%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for David Orme at 2011-05-30 15:25:22 +0100 


%% Saved with string encoding Unicode (UTF-8) 



@article{Garland.Ives.2000.a,
	Abstract = {Two phylogenetic comparative methods, independent contrasts and generalized least squares models, can be used to determine the statistical relationship between two or more traits. We show that the two approaches are functionally identical and that either can be used to make statistical inferences about values at internal nodes of a phylogenetic tree (hypothetical ancestors), to estimate relationships between characters, and to predict values for unmeasured species. Regression equations derived from independent contrasts can be placed back onto the original data space, including computation of both confidence intervals and prediction intervals for new observations. Predictions for unmeasured species (including extinct forms) can be made increasingly accurate and precise as the specificity of their placement on a phylogenetic tree increases, which can greatly increase statistical power to detect, for example, deviation of a single species from an allometric prediction. We reexamine published data for basal metabolic rates (BMR) of birds and show that conventional and phylogenetic allometric equations differ significantly. In new results, we show that, as compared with nonpasserines, passerines exhibit a lower rate of evolution in both body mass and mass-corrected BMR; passerines also have significantly smaller body masses than their sister clade. These differences may justify separate, clade-specific allometric equations for prediction of avian basal metabolic rates.},
	Address = {5720 SOUTH WOODLAWN AVE, CHICAGO, IL 60637-1603 USA},
	Author = {Garland, Jr, Theodore and Ives, Anthony R.},
	Date-Added = {2011-05-20 08:38:02 +0100},
	Date-Modified = {2011-05-20 08:38:31 +0100},
	Isi = {000086444100005},
	Isi-Recid = {114497756},
	Isi-Ref-Recids = {110890061 106822152 88567074 94732619 110825903 103375501 110281506 53742605 89170749 105362459 106788342 76174554 75073628 95243159 98297541 108228217 97185685 96919564 54497548 108971317 86645752 102791424 80535801 110281521 80759959 89170746 112176407 84822622 71141655 98460480 97088799 102791328 106880547 75043716 56238547 99145988 98509406 89170750 98839564 98053151 114497757 76218624 99676097 106209247 96176544 94842174 91434282 85463423 87630012 111262324 94796213 85105165 105408080 86763569 85938648 95821558 103730521 53951954 75537460 75537462 86043599 93664542 95589274 82986870},
	Journal = {American Naturalist},
	Keywords = {allometry; ancestor reconstruction; comparative method; metabolic rate; phylogeny; regression},
	Month = mar,
	Number = {3},
	Pages = {346--364},
	Publisher = {UNIV CHICAGO PRESS},
	Times-Cited = {298},
	Title = {Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods},
	Volume = {155},
	Year = {2000},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000086444100005}}

@article{Webb.Ackerly.ea.2002.a,
	Abstract = { ▪ Abstract  As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research. },
	Author = {Webb, Campbell O. and Ackerly, David D. and McPeek, Mark A. and Donoghue, Michael J.},
	Date-Added = {2011-05-18 12:00:09 +0100},
	Date-Modified = {2011-05-18 12:02:50 +0100},
	Doi = {10.1146/annurev.ecolsys.33.010802.150448},
	Eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.33.010802.150448},
	Journal = {Annual Review of Ecology and Systematics},
	Number = {1},
	Pages = {475-505},
	Title = {Phylogenies and community ecology},
	Url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150448},
	Volume = {33},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.33.010802.150448},
	Bdsk-Url-2 = {http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150448}}

@article{Faith.1992.a,
	Abstract = {
Protecting biological diversity with limited resources may require placing conservation priorities on different taxa. A system of priorities that reflects the value of taxonomic diversity can be achieved by setting priorities such that the subset of taxa that is protected has maximum underlying feature diversity. Such feature diversity of taxon subsets is difficult to estimate directly, but can be predicted by the cladistic/phylogenetic relationships among the taxa. In this study, a simple measure of phylogenetic diversity is defined based on cladistic information. The measure of phylogenetic diversity, PD, is contrasted with a measure of taxic diversity recently developed by Vane-Wright et al. (Biol. Conserv., 55, 1991). In re-examining reserve-selection scenarios based on a phylogeny of bumble bees (Apidae), PD produces quite different priorities for species conservation, relative to taxic diversity. The potential application of PD at levels below that of the species is then illustrated using a mtDNA phylogeny for populations of crested newts Triturus cristatus. Calculation of PD for different population subsets shows that protection of populations at either of two extremes of the geographic range of the group can significantly increase the phylogenetic diversity that is protected.},
	Author = {Daniel P. Faith},
	Date-Added = {2011-05-18 11:56:50 +0100},
	Date-Modified = {2011-05-18 12:02:44 +0100},
	Doi = {DOI: 10.1016/0006-3207(92)91201-3},
	Issn = {0006-3207},
	Journal = {Biological Conservation},
	Number = {1},
	Pages = {1 - 10},
	Title = {Conservation evaluation and phylogenetic diversity},
	Url = {http://www.sciencedirect.com/science/article/B6V5X-48XKBRG-VP/2/92106791e1bac03e76b8dbe7fa5ca7c2},
	Volume = {61},
	Year = {1992},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6V5X-48XKBRG-VP/2/92106791e1bac03e76b8dbe7fa5ca7c2},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/0006-3207(92)91201-3}}

@article{Pagel.1994.a,
	Abstract = {I present a new statistical method for analysing the relationship between two discrete characters that are measured across a group of hierarchically evolved species or populations. The method assesses whether a pattern of association across the group is evidence for correlated evolutionary change in the two characters. The method takes into account information on the lengths of the branches of phylogenetic trees, develops estimates of the rates of change of the discrete characters, and tests the hypothesis of correlated evolution without relying upon reconstructions of the ancestral character states. A likelihood ratio test statistic is used to discriminate between two models that are fitted to the data: one allowing only for independent evolution of the two characters, the other allowing for correlated evolution. Tests of specific directional hypotheses can also be made. The method is illustrated with an application to the Hominoidea.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Pagel, Mark D},
	Date-Added = {2011-05-18 11:17:19 +0100},
	Date-Modified = {2011-05-18 11:17:49 +0100},
	Isi = {A1994MT55500006},
	Isi-Recid = {86050888},
	Isi-Ref-Recids = {29953984 7648489 86050889 54497548 43930323 50927113 81631248 74123377 82166166 71141655 76517571 75043716 57684838 80080593 20683055 41807846 25228715 26444328 86050890 76218624 86050891 70999827 80134800 86050892 49537754 75070617 65066140},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Month = jan,
	Number = {1342},
	Pages = {37--45},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {457},
	Title = {DETECTING CORRELATED EVOLUTION ON PHYLOGENIES - A GENERAL-METHOD FOR THE COMPARATIVE-ANALYSIS OF DISCRETE CHARACTERS},
	Volume = {255},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994MT55500006}}

@manual{R-Hackathon.Bolker.ea.2011.a,
	Author = {{R Hackathon}, {alphabetically:}, {} and Ben Bolker and Marguerite Butler and Peter Cowan and Damien de Vienne and Dirk Eddelbuettel and Mark Holder and Thibaut Jombart and Steve Kembel and Francois Michonneau and David Orme and Brian O'Meara and Emmanuel Paradis and Jim Regetz and Derrick Zwickl)},
	Date-Added = {2011-05-18 10:40:39 +0100},
	Date-Modified = {2011-05-18 10:44:36 +0100},
	Note = {R package version 0.6.3},
	Title = {phylobase: Base package for phylogenetic structures and comparative data},
	Url = {http://CRAN.R-project.org/package=phylobase},
	Year = {2011},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=phylobase}}

@manual{R-Development-Core-Team.2011.a,
	Address = {Vienna, Austria},
	Author = {{R Development Core Team}},
	Date-Added = {2011-05-17 15:23:24 +0100},
	Date-Modified = {2011-05-17 15:23:30 +0100},
	Note = {{ISBN} 3-900051-07-0},
	Organization = {R Foundation for Statistical Computing},
	Title = {R: A Language and Environment for Statistical Computing},
	Url = {http://www.R-project.org/},
	Year = {2011},
	Bdsk-Url-1 = {http://www.R-project.org/}}

@article{Felsenstein.1989.a,
	Author = {Felsenstein, Joseph},
	Date-Added = {2011-05-17 15:08:42 +0100},
	Date-Modified = {2011-05-17 15:10:10 +0100},
	Journal = {Cladistics},
	Number = {164-166},
	Title = {{PHYLIP -- Phylogeny Inference Package (Version 3.2).}},
	Volume = {5},
	Year = {1989}}

@url{Pagel.Meade.2011.a,
	Author = {Pagel, Mark and Meade, Andrew},
	Date-Added = {2011-05-17 14:42:50 +0100},
	Date-Modified = {2011-05-30 15:24:54 +0100},
	Lastchecked = {2011},
	Organization = {University of Reading},
	Title = {{BayesTraits}},
	Url = {http://www.evolution.rdg.ac.uk/},
	Urldate = {2011},
	Year = {2011},
	Bdsk-Url-1 = {http://www.evolution.rdg.ac.uk/}}

@manual{Martins.2004.a,
	Address = {Bloomington IN.},
	Author = {Martins, Em{\'\i}lia P},
	Date-Added = {2011-05-17 14:38:15 +0100},
	Date-Modified = {2011-05-17 14:41:05 +0100},
	Organization = {Department of Biology, Indiana University},
	Title = {COMPARE, version 4.6b. Computer programs for the statistical analysis of comparative data.},
	Url = {http://compare.bio.indiana.edu/},
	Year = {2004},
	Bdsk-Url-1 = {http://compare.bio.indiana.edu/}}

@manual{Diaz-Uriarte.Garland.ea.2010.a,
	Author = {Diaz-Uriarte, Ramon and Garland, Jr, Theodore},
	Date-Added = {2011-05-17 14:35:09 +0100},
	Date-Modified = {2011-05-17 14:36:41 +0100},
	Note = {R package version 1.0.7},
	Title = {PHYLOGR: Functions for phylogenetically based statistical analyses},
	Url = {http://CRAN.R-project.org/package=PHYLOGR},
	Year = {2010},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=PHYLOGR}}

@article{Price.1997.a,
	Abstract = {The use of the independent contrast method in comparative tests is studied. It is assumed that: (i) the traits under investigation are subject to natural selection; (ii) closely related species are similar because they share many characteristics of their niche, inherited from a common ancestor; and (iii) the current adaptive significance of the traits is the focus of investigation. The main objection to the use of species values in this case is that third variables which are shared by closely related species confound the relationship between the focal traits. In this paper, I argue that third variables are largely not controlled by the contrast methods, which are designed to estimate correlated evolution. To the extent that third variables also show correlated evolution, the true relationship among the traits of interest will remain obscured. Although the independent contrast method does not resolve the influence of third traits it does, in principle, provide a greater resolution than the use of the species mean values. However, its validity depends on the applicability of an evolutionary model which has a substantial stochastic component. To illustrate the consequences of relaxing this assumption I consider an alternative model of an adaptive radiation, where species come to fill a fixed niche space. Under this model, the expected value for the contrast correlation differs from that for the species correlation. The two correlations differ because contrasts reflect the historical pattern of diversification among species, whereas the species values describe the present-day relationships among the species. If the latter is of interest, I suggest that assessing significance based on the species correlations can be justified, providing that attention is paid to the role of potentially confounding third traits. Often, differences between contrast and species correlations may be biologically informative, reflecting changes in correlations between traits as an adaptive radiation proceeds; contrasts may be particularly useful as a means of investigating past history, rather than current utility of traits.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Price, Trevor D.},
	Date-Added = {2011-05-17 14:03:59 +0100},
	Date-Modified = {2011-05-17 14:05:22 +0100},
	Isi = {A1997WX80400007},
	Isi-Recid = {100359553},
	Isi-Ref-Recids = {93885554 100359554 87572567 78800747 89124410 64051071 90158710 94432303 85466159 95243159 54497548 86933228 80535801 78279598 82254350 89170746 80759959 38299061 45679224 71141655 76260364 75043716 91702658 76254733 44724435 86717196 72353824 73339062 89170750 88319323 74999557 100359555 93579196 82613328 85835715 85835721 76218624 85137610 88018481 85105165 80134800 69468637 85824140 79151113 81735835 78723504 98068978 68312352 77442502 87624979 82828458 64284742 85964673 89395075 87325257 81980866 96316169},
	Journal = {Philosophical Transactions of the Royal Society of London Series B-Biological Sciences},
	Month = apr,
	Number = {1352},
	Pages = {519--529},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {219},
	Title = {Correlated evolution and independent contrasts},
	Volume = {352},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WX80400007}}

@article{Pagel.Harvey.1989.a,
	Address = {ALLSCHWILERSTRASSE 10, CH-4009 BASEL, SWITZERLAND},
	Author = {Pagel, Mark D and Harvey, Paul H.},
	Date-Added = {2011-05-17 11:56:23 +0100},
	Date-Modified = {2011-05-17 11:57:12 +0100},
	Isi = {A1989CD67900014},
	Isi-Recid = {70999827},
	Isi-Ref-Recids = {38106522 68958032 58218260 9364142 14019453 45021262 57561095 70234465 32479674 32691204 38299032 60318406 54497548 50754984 56562694 29726999 45679224 70999828 13502010 43711438 58372656 46169363 36051126 36005627 57696592 13641258 32236798 63652685 67167571 15174403 16654307 37222085 53205154 70999829 39788521 24280831 70999826 52265466 43711448 54334185 67167574 67804616 69468637 70999830 57400978 70999831 61121546 49537754 70999832 50428468 27797588},
	Journal = {Folia Primatologica},
	Number = {1-4},
	Pages = {203--220},
	Publisher = {KARGER},
	Times-Cited = {117},
	Title = {COMPARATIVE METHODS FOR EXAMINING ADAPTATION DEPEND ON EVOLUTIONARY MODELS},
	Volume = {53},
	Year = {1989},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1989CD67900014}}

@book{Harvey.Pagel.1991.a,
	Author = {Harvey, Paul H. and Pagel, Mark D},
	Date-Added = {2011-05-17 11:48:43 +0100},
	Date-Modified = {2011-05-17 11:49:40 +0100},
	Publisher = {Oxford University Press, Oxford},
	Title = {The comparative method in evolutionary biology},
	Year = {1991}}

@article{Grafen.Ridley.1997.a,
	Abstract = {The paper provides an explicit justification for the principle that a uniform taxon should contribute only one datapoint in comparative analyses with discrete variables. The justification is that phylogenetic patterns in variables unincluded in the proposed test vitiate the assumption of independence, both at the level of species and at the level of branch segments. The consequence is that a uniform taxon cannot safely be counted as more than one datapoint. The arguments use a branching discrete Markov process in continuous time, with the new feature that the tested variables are only a subset of the evolving characters. This model is proposed as a useful criterion for measuring the merit of proposed tests, and illustrates the necessity for models in evaluating comparative methods. (C) 1997 Academic Press Limited},
	Address = {24-28 OVAL RD, LONDON, ENGLAND NW1 7DX},
	Author = {Grafen, A and Ridley, M},
	Date-Added = {2011-05-17 11:42:19 +0100},
	Date-Modified = {2011-05-17 11:42:19 +0100},
	Isi = {A1997WB69800002},
	Isi-Recid = {98839563},
	Isi-Ref-Recids = {50339923 76218625 32028122 25715300 98460480 71141655 9786697 75043716 86002423 71047462 72714421 76996737 98839564 85463423 79168459 86050888 76218628 90629508 49537754 98460486 78548583 75914987 86678878 67476527},
	Journal = {Journal of Theoretical Biology},
	Month = jan,
	Number = {1},
	Pages = {7--14},
	Publisher = {ACADEMIC PRESS LTD},
	Times-Cited = {7},
	Title = {A new model for discrete character evolution},
	Volume = {184},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WB69800002}}

@article{Grafen.Ridley.1996.a,
	Abstract = {Four methods have been proposed that can be used to test for associations between the states of discrete characters in cross-species data and that do not suffer from non-independence due to overcounting of data points. The tests are those of Ridley (1983), Burt (1989), Grafen (1989), and a new test called the ICDE test. The aim of the paper is to measure the Type I error rates for these methods with simulated null distributions of discrete characters. The null data is generated by a model of discrete character evolution, using three shapes of phylogeny: tetratomous, dichotomous, and realistic. Ridley's and Burt's tests are both reasonably valid with the realistic phylogeny but biased with the tetratomous and dichotomous phylogenies. Grafen's phylogenetic regression is reasonably valid with all tree shapes. One version of the ICDE test was valid, the other less so. The invalid results are explained in terms of two kinds of statistical non-independence that arise in discrete data: non-independence due to the reconstruction of character states by parsimony, and the ''family problem'' in which similar patterns are found in null data in many separate radiations because all the radiations began from the same ancestral state. (C) 1996 Academic Press Limited},
	Address = {24-28 OVAL RD, LONDON, ENGLAND NW1 7DX},
	Author = {Grafen, A and Ridley, M},
	Date-Added = {2011-05-17 11:41:51 +0100},
	Date-Modified = {2011-05-17 11:41:51 +0100},
	Isi = {A1996VX06200003},
	Isi-Recid = {98460480},
	Isi-Ref-Recids = {98460481 76218625 71141655 98460482 98460483 98460484 98460485 75043716 44406036 72714421 79168459 86050888 90629508 49537754 98460486 67476527},
	Journal = {Journal of Theoretical Biology},
	Month = dec,
	Number = {3},
	Pages = {255--267},
	Publisher = {ACADEMIC PRESS LTD},
	Times-Cited = {23},
	Title = {Statistical tests for discrete cross-species data},
	Volume = {183},
	Year = {1996},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1996VX06200003}}

@article{Grafen.1989.a,
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Grafen, Alan},
	Date-Added = {2011-05-17 11:40:29 +0100},
	Date-Modified = {2011-05-17 11:42:48 +0100},
	Isi = {A1989CG15400001},
	Isi-Recid = {71141655},
	Isi-Ref-Recids = {26817014 54497548 67535675 22364280 68259716 67804616 64776245 61121546 49537754 71141656 71141657 64284742 66631130 65066140 28370940},
	Journal = {Philosophical Transactions of the Royal Society of London Series B-Biological Sciences},
	Month = dec,
	Number = {1233},
	Pages = {119--157},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {612},
	Title = {The phylogenetic regression},
	Volume = {326},
	Year = {1989},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1989CG15400001}}

@article{Clutton-Brock.Harvey.1977.a,
	Address = {GREAT CLARENDON ST, OXFORD, ENGLAND OX2 6DP},
	Author = {Clutton-Brock, Tim H and Harvey, Paul H.},
	Date-Added = {2011-05-17 10:42:41 +0100},
	Date-Modified = {2011-05-17 10:45:07 +0100},
	Isi = {A1977DU45100001},
	Isi-Recid = {32479674},
	Isi-Ref-Recids = {21029093 19981547 26321811 24865409 21237112 10161136 22565412 21118267 31491859 14679054 16551923 28216277 7741843 27275644 28900737 10161144 14832627 21182214 21621496 32479675 27845240 32479676 29118391 27026511 16551946 25811531 27640417 28339149 27108395 29953984 25281666 32479677 32479678 24841543 26614705 21798308 28371035 31744861 29241190 12169825 12898674 26938839 19981548 700383 28161313 20462159 19579245 11057752 20784969 32479679 21923680 25784524 32479680 32479681 32479682 27867284 21182208 24865502 14832634 27338890 28281521 9196954 25566180 32479683 32479684 21182226 18833854 32479685 22818469 21182228 32479686 22837505 24865381 31744805 21784810 21293043 20714522 24433232 30528 12898836 8332493 12305676 21695517 28161312 2044469 13836561 5344853 27845254 32479687 23765343 27108399 2196721 5406434 24515184 32479688 32479689 22498960 15708482 15736688 27756307 24865277 32479690 25657513 23738744 20535217 32479691 32479692 21798305 30386149 22031631 9623817 15984423 16394797 25520011 32479693 24841539 18298808 21060215 17224525 32479694 8505205 28540378 20240050 11520853 32479695 14457378 15114507 21293054 7339258 32479696 32479697 24324251 32479698 17453273 7058002 12588604 21182248 9457767 32479699 16551926 18017477 32479700 11448623 19870831 32479701 27300129 32479702 22837504 12459555 32479703 13669573 22031637 19575577 16334866 14819621 4265629 12332140 27551055 11057786 15002625 16632137 11057787 23439597 13996950 13175641 17031612 29442613 14679062 22837511 32479704 32479705 31255167 32479706 14679064 32479707 27338886 20462166 25892777 15736684 18078362 18716885 7819415 28143519 28143522 32479708 16241210 11835204 9931492 20837718 19534805 32479709 26976057 28276644 27300110 26277858 29131318 17925174 12594616 20100815},
	Journal = {Journal of Zoology},
	Number = {SEP},
	Pages = {1--39},
	Publisher = {OXFORD UNIV PRESS},
	Times-Cited = {571},
	Title = {Primate ecology and social organization},
	Volume = {183},
	Year = {1977},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1977DU45100001}}

@article{Harvey.Clutton-Brock.1985.a,
	Address = {810 E 10TH STREET, LAWRENCE, KS 66044},
	Author = {Harvey, Paul H. and Clutton-Brock, Tim H},
	Date-Added = {2011-05-17 10:41:20 +0100},
	Date-Modified = {2011-05-17 10:41:53 +0100},
	Isi = {A1985AJY2600007},
	Isi-Recid = {55865463},
	Isi-Ref-Recids = {49190597 55865464 55865465 31718262 55605264 53977880 53977881 39607216 32479674 34320581 39607218 43563747 38972841 47426144 29273802 45226659 34787522 46169363 55865466 45329826 50706089 38980895 24515184 25132987 27756307 21736329 16394797 37222085 55865467 29779152 36248191 49168701 54794932 54508284 55865468 54334185 55865469 40541157 34556933 29892148 32276855 55865470 55865471 49537754 55865472 25461721 6371901 50364888 50428468 38880084 46871442},
	Journal = {Evolution},
	Number = {3},
	Pages = {559--581},
	Publisher = {SOC STUDY EVOLUTION},
	Times-Cited = {301},
	Title = {LIFE-HISTORY VARIATION IN PRIMATES},
	Volume = {39},
	Year = {1985},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1985AJY2600007}}

@article{Thuiller.Lavergne.ea.2011.a,
	Abstract = {Many species are projected to become vulnerable to twenty-first-century climate changes, with consequent effects on the tree of life. If losses were not randomly distributed across the tree of life, climate change could lead to a disproportionate loss of evolutionary history. Here we estimate the consequences of climate change on the phylogenetic diversities of plant, bird and mammal assemblages across Europe. Using a consensus across ensembles of forecasts for 2020, 2050 and 2080 and high-resolution phylogenetic trees, we show that species vulnerability to climate change clusters weakly across phylogenies. Such phylogenetic signal in species vulnerabilities does not lead to higher loss of evolutionary history than expected with a model of random extinctions. This is because vulnerable species have neither fewer nor closer relatives than the remaining clades. Reductions in phylogenetic diversity will be greater in southern Europe, and gains are expected in regions of high latitude or altitude. However, losses will not be offset by gains and the tree of life faces a trend towards homogenization across the continent.},
	Author = {Thuiller, Wilfried and Lavergne, S{\'e}bastien and Roquet, Cristina and Boulangeat, Isabelle and Lafourcade, Bruno and Araujo, Miguel B},
	Date-Added = {2011-05-16 15:58:24 +0100},
	Date-Modified = {2011-05-16 15:58:24 +0100},
	Doi = {10.1038/nature09705},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Biodiversity; Birds; Climate Change; Europe; Extinction, Biological; Human Activities; Mammals; Models, Theoretical; Phylogeny; Plants; Species Specificity},
	Month = {Feb},
	Number = {7335},
	Pages = {531-4},
	Pmid = {21326204},
	Pst = {ppublish},
	Title = {Consequences of climate change on the tree of life in Europe},
	Volume = {470},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{Whitton.Purvis.ea.2011.a,
	Abstract = {ABSTRACT
Aim  Species geographic ranges are the `fundamental units' of macroecology. Range size is a major correlate of extinction risk in many groups, and is also critical in studies of biotic responses to climate change. Despite this, there is a lack of studies exploring the role of environmental, historical and anthropogenic processes in determining large-scale patterns in range size. We perform the first global analysis of putative drivers of range size variation in any group, choosing amphibians as our study taxon. Our aims are to disentangle the many hypothesized causes of range size variation and evaluate support for `Rapoport's rule', the observation that range size correlates with latitude.Location  Global.Methods  We develop a global map of gridded median range size using the International Union for Conservation of Nature (IUCN) distribution maps. From this we perform spatial and non-spatial regressions to explore relationships between range size and nine hypothesized variables in six biogeographic realms. We use information-theoretic model selection to compare multiple competing variables, simultaneously evaluating the relative support for each one.Results  Current climate -- environmental water and energy, and temperature seasonality -- is consistently highly ranked in spatial and non-spatial analyses. Human impacts and other environmental measures (topographic and landscape complexity, effective area, climate extremes) show mixed support, and glacial history is consistently unimportant. Our findings add further evidence to the view that Rapoport's rule is a regional, not global, phenomenon.Main conclusions  The primary importance of temperature seasonality may explain why Rapoport's rule is largely restricted to northern latitudes, as this is where seasonality is most pronounced. More generally, the dominance of contemporary climate in our analyses (even when accounting for space) has stark implications for the future status of amphibians. Changes in climate will almost certainly interact with the anthropogenic processes already threatening a third of amphibians globally, with the effects being most keenly felt by species with a restricted range.},
	Author = {Whitton, Felix J. S. and Purvis, Andy and Orme, C. David L. and Olalla-T{\'a}rraga, Miguel {\'A}.},
	Date-Added = {2011-05-16 12:01:41 +0100},
	Date-Modified = {2011-05-16 12:02:33 +0100},
	Doi = {10.1111/j.1466-8238.2011.00660.x},
	Issn = {1466-8238},
	Journal = {Global Ecology and Biogeography},
	Keywords = {Amphibians, climate variability, energy--water balance, environmental gradients, geographic range size, global, information theory, model selection, Rapoport's rule, simultaneous autoregressive model},
	Pages = {no--no},
	Publisher = {Blackwell Publishing Ltd},
	Title = {Understanding global patterns in amphibian geographic range size: does Rapoport rule?},
	Url = {http://dx.doi.org/10.1111/j.1466-8238.2011.00660.x},
	Year = {2011},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2011.00660.x}}

@article{McInnes.Baker.ea.2011.a,
	Abstract = {On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, 'Integrating Ecology into Macroevolutionary Research'. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns.},
	Author = {McInnes, Lynsey and Baker, William J and Barraclough, Timothy G and Dasmahapatra, Kanchon K and Goswami, Anjali and Harmon, Luke J and Morlon, H{\'e}l{\`e}ne and Purvis, Andy and Rosindell, James and Thomas, Gavin H and Turvey, Samuel T and Phillimore, Albert B},
	Date-Added = {2011-05-16 11:57:48 +0100},
	Date-Modified = {2011-05-16 11:57:48 +0100},
	Doi = {10.1098/rsbl.2011.0358},
	Journal = {Biol Lett},
	Journal-Full = {Biology letters},
	Month = {Apr},
	Pmid = {21527505},
	Pst = {aheadofprint},
	Title = {Integrating ecology into macroevolutionary research},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{Isaac.Turvey.ea.2007.a,
	Abstract = {Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species) do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.},
	Address = {185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA},
	Author = {Isaac, Nick J. B. and Turvey, Samuel T. and Collen, Ben and Waterman, Carly and Baillie, Jonathan E. M.},
	Date-Added = {2011-05-05 00:08:11 +0100},
	Date-Modified = {2011-05-05 00:09:37 +0100},
	Doi = {DOI 10.1371/journal.pone.0000296},
	Isi = {000207444800019},
	Isi-Recid = {157732122},
	Isi-Ref-Recids = {151669389 174911301 134425482 122980588 125133468 185797046 110292786 135331243 126939792 163056691 142475168 103222988 134534005 143543217 185797047 76811901 79838892 123378631 108501518 118558512 104010943 156651897 114401484 136433706 117638467 77776705 163165350 146894422 183564303 129789678 114485288 73520451 111425243 113913990 102480485 122306281 145723116 115948993 144470970 109553965 92086876 92133321 163056695 114485286 153625761 124090639 133945986 123706614 146525762 105541171 145646213 74302138 107489644 150507443 84478843 90027651},
	Journal = {Plos One},
	Month = mar,
	Number = {3},
	Pages = {e296},
	Publisher = {PUBLIC LIBRARY SCIENCE},
	Rating = {0},
	Times-Cited = {45},
	Title = {Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny},
	Volume = {2},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000207444800019}}

@article{Jones.Purvis.1997.a,
	Abstract = {1. The distribution of body sizes among mammalian species has been modelled by Brown, Marquet & Taper (1993), who suggest that reproductive power (the rate at which energy from the environment is channelled into offspring production) is maximized at a size of 100 g, and the observed size distribution among species reflects the way reproductive power depends on size. The model makes a testable prediction about life-history allometries: namely, that components of reproductive power should not scale linearly with body size but should change sign at the optimum size.2. A large set of life-history data from a single clade of small mammals, the bats (Order: Chiroptera), was analysed to test this key prediction. The analyses in this study offer no support for the idea that allometries of reproductive power change sign in bats, either at 100 g or at any other size. Furthermore the life-history allometries of bats, which are mostly below the 100 g optimum, were broadly the same as in mammalian taxa larger than the optimum size.3. These findings together contradict a key prediction of Brown et al.'s (1993) model to explain the skewed body size distribution across mammalian species.},
	Author = {Jones, Kate E. and Purvis, Andy},
	Date-Added = {2011-04-21 16:36:46 +0100},
	Date-Modified = {2011-04-21 16:38:06 +0100},
	Doi = {10.1046/j.1365-2435.1997.00149.x},
	Issn = {1365-2435},
	Journal = {Functional Ecology},
	Keywords = {Body size distribution, Chiroptera, independent contrasts, life history, reproductive power},
	Number = {6},
	Pages = {751--756},
	Publisher = {Blackwell Science Ltd},
	Title = {An optimum body size for mammals? Comparative evidence from bats},
	Url = {http://dx.doi.org/10.1046/j.1365-2435.1997.00149.x},
	Volume = {11},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1046/j.1365-2435.1997.00149.x}}

@article{Meiri.Cooper.ea.2008.a,
	Abstract = {The island rule is a hypothesis whereby small mammals evolve larger size on islands while large insular mammals dwarf. The rule is believed to emanate from small mammals growing larger to control more resources and enhance metabolic efficiency, while large mammals evolve smaller size to reduce resource requirements and increase reproductive output. We show that there is no evidence for the existence of the island rule when phylogenetic comparative methods are applied to a large, high-quality dataset. Rather, there are just a few clade-specific patterns: carnivores; heteromyid rodents; and artiodactyls typically evolve smaller size on islands whereas murid rodents usually grow larger. The island rule is probably an artefact of comparing distantly related groups showing clade-specific responses to insularity. Instead of a rule, size evolution on islands is likely to be governed by the biotic and abiotic characteristics of different islands, the biology of the species in question and contingency.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Meiri, Shai and Cooper, Natalie and Purvis, Andy},
	Date-Added = {2011-04-21 16:33:12 +0100},
	Date-Modified = {2011-04-21 16:33:12 +0100},
	Doi = {DOI 10.1098/rspb.2007.1056},
	Isi = {000251724500004},
	Isi-Recid = {159699770},
	Isi-Ref-Recids = {126806292 150035229 89992923 54697085 122752833 98458108 155066183 128732855 134700673 157316089 85211999 136696429 145845813 34458220 125716018 85040241 106859608 137447091 9815839 80759959 81631248 121243136 159699771 33995251 134696308 62379741 98966355 152250022 148416763 103642851 44873788 133342926 54697091 146272985 159699772 143230338 158662027 151639051 143184295 146683005 126532253 144822819 112080936 159699773 112336304 153920107 92213623 152202313 159699774 93033347 151524900 109690800 80047580 121623035 27243773 153608173 84478843},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {body size evolution; dwarfism; gigantism; island rule; mammals; phylogenetic comparative methods},
	Month = jan,
	Number = {1631},
	Pages = {141--148},
	Publisher = {ROYAL SOC},
	Times-Cited = {34},
	Title = {The island rule: made to be broken?},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000251724500004}}

@manual{Purvis.Rambaut.1995.b,
	Author = {Purvis, Andy and Rambaut, Andrew},
	Date-Added = {2011-04-21 15:27:06 +0100},
	Date-Modified = {2011-04-21 15:29:02 +0100},
	Title = {Comparative Analysis by Independent Contrasts (CAIC) User's Guide},
	Year = {1995},
	Bdsk-File-1 = { }}

@article{Thomas.2008.a,
	Abstract = {Recent studies suggest that species' life histories and ecology can be used to forecast future extinction risk. Threatened species often share similar traits such that if a trait predisposing a species to decline or extinction is evolutionarily conserved, then close relatives of threatened species are themselves likely to be at risk. The phylogenetic distribution of current threat has been argued to provide insight into the species that could be threatened in the future when trait data are not available. Conservation criteria are typically based on multiple indices that capture different symptoms of threat including population trends and range contraction. However, there is no reason to assume consistent phylogenetic distributions of different symptoms. I construct a molecular phylogeny of 249 species of British birds (more than 93\% of the breeding and wintering species) and use this to show that the species that are threatened due to population declines are phylogenetically more closely related than expected by chance alone. However, species that are listed for other reasons, including range contraction, are distributed randomly with respect to phylogeny. I suggest that while phylogeny can be informative with respect to identifying clades that are susceptible to some measures of extinction risk, such patterns are likely to be idiosyncratic with respect to symptom and taxa.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Thomas, Gavin H.},
	Date-Added = {2011-04-20 08:56:41 +0100},
	Date-Modified = {2011-04-20 08:56:41 +0100},
	Doi = {DOI 10.1098/rspb.2008.0549},
	Isi = {000258091800003},
	Isi-Recid = {172212957},
	Isi-Ref-Recids = {161650422 158371039 172212958 149687869 53297234 135798305 149555681 160545023 163056688 160320221 172212959 150369836 151136018 153615914 79838892 131246339 154402909 143375520 148658244 143568636 172212960 112799139 117111000 104377069 117111095 85953935 128817195 93125040 157732122 141991244 125853805 155784153 129789678 163056694 129879513 150662431 133723992 116955607 172212961 172212962 153625761 163510885 147758555 31549538 75537460 153973767 133684292 151311502 127725576 153818552 150198030 163100489},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {phylogeny; British birds; population decline; range contraction},
	Month = sep,
	Number = {1647},
	Pages = {2077--2083},
	Publisher = {ROYAL SOC},
	Times-Cited = {12},
	Title = {Phylogenetic distributions of British birds of conservation concern},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000258091800003}}

@article{Fritz.Purvis.2010.a,
	Abstract = {The strength of phylogenetic signal in extinction risk can give insight into the mechanisms behind species' declines. Nevertheless, no existing measure of phylogenetic pattern in a binary trait, such as extinction-risk status, measures signal strength in a way that can be compared among data sets. We developed a new measure for phylogenetic signal of binary traits, D, which simulations show gives robust results with data sets of more than 50 species, even when the proportion of threatened species is low. We applied D to the red-list status of British birds and the world's mammals and found that the threat status for both groups exhibited moderately strong phylogenetic clumping. We also tested the hypothesis that the phylogenetic pattern of species threatened by harvesting will be more strongly clumped than for those species threatened by either habitat loss or invasive species because the life-history traits mediating the effects of harvesting show strong evolutionary pattern. For mammals, our results supported our hypothesis; there was significant but weaker phylogenetic signal in the risk caused by the other two drivers (habitat loss and invasive species). We conclude that D is likely to be a useful measure of the strength of phylogenetic pattern in many binary traits.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Fritz, Susanne A. and Purvis, Andy},
	Date-Added = {2011-04-19 16:39:42 +0100},
	Date-Modified = {2011-04-19 16:39:42 +0100},
	Doi = {DOI 10.1111/j.1523-1739.2010.01455.x},
	Isi = {000280148600016},
	Isi-Recid = {190634712},
	Isi-Ref-Recids = {173241471 161666750 99916428 149687869 175140281 174391246 129554126 100149753 149555681 181395347 163056688 172659403 136542103 145965797 54497548 175404022 127500623 180385747 128817195 159735607 77339811 136510614 190634713 142988388 110407478 125853805 96464811 159750512 103223104 99631610 190634714 117223810 112336304 157261187 159559576 175141761 114485286 182711312 108014312 122319672 148382624 149328871 137301762 172212957 127725576 174412985},
	Journal = {Conservation Biology},
	Keywords = {extinction risk; habitat loss; harvesting; phylogenetic selectivity; phylogenetic signal},
	Month = aug,
	Number = {4},
	Pages = {1042--1051},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {1},
	Title = {Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits},
	Volume = {24},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000280148600016}}

@article{Isaac.Agapow.ea.2003.a,
	Abstract = {Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t-test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness.},
	Address = {810 E 10TH STREET, LAWRENCE, KS 66044 USA},
	Author = {Isaac, NJB and Agapow, PM and Harvey, PH and Purvis, A},
	Date-Added = {2011-04-19 14:22:22 +0100},
	Date-Modified = {2011-04-19 14:22:22 +0100},
	Isi = {000181156600002},
	Isi-Recid = {128447859},
	Isi-Ref-Recids = {117556278 124134013 116671108 110653595 106629188 90616320 128447860 118876512 68770968 67019755 95243159 110894175 29451809 106191437 54497548 108971389 84822622 80759959 103859677 71141655 89651281 75043716 118078912 114401484 98458397 120655815 86678876 66311374 93216587 90565226 71047462 76218624 115625970 85354831 75468688 66690949 99631610 119968552 99631614 80791779 124134011 110178480 112336304 80134799 86763569 92133314 113655968 99631616 117605548 90871598 116873340 74123390 104149213 22842046 949309 69534315 91809311},
	Journal = {Evolution},
	Keywords = {comparative methods; MacroCAIC; macroevolution; phylogeny; sister-clade comparisons; species richness; validity},
	Month = jan,
	Number = {1},
	Pages = {18--26},
	Publisher = {SOC STUDY EVOLUTION},
	Times-Cited = {26},
	Title = {Phylogenetically nested comparisons for testing correlates of species richness: A simulation study of continuous variables},
	Volume = {57},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000181156600002}}

@article{Isaac.Jones.ea.2005.a,
	Abstract = {We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism.},
	Address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA},
	Author = {Isaac, NJB and Jones, KE and Gittleman, JL and Purvis, A},
	Date-Added = {2011-04-18 15:36:23 +0100},
	Date-Modified = {2011-04-18 15:36:23 +0100},
	Isi = {000228094100009},
	Isi-Recid = {143540586},
	Isi-Ref-Recids = {124134013 134425482 127935544 116671108 106629188 90616320 110292786 135331243 4970904 135840799 135511857 48579746 127935581 68770968 116833556 78027514 131246339 127481253 108971389 80759959 87769416 126173490 113914042 87452709 103859677 143540587 123729316 128447859 135257490 136433706 105972911 127322636 124980495 136510616 120655815 75468688 104155499 66690949 99631610 143260236 80791779 63629423 125430245 110178480 104155555 50798003 135840801 92133314 143540588 92133321 116955607 70790989 68015879 143540589 102814501 100920016 128908133 130158038 86317130 84478843},
	Journal = {American Naturalist},
	Keywords = {nested sister clade comparisons; species richness; phylogeny; speciation; extinction},
	Month = may,
	Number = {5},
	Pages = {600--607},
	Publisher = {UNIV CHICAGO PRESS},
	Times-Cited = {24},
	Title = {Correlates of species richness in mammals: Body size, life history, and ecology},
	Volume = {165},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000228094100009}}

@article{Burt.1989.a,
	Author = {Burt, Austin},
	Date-Added = {2011-04-18 11:02:07 +0100},
	Date-Modified = {2011-04-18 11:03:10 +0100},
	Journal = {Oxford Surveys in Evolutionary Biology},
	Pages = {33-53},
	Title = {Comparative methods using phylogenetically independent contrasts.},
	Volume = {6},
	Year = {1989}}

@article{Lislevand.Thomas.2006.a,
	Abstract = {In bird species where males incubate but are smaller than females, egg size may be constrained by male body size, and hence ability to incubate the eggs. Using data from 71 such shorebird species, we show that egg size decreases as the degree of female-biased sexual size dimorphism increases, after controlling for female body mass. Relative egg size was not related to mean clutch size. However, when controlling for mating system, the relationship between female-biased sexual size dimorphism and relative egg size was only significant in polyandrous species. The relatively small eggs of socially polyandrous shorebirds have previously been explained as an energy-saving strategy associated with the production of multiple clutches. Our findings suggest that egg size evolution is better explained by male incubation limitation in these birds.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Lislevand, Terje and Thomas, Gavin H.},
	Date-Added = {2011-04-18 08:58:46 +0100},
	Date-Modified = {2011-04-18 08:58:46 +0100},
	Doi = {DOI 10.1098/rsbl.2005.0428},
	Isi = {000241862500012},
	Isi-Recid = {153096333},
	Isi-Ref-Recids = {56780729 110512008 82585835 123737823 131023506 127500623 136510580 104582742 1980801 131023503 122481379 21148836 100985792 114793100 112336304 117263033 36931383 59827322 97280540 136059106 136180329 99797294 25511169 88862780 111095335},
	Journal = {Biology Letters},
	Keywords = {brood patch; egg size; incubation; shorebirds; waders},
	Month = jun,
	Number = {2},
	Pages = {206--208},
	Publisher = {ROYAL SOCIETY},
	Times-Cited = {3},
	Title = {Limited male incubation ability and the evolution of egg size in shorebirds},
	Volume = {2},
	Year = {2006},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000241862500012}}

@article{Strassburg.Kelly.ea.2010.a,
	Abstract = {Deforestation is a main driver of climate change and biodiversity loss. An incentive mechanism to reduce emissions from deforestation and forest degradation (REDD) is being negotiated under the United Nations Framework Convention on Climate Change. Here we use the best available global data sets on terrestrial biodiversity and carbon storage to map and investigate potential synergies between carbon and biodiversity-oriented conservation. A strong association (r(S) = 0.82) between carbon stocks and species richness suggests that such synergies would be high, but unevenly distributed. Many areas of high value for biodiversity could be protected by carbon-based conservation, while others could benefit from complementary funding arising from their carbon content. Some high-biodiversity regions, however, would not benefit from carbon-focused conservation, and could become under increased pressure if REDD is implemented. Our results suggest that additional gains for biodiversity conservation are possible, without compromising the effectiveness for climate change mitigation, if REDD takes biodiversity distribution into account.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Strassburg, Bernardo B. N. and Kelly, Annabel and Balmford, Andrew and Davies, Richard G. and Gibbs, Holly K. and Lovett, Andrew and Miles, Lera and Orme, C. David L. and Price, Jeff and Turner, R. Kerry and Rodrigues, Ana S. L.},
	Date-Added = {2011-04-13 11:35:48 +0100},
	Date-Modified = {2011-04-13 11:35:48 +0100},
	Doi = {DOI 10.1111/j.1755-263X.2009.00092.x},
	Isi = {000279224000005},
	Isi-Recid = {189787554},
	Isi-Ref-Recids = {187113272 151542795 171522027 96759948 189787555 157586406 162872677 176083133 162235196 184857701 155666782 124704699 111867963 172341781 134819967 176529376 185862245 160871088 162872681 179972484 145723116 145042369 161701303 177083112 143214016 148031793 185541219 133729253 173302047 156136210 181164977 137301762 132624207 150371181 112464784 107489487 187796789},
	Journal = {Conservation Letters},
	Keywords = {Biodiversity; climate change; deforestation; REDD; cobenefits; biological conservation; carbon stocks; UNFCCC; CBD; ecosystem services},
	Month = apr,
	Number = {2},
	Pages = {98--105},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {1},
	Title = {Global congruence of carbon storage and biodiversity in terrestrial ecosystems},
	Volume = {3},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000279224000005}}

@article{Baldwin.Sanderson.1998.a,
	Abstract = {Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an "external" calibration using paleoclimatic and Fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 +/- 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (less than or equal to 5.1 +/- 0.2 million years ago), By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 +/- 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Baldwin, BG and Sanderson, MJ},
	Date-Added = {2011-04-13 11:34:29 +0100},
	Date-Modified = {2011-04-13 11:34:29 +0100},
	Isi = {000075246600062},
	Isi-Recid = {106499516},
	Isi-Ref-Recids = {87626308 89134299 63063266 103692980 75162965 94842176 81713754 103590120 103590125 58582692 95976711 94930397 93736157 38670375 4061475 87253760 92862656 78676418 99953169 84933676 67748941 87626304 103868924 107471364 74710733 99996694 83742849 69325647 318514 93216587 106499517 87408719 87271066 84111634 36103231 78239325 45026494 106499518 95661814 96750226 76953412 68574078 97090834},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = aug,
	Number = {16},
	Pages = {9402--9406},
	Publisher = {NATL ACAD SCIENCES},
	Times-Cited = {307},
	Title = {Age and rate of diversification of the Hawaiian silversword alliance (Compositae)},
	Volume = {95},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000075246600062}}

@article{Abouheif.1999.a,
	Abstract = {When making a comparison between two or more traits across taxa, the assumption of phylogenetic independence must be tested. Empirically determining the validity of this assumption before and after applying a phylogenetically based comparative method (PCM) can provide researchers with a rigorous methodological approach for analysing comparative data. This approach can help resolve current debates regarding whether it is always appropriate to apply a PCM, and whether PCMs are in fact successful in accounting for all of the historical non-independence in comparative data. To use this methodological approach, however, a generally applicable statistical diagnostic that can test the assumption of phylogenetic independence in comparative data is required. In this context, I present the application of a statistical diagnostic called the 'test for serial independence'. This diagnostic can be applied to almost all currently employed PCMs, including Felsenstein's (1985) independent contrasts. Furthermore, I demonstrate the application of the test for serial independence by analysing three data sets from the literature. The results of these analyses show that this diagnostic can successfully detect different degrees of phylogenetic autocorrelation in small and large phylogenies as well as in different types of phenotypic characters. The challenges and difficulties associated with applying the proposed methodological approach and the test for serial independence are discussed.},
	Address = {UNIV ARIZONA, 321 BIOSCIENCES WEST, TUCSON, AZ 85721 USA},
	Author = {Abouheif, E},
	Date-Added = {2011-04-13 11:33:42 +0100},
	Date-Modified = {2011-04-13 11:33:42 +0100},
	Isi = {000084534400001},
	Isi-Recid = {113189346},
	Isi-Ref-Recids = {99456255 106822152 107818594 68958032 93885554 57561095 43397840 95243159 108228217 107655117 97718910 67535675 54497548 84822622 80759959 92373448 74123377 99676099 102328220 38299061 97260513 75043716 91702658 88319323 94842174 76218624 94842170 98053151 88083507 85463272 85463423 1744994 101432044 100359553 86763569 85938648 87248412 95908302 98068978 104099654 64284742 90496259 694448 91702663 366538 53877170},
	Journal = {Evolutionary Ecology Research},
	Keywords = {comparative method; independent contrasts; phylogeny; phylogenetic autocorrelation; test for serial independence},
	Month = dec,
	Number = {8},
	Pages = {895--909},
	Publisher = {EVOLUTIONARY ECOLOGY LTD},
	Times-Cited = {124},
	Title = {A method for testing the assumption of phylogenetic independence in comparative data},
	Volume = {1},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000084534400001}}

@article{Elith.Phillips.ea.2011.a,
	Abstract = {MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Elith, Jane and Phillips, Steven J. and Hastie, Trevor and Dudik, Miroslav and Chee, Yung En and Yates, Colin J.},
	Date-Added = {2011-04-13 10:26:13 +0100},
	Date-Modified = {2011-04-13 10:26:13 +0100},
	Doi = {DOI 10.1111/j.1472-4642.2010.00725.x},
	Isi = {000285246700005},
	Isi-Recid = {193892758},
	Isi-Ref-Recids = {192725336 127164622 150224621 163239017 160690853 175909848 193892759 158705059 157636498 185132934 149708427 193892760 184940744 185132935 152799144 183403700 173684324 173834960 142452031 182475894 171923227 108193800 187135432 147499455 143017698 183084212 175858077 186239014 150224625 153708767 147728857 176718900 161503292 66814352 150194522 157416762 184821517 145454604 159510062 134939284 76042162 94542735 178779941 180704071 184472925 177014905 181408100 193892761 193892762 180919924 157318499 181393792 135162269 174724285 186170385 152653070 182922056 147728867},
	Journal = {Diversity and Distributions},
	Keywords = {Absence; ecological niche; entropy; machine learning; presence-only; species distribution model},
	Month = jan,
	Number = {1},
	Pages = {43--57},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {0},
	Title = {A statistical explanation of MaxEnt for ecologists},
	Volume = {17},
	Year = {2011},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000285246700005}}

@article{Hijmans.Cameron.ea.2005.a,
	Abstract = {We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950-2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and cross validation. Elevation bias tended to be negative (stations lower than expected) at high latitudes but positive in the tropics. Uncertainty is highest in mountainous and in poorly sampled areas. Data partitioning showed high uncertainty of the surfaces on isolated islands, e.g. in the Pacific. Aggregating the elevation and climate data to 10 arc min resolution showed an enormous variation within grid cells, illustrating the value of high-resolution surfaces. A comparison with an existing data set at 10 arc min resolution showed overall agreement, but with significant variation in some regions. A comparison with two high-resolution data sets for the United States also identified areas with large local differences, particularly in mountainous areas. Compared to previous global climatologies, ours has the following advantages: the data are at a higher spatial resolution (400 times greater or more); more weather station records were used; improved elevation data were used; and more information about spatial patterns of uncertainty in the data is available. Owing to the overall low density of available climate stations, our surfaces do not capture of all variation that may occur at a resolution of 1 km, particularly of precipitation in mountainous areas. In future work, such variation might be captured through knowledge-based methods and inclusion of additional co-variates, particularly layers obtained through remote sensing. Copyright (c) 2005 Royal Meteorological Society.},
	Address = {THE ATRIUM, SOUTHERN GATE, CHICHESTER PO19 8SQ, W SUSSEX, ENGLAND},
	Author = {Hijmans, RJ and Cameron, SE and Parra, JL and Jones, PG and Jarvis, A},
	Date-Added = {2011-04-12 17:02:25 +0100},
	Date-Modified = {2011-04-12 17:02:25 +0100},
	Doi = {DOI 10.1002/joc.1276},
	Isi = {000234519700002},
	Isi-Recid = {148243617},
	Isi-Ref-Recids = {148243618 148243619 128990038 126110729 94398824 126983113 91240741 122673846 128990035 148243620 92568809 148243621 120247308 148243622 82627875 144706642 109283576 126110725 148243623 134645858 104190308 107017607 88154269 101058115 137346575},
	Journal = {International Journal of Climatology},
	Keywords = {ANUSPLIN; climate; error; GIS; interpolation; temperature; precipitation; uncertainty},
	Month = dec,
	Number = {15},
	Pages = {1965--1978},
	Publisher = {JOHN WILEY \& SONS LTD},
	Times-Cited = {801},
	Title = {Very high resolution interpolated climate surfaces for global land areas},
	Volume = {25},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000234519700002}}

@article{Tarroso.Rebelo.2010.a,
	Abstract = {There are an increasing number of studies that are now focussing on the influence of climate change on species' distributions. However, access to predictive climatic datasets for future scenarios is difficult due to their specific formats and/or the need to be geographically downscaled. The TYN dataset is freely available to users and provides a synthetic format with several climatic models and IPCC future climate scenarios. Moreover, the CRU historical dataset (1901-2000) is also available which allows users to create baseline models for current climatic variables. E-clic is a free, user-friendly software package that offers three different ways to convert these two datasets into a spatially explicit raster format which is compatible with the most common geographic information systems and usable on different platforms.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Tarroso, Pedro and Rebelo, Hugo},
	Date-Added = {2011-04-12 17:00:21 +0100},
	Date-Modified = {2011-04-12 17:00:21 +0100},
	Doi = {DOI 10.1111/j.1600-0587.2009.05969.x},
	Isi = {000280457500021},
	Isi-Recid = {190640078},
	Isi-Ref-Recids = {152115711 118133611 127654673 155905640 68391995 153798263 145143496 144706642 126064327 127580979 161902184 132624207 133449200 144745203},
	Journal = {Ecography},
	Month = jun,
	Number = {3},
	Pages = {617--620},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {0},
	Title = {E-Clic - easy climate data converter},
	Volume = {33},
	Year = {2010},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000280457500021}}

@techreport{Mitchell.Carter.ea..a,
	Author = {Timothy D. Mitchell and Timothy R. Carter and Philip D. Jones and Mike Hulme and Mark New},
	Date-Added = {2011-04-12 16:55:45 +0100},
	Date-Modified = {2011-04-12 16:58:37 +0100},
	Institution = {Tyndall Centre for Climate Change Research},
	Number = {55},
	Title = {A comprehensive set of high-resolution grids of monthly climate for Europe and the globe: the observed record (1901-2000) and 16 scenarios (2001-2100).},
	Type = {Working Paper},
	Url = {http://www.tyndall.ac.uk/biblio/working-papers},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Mitchell.Jones.2005.a,
	Abstract = {A database of monthly climate observations from meteorological stations is constructed. The database includes six climate elements and extends over the global land surface. The database is checked for inhomogeneities in the station records using an automated method that refines previous methods by using incomplete and partially overlapping records and by detecting inhomogeneities with opposite signs in different seasons. The method includes the development of reference series using neighbouring stations. Information from different sources about a single station may be combined, even without an overlapping period, using a reference series. Thus, a longer station record may be obtained and fragmentation of records reduced. The reference series also enables 1961-90 normals to be calculated for a larger proportion of stations.

The station anomalies are interpolated onto a 0.5 degrees grid covering the global land surface (excluding Antarctica) and combined with a published normal from 1961-90. Thus, climate grids are constructed for nine climate variables (temperature, diurnal temperature range, daily minimum and maximum temperatures, precipitation, wet-day frequency, frost-day frequency, vapour pressure, and cloud cover) for the period 1901-2002. This dataset is known as CRU TS 2.1 and is publicly available (http://www.cru.uea.ac.uk/). Copyright (c) 2005 Royal Meteorological Society.},
	Address = {THE ATRIUM, SOUTHERN GATE, CHICHESTER PO19 8SQ, W SUSSEX, ENGLAND},
	Author = {Mitchell, T D and Jones, P D},
	Date-Added = {2011-04-12 16:55:31 +0100},
	Date-Modified = {2011-04-13 15:28:43 +0100},
	Doi = {DOI 10.1002/joc.1181},
	Isi = {000229688800001},
	Isi-Recid = {144706642},
	Isi-Ref-Recids = {144706643 129575163 132311240 128368731 110616525 129520306 91240741 128115590 144706644 64234424 99422451 106726253 89302180 127987344 130962717 144706645 131741710 109283576 116061752 104190308 102679508 88154269 107017607 107664336 107420317 101583188 93860971 102978235},
	Journal = {International Journal of Climatology},
	Keywords = {climate; observations; grids; homogeneity; temperature; precipitation; vapour; cloud},
	Month = may,
	Number = {6},
	Pages = {693--712},
	Publisher = {JOHN WILEY \& SONS LTD},
	Times-Cited = {632},
	Title = {An improved method of constructing a database of monthly climate observations and associated high-resolution grids},
	Volume = {25},
	Year = {2005},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000229688800001}}

@article{Conde.Flesness.ea.2011.a,
	Address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA},
	Author = {Conde, D. A. and Flesness, N. and Colchero, F. and Jones, O. R. and Scheuerlein, A.},
	Date-Added = {2011-04-06 08:54:59 +0100},
	Date-Modified = {2011-04-06 08:54:59 +0100},
	Doi = {DOI 10.1126/science.1200674},
	Isi = {000288504000023},
	Isi-Recid = {195771484},
	Isi-Ref-Recids = {195771485 182494235 159664793 152293108 195771486 195771487 195112766 119763634 152836347 195771488 193495509 115948948 162242510 195771489 123378411 157354273 110366805 118875290 96939233 144323732},
	Journal = {Science},
	Month = mar,
	Number = {6023},
	Pages = {1390--1391},
	Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
	Times-Cited = {0},
	Title = {An Emerging Role of Zoos to Conserve Biodiversity},
	Type = {Editorial Material},
	Volume = {331},
	Year = {2011},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000288504000023}}

@article{Philippe.Brinkmann.ea.2011.a,
	Author = {Philippe, Herv{\'e} and Brinkmann, Henner and Lavrov, Dennis V and Littlewood, D Timothy J and Manuel, Michael and W{\"o}rheide, Gert and Baurain, Denis},
	Date-Added = {2011-04-06 08:31:39 +0100},
	Date-Modified = {2011-04-06 08:31:39 +0100},
	Doi = {10.1371/journal.pbio.1000602},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Month = {Mar},
	Number = {3},
	Pages = {e1000602},
	Pmc = {PMC3057953},
	Pmid = {21423652},
	Pst = {ppublish},
	Title = {Resolving difficult phylogenetic questions: why more sequences are not enough},
	Volume = {9},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{Grueber.Nakagawa.ea.2011.a,
	Abstract = {Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.},
	Author = {Grueber, C E and Nakagawa, S and Laws, R J and Jamieson, I G},
	Date-Added = {2011-03-25 10:30:04 +0000},
	Date-Modified = {2011-03-25 10:30:04 +0000},
	Doi = {10.1111/j.1420-9101.2010.02210.x},
	Journal = {J Evol Biol},
	Journal-Full = {Journal of evolutionary biology},
	Month = {Apr},
	Number = {4},
	Pages = {699-711},
	Pmid = {21272107},
	Pst = {ppublish},
	Title = {Multimodel inference in ecology and evolution: challenges and solutions},
	Volume = {24},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{McInnes.Orme.ea.2011.a,
	Abstract = {Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a-probably untenable-model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.},
	Author = {McInnes, Lynsey and Orme, C David L and Purvis, A},
	Date-Added = {2011-03-25 10:26:12 +0000},
	Date-Modified = {2011-03-25 10:26:12 +0000},
	Doi = {10.1098/rspb.2011.0241},
	Journal = {Proc Biol Sci},
	Journal-Full = {Proceedings. Biological sciences / The Royal Society},
	Month = {Mar},
	Pmid = {21429924},
	Pst = {aheadofprint},
	Title = {Detecting shifts in diversity limits from molecular phylogenies: what can we know?},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{OHara.Kotze.2010.a,
	Author = {O'Hara, Robert B. and Kotze, D. Johan},
	Date-Added = {2011-03-18 09:34:35 +0000},
	Date-Modified = {2011-03-18 09:36:53 +0000},
	Journal = {Methods in Ecology and Evolution},
	Pages = {118-122},
	Title = {Do not log-transform count data},
	Volume = {1},
	Year = {2010},
	Bdsk-File-1 = { }}

@incollection{Purvis.Orme.ea.2002.a,
	Author = {Purvis, Andy and Orme, C. David L. and Dolphin, Konrad},
	Booktitle = {Macroecology: Concepts and Consequences},
	Date-Added = {2011-03-08 17:41:40 +0000},
	Date-Modified = {2011-03-08 17:44:04 +0000},
	Editor = {Gaston, Kevin J. and Blackburn, Tim M.},
	Publisher = {Blackwell Publishing Ltd},
	Title = {Why are most species small-bodied? A phylogenetic view},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Hopcraft.Sinclair.ea.2005.a,
	Abstract = {1. We used long-term radio-telemetry data to investigate how Serengeti lions (Panthera leo) distribute themselves with respect to hunting opportunities. Specifically, we investigate whether lions hunt in areas where prey are easy to capture or where prey are locally abundant.

2. We used resource-selection functions (logistic regressions) to measure the location of kills/carcasses with respect to five different habitats: the view-sheds from large rocky outcrops, river confluences, woodland vegetation, erosion embankments and water sources.

3. As expected for a sit-and-wait predator, resting lions spent more time in areas with good cover. On a broad-scale, lions shifted their ranges according to the seasonal movement of prey, but at a finer scale (< 100 m) lions fed in areas with high prey 'catchability' rather than high prey density. Plains lions selected erosion embankments, view-sheds from rocky outcrops, and access to free water. Woodland lions tended to use erosion embankments, and woody vegetation.

4. The results emphasize the importance of fine-scale landscape and habitat features when assessing predator-prey theory and conservation.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DG, OXON, ENGLAND},
	Author = {Hopcraft, JGC and Sinclair, ARE and Packer, C},
	Date-Added = {2011-03-08 17:20:16 +0000},
	Date-Modified = {2011-03-08 17:20:16 +0000},
	Doi = {DOI 10.1111/j.1365-2656.2005.00955.x},
	Isi = {000229283500017},
	Isi-Recid = {144490497},
	Isi-Ref-Recids = {119495220 110765974 123976899 86912056 75530908 54025971 124604387 98140810 32939273 91066417 119905853 104739160 120670206 112451531 91866241 89725152 13221617 108178384 72637046 123267536 59422819 72874304 45155491 131700041 50141727 63699641 106313932 89536531 73561838 100145671 122208915 27358445 37177792 111253165 69083107 111133800 24591933 82429299 75869174 91066415 46218394 56871571 126508208 79152118 92125943 98302642 72203369 129728675 52470697},
	Journal = {Journal of Animal Ecology},
	Keywords = {ambush predator; habitat selection; predator-sensitive foraging; predator-prey interaction; prey abundance; resource selection},
	Month = may,
	Number = {3},
	Pages = {559-566},
	Publisher = {BLACKWELL PUBLISHING},
	Times-Cited = {47},
	Title = {Planning for success: Serengeti lions seek prey accessibility rather than abundance},
	Volume = {74},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000229283500017}}

@article{Pettorelli.Hilborn.ea.2009.a,
	Abstract = {Understanding the basis of habitat choice having important implications for explaining the distribution of organisms, as well as helping to differentiate between habitats of different quality for effective management. In this study, the effects of sex, age and reproductive status on habitat use patterns of cheetahs Acinonyx jubatus in the Serengeti plains were explored using Ecological Niche Factor Analysis (ENFA). Our results showed that gender and territoriality did not affect patterns of habitat use. However, females tended to be more specialized when they were young than when they were older, displaying a more restricted ecological niche. Likewise, older females without cubs were more specialized than the same adult females with young cubs. This result did not hold for younger females. Altogether, the ENFA approach allowed us to (1) use the large amount of incidental sighting data collected over 12 years on cheetah spatial distribution; (2) identify the importance of reproductive status and age on the relationship between animals and their habitat; (3) further demonstrate that ENFA is applicable in a wide range of situations, including for exploring individual variation in niche definition.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Pettorelli, N. and Hilborn, A. and Broekhuis, F. and Durant, S. M.},
	Date-Added = {2011-03-08 17:19:44 +0000},
	Date-Modified = {2011-03-08 17:19:44 +0000},
	Doi = {DOI 10.1111/j.1469-7998.2008.00522.x},
	Isi = {000262678200008},
	Isi-Recid = {176289185},
	Isi-Ref-Recids = {116955616 160690770 154852406 131921328 134754207 151764361 135798305 61800472 76430895 89367642 142103748 108640688 68036978 133522015 156472957 105564217 102054341 74210797 127412683 142587027 125571143 153910051 153122142 144490497 85495376 123378530 3097843 117298042 92877020 89367640 176289186 131164037 176289187 136717503 104893388 130178603 148450393 143780550 56489091 159417440 129304929 157636641 150894712 150714995 158898300 93072885 157780850 90496259 154231804 48372010 105790213},
	Journal = {Journal of Zoology},
	Keywords = {Acinonyx jubatus; Serengeti; ENFA; carnivores; Africa},
	Month = feb,
	Number = {2},
	Pages = {141-148},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {1},
	Title = {Exploring habitat use by cheetahs using ecological niche factor analysis},
	Volume = {277},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000262678200008}}

@article{Hoorn.Wesselingh.ea.2010.a,
	Abstract = {The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this "Andean" substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.},
	Author = {Hoorn, C and Wesselingh, F P and ter Steege, H and Bermudez, M A and Mora, A and Sevink, J and Sanmart{\'\i}n, I and Sanchez-Meseguer, A and Anderson, C L and Figueiredo, J P and Jaramillo, C and Riff, D and Negri, F R and Hooghiemstra, H and Lundberg, J and Stadler, T and S{\"a}rkinen, T and Antonelli, A},
	Date-Added = {2011-03-02 14:31:47 +0000},
	Date-Modified = {2011-03-02 14:31:47 +0000},
	Doi = {10.1126/science.1194585},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Biodiversity; Climate Change; Ecosystem; Fossils; Geography; Geological Phenomena; Phylogeny; Rivers; South America; Time; Trees; Wetlands},
	Month = {Nov},
	Number = {6006},
	Pages = {927-31},
	Pmid = {21071659},
	Pst = {ppublish},
	Title = {Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity},
	Volume = {330},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Lyons.Wagner.ea.2010.a,
	Abstract = {Understanding and predicting how species' distributions will shift as climate changes are central questions in ecology today. The late Quaternary of North America represents a natural experiment in which we can evaluate how species responded during the expansion and contraction of the glaciers. Here, we ask whether species' range shifts differ because of taxonomic affinity, life-history traits, body size or topographic heterogeneity and whether the species survived the megafaunal extinction. There was no difference in range shifts between victims and survivors of the megafaunal extinction. In general, the change in the size of a species' range is not well correlated with any of the ecological or life-history traits evaluated. However, there are significant relationships between some variables and the movements of the centroids of ranges. Differences in the distances shifted exist among orders, although this is probably a result of body size differences as larger bodied species show larger shifts. Although there are a few exceptions, the distance that species shifted their range was weakly correlated with life-history traits. Finally, species in more topographically heterogeneous areas show smaller shifts than species in less-diverse areas. Overall, these results indicate that when trying to predict species range shifts in the future, body size, lifespan and the topographic relief of the landscape should be taken into account.},
	Author = {Lyons, S Kathleen and Wagner, Peter J and Dzikiewicz, Katherine},
	Date-Added = {2011-03-02 14:31:28 +0000},
	Date-Modified = {2011-03-02 14:31:28 +0000},
	Doi = {10.1098/rstb.2010.0263},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Mesh = {Adaptation, Biological; Animals; Body Size; Climate Change; Databases, Factual; Demography; Fossils; Geography; Mammals; Phylogeny; Statistics, Nonparametric; United States},
	Month = {Nov},
	Number = {1558},
	Pages = {3681-93},
	Pmc = {PMC2981999},
	Pmid = {20980316},
	Pst = {ppublish},
	Title = {Ecological correlates of range shifts of Late Pleistocene mammals},
	Volume = {365},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Benton.2010.a,
	Abstract = {Comparative studies of large phylogenies of living and extinct groups have shown that most biodiversity arises from a small number of highly species-rich clades. To understand biodiversity, it is important to examine the history of these clades on geological time scales. This is part of a distinct 'phylogenetic expansion' view of macroevolution, and contrasts with the alternative, non-phylogenetic 'equilibrium' approach to the history of biodiversity. The latter viewpoint focuses on density-dependent models in which all life is described by a single global-scale model, and a case is made here that this approach may be less successful at representing the shape of the evolution of life than the phylogenetic expansion approach. The terrestrial fossil record is patchy, but is adequate for coarse-scale studies of groups such as vertebrates that possess fossilizable hard parts. New methods in phylogenetic analysis, morphometrics and the study of exceptional biotas allow new approaches. Models for diversity regulation through time range from the entirely biotic to the entirely physical, with many intermediates. Tetrapod diversity has risen as a result of the expansion of ecospace, rather than niche subdivision or regional-scale endemicity resulting from continental break-up. Tetrapod communities on land have been remarkably stable and have changed only when there was a revolution in floras (such as the demise of the Carboniferous coal forests, or the Cretaceous radiation of angiosperms) or following particularly severe mass extinction events, such as that at the end of the Permian.},
	Author = {Benton, Michael J},
	Date-Added = {2011-03-02 14:31:04 +0000},
	Date-Modified = {2011-03-02 14:31:04 +0000},
	Doi = {10.1098/rstb.2010.0269},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Mesh = {Adaptation, Biological; Animals; Biodiversity; Biological Evolution; Ecosystem; Environment; Fossils; Models, Theoretical; Phylogeny; Vertebrates},
	Month = {Nov},
	Number = {1558},
	Pages = {3667-79},
	Pmc = {PMC2982001},
	Pmid = {20980315},
	Pst = {ppublish},
	Title = {The origins of modern biodiversity on land},
	Volume = {365},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Paradis.Baillie.ea.2002.a,
	Abstract = {We present an approach to analyze dispersal distance data. This approach allows one to take into account accuracy of the recorded dispersal distances. Three distributions were used, all assuming continuous space; a maximum likelihood approach was used for parameter estimation and model selection. Numerical simulations showed that our method is statistically consistent since it selected the correct model with increasing frequency when sample size increased. Ringing data on two species of tits (Parus caeruleus and Parus major) in Britain and Ireland were used to illustrate the potentialities of our method. In both species, adults dispersed significantly further than juveniles. The differences between species within an age-class were not statistically significant. In all species and age-classes, the model finally selected was the one assuming a heavy-tailed half-Cauchy distribution where long-distance dispersers are predicted to be more frequent than in the exponential model. The proposed methodology can potentially be applied to any organisms, and the model selection procedure can be used with any model of the distribution of dispersal distances (DE)D). Several extensions are presented in the discussion, such as generalized linear modeling of the dispersal parameters, or interfacing with capture-recapture models. (C) 2002 Elsevier Science B.V. All rights reserved.},
	Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
	Author = {Paradis, E and Baillie, SR and Sutherland, WJ},
	Date-Added = {2011-03-02 14:30:30 +0000},
	Date-Modified = {2011-03-02 14:30:30 +0000},
	Isi = {000176080300010},
	Isi-Recid = {125067245},
	Isi-Ref-Recids = {125067246 70949349 101969046 117110993 92710971 66198249 86060937 107196536 106348612 106208535 106465810 103230041 120150432 90487881 51762062 81996203 43166031 99712630 115425185 85953935 47545206 41638097 110562555 20522612 104582742 97806670 96002869 110835268 99801814 104751570 83877553 8143328 100126207 103227721 115625954 104952468 68617361 106465807 71750445 46553331 93124036 84361140 100786441 125067247 90880389 103988697 93869006 116433793},
	Journal = {Ecological Modelling},
	Keywords = {dispersal; estimation; hypothesis testing; likelihood; model; spatial scale},
	Month = jun,
	Number = {2-3},
	Pages = {279-292},
	Publisher = {ELSEVIER SCIENCE BV},
	Times-Cited = {33},
	Title = {Modeling large-scale dispersal distances},
	Volume = {151},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000176080300010}}

@article{Stone.Nee.ea.2011.a,
	Author = {Stone, Graham N. and Nee, Sean and Felsenstein, Joseph},
	Date-Added = {2011-03-02 14:27:53 +0000},
	Date-Modified = {2011-03-02 14:29:04 +0000},
	Journal = {Philosophical Transactions of the Royal Society B-Biological Sciences},
	Title = {Controlling for non-independence in comparative analysis of patterns across populations within species},
	Year = {In press},
	Bdsk-File-1 = { }}

@article{Hartmann.Wong.ea.2010.a,
	Abstract = {A wide range of evolutionary models for species-level (and higher) diversification have been developed. These models can be used to test evolutionary hypotheses and provide comparisons with phylogenetic trees constructed from real data. To carry out these tests and comparisons, it is often necessary to sample, or simulate, trees from the evolutionary models. Sampling trees from these models is more complicated than it may appear at first glance, necessitating careful consideration and mathematical rigor. Seemingly straightforward sampling methods may produce trees that have systematically biased shapes or branch lengths. This is particularly problematic as there is no simple method for determining whether the sampled trees are appropriate. In this paper, we show why a commonly used simple sampling approach (SSA)-simulating trees forward in time until n species are first reached-should only be applied to the simplest pure birth model, the Yule model. We provide an alternative general sampling approach (GSA) that can be applied to most other models. Furthermore, we introduce the constant-rate birth-death model sampling approach, which samples trees very efficiently from a widely used class of models. We explore the bias produced by SSA and identify situations in which this bias is particularly pronounced. We show that using SSA can lead to erroneous conclusions: When using the inappropriate SSA, the variance of a gradually evolving trait does not correlate with the age of the tree; when the correct GSA is used, the trait variance correlates with tree age. The algorithms presented here are available in the Perl Bio::Phylo package, as a stand-alone program TreeSample, and in the R TreeSim package.},
	Author = {Hartmann, Klaas and Wong, Dennis and Stadler, Tanja},
	Date-Added = {2011-03-02 14:21:03 +0000},
	Date-Modified = {2011-03-02 14:21:03 +0000},
	Doi = {10.1093/sysbio/syq026},
	Journal = {Syst Biol},
	Journal-Full = {Systematic biology},
	Mesh = {Biological Evolution; Computer Simulation; Genetic Speciation; Models, Genetic; Selection Bias},
	Month = {Jul},
	Number = {4},
	Pages = {465-76},
	Pmid = {20547782},
	Pst = {ppublish},
	Title = {Sampling trees from evolutionary models},
	Volume = {59},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Bokma.2010.a,
	Author = {Bokma, Folmer},
	Date-Added = {2011-03-02 14:20:54 +0000},
	Date-Modified = {2011-03-02 14:20:54 +0000},
	Doi = {10.1093/sysbio/syq029},
	Journal = {Syst Biol},
	Journal-Full = {Systematic biology},
	Mesh = {Bayes Theorem; Biological Evolution; Genetic Variation; Likelihood Functions; Neural Networks (Computer); Phenotype; Phylogeny},
	Month = {Oct},
	Number = {5},
	Pages = {602-7},
	Pmid = {20926600},
	Pst = {ppublish},
	Title = {Time, species, and separating their effects on trait variance in clades},
	Volume = {59},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Vorosmarty.McIntyre.ea.2010.a,
	Abstract = {Protecting the world's freshwater resources requires diagnosing threats over a broad range of scales, from global to local. Here we present the first worldwide synthesis to jointly consider human and biodiversity perspectives on water security using a spatial framework that quantifies multiple stressors and accounts for downstream impacts. We find that nearly 80\% of the world's population is exposed to high levels of threat to water security. Massive investment in water technology enables rich nations to offset high stressor levels without remedying their underlying causes, whereas less wealthy nations remain vulnerable. A similar lack of precautionary investment jeopardizes biodiversity, with habitats associated with 65\% of continental discharge classified as moderately to highly threatened. The cumulative threat framework offers a tool for prioritizing policy and management responses to this crisis, and underscores the necessity of limiting threats at their source instead of through costly remediation of symptoms in order to assure global water security for both humans and freshwater biodiversity.},
	Author = {V{\"o}r{\"o}smarty, C J and McIntyre, P B and Gessner, M O and Dudgeon, D and Prusevich, A and Green, P and Glidden, S and Bunn, S E and Sullivan, C A and Liermann, C Reidy and Davies, P M},
	Date-Added = {2011-03-02 14:20:11 +0000},
	Date-Modified = {2011-03-02 14:20:11 +0000},
	Doi = {10.1038/nature09440},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Biodiversity; Conservation of Natural Resources; Fisheries; Geography; Internationality; Population Density; Rivers; Water Supply},
	Month = {Sep},
	Number = {7315},
	Pages = {555-61},
	Pmid = {20882010},
	Pst = {ppublish},
	Title = {Global threats to human water security and river biodiversity},
	Volume = {467},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Foufopoulos.Kilpatrick.ea.2011.a,
	Abstract = {Recent climate change has caused the distributions of many species to shift poleward, yet few empirical studies have addressed which species will be vulnerable to longer-term climate changes. To investigate past consequences of climate change, we calculated the population extinction rates of 35 reptile species from 87 Greek land-bridge islands in the Mediterranean that occurred over the past 16,000 years. Population extinction rates were higher for those species that today have more northern distributions. We further found that northern species requiring cool, mesic habitats had less available suitable habitat among islands, implicating loss of suitable habitat in their elevated extinction rates. These extinctions occurred in the context of increasing habitat fragmentation, with islands shrinking and separating as sea levels rose. Thus, the circumstances faced by reptiles on the islands are similar to challenges for numerous species today that must cope with a changing climate while living in an increasingly human-fragmented landscape. Our island-biogeographical approach to investigating historical population extinctions gives insight into the long-term patterns of species responses to climate change.},
	Author = {Foufopoulos, Johannes and Kilpatrick, A Marm and Ives, Anthony R},
	Date-Added = {2011-02-18 12:19:59 +0000},
	Date-Modified = {2011-02-18 12:19:59 +0000},
	Doi = {10.1086/657624},
	Journal = {Am Nat},
	Journal-Full = {The American naturalist},
	Month = {Jan},
	Number = {1},
	Pages = {119-29},
	Pmid = {21091198},
	Pst = {ppublish},
	Title = {Climate change and elevated extinction rates of reptiles from Mediterranean Islands},
	Volume = {177},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{Rabosky.2010.a,
	Abstract = {The disparity in species richness across the tree of life is one of the most striking and pervasive features of biological diversity. Some groups are exceptionally diverse, whereas many other groups are species poor. Differences in diversity among groups are frequently assumed to result from primary control by differential rates of net diversification. However, a major alternative explanation is that ecological and other factors exert primary control on clade diversity, such that apparent variation in net diversification rates is a secondary consequence of ecological limits on clade growth. Here, I consider a likelihood framework for distinguishing between these competing hypotheses. I incorporate hierarchical modeling to explicitly relax assumptions about the constancy of diversification rates across clades, and I propose several statistics for a posteriori evaluation of model adequacy. I apply the framework to a recent dated phylogeny of ants. My results reject the hypothesis that net diversification rates exert primary control on species richness in this group and demonstrate that clade diversity is better explained by total time-integrated speciation. These results further suggest that it may not possible to estimate meaningful speciation and extinction rates from higher-level phylogenies of extant taxa only.},
	Author = {Rabosky, Daniel L},
	Date-Added = {2011-02-18 12:16:09 +0000},
	Date-Modified = {2011-02-18 12:16:09 +0000},
	Doi = {10.1093/sysbio/syq060},
	Journal = {Syst Biol},
	Journal-Full = {Systematic biology},
	Mesh = {Animals; Biodiversity; Genetic Speciation; Likelihood Functions; Models, Genetic},
	Month = {Dec},
	Number = {6},
	Pages = {634-45},
	Pmid = {20926597},
	Pst = {ppublish},
	Title = {Primary controls on species richness in higher taxa},
	Volume = {59},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Fisher.Blomberg.2010.a,
	Abstract = {Extinction is difficult to detect, even in well-known taxa such as mammals. Species with long gaps in their sighting records, which might be considered possibly extinct, are often rediscovered. We used data on rediscovery rates of missing mammals to test whether extinction from different causes is equally detectable and to find which traits affect the probability of rediscovery. We find that species affected by habitat loss were much more likely to be misclassified as extinct or to remain missing than those affected by introduced predators and diseases, or overkill, unless they had very restricted distributions. We conclude that extinctions owing to habitat loss are most difficult to detect; hence, impacts of habitat loss on extinction have probably been overestimated, especially relative to introduced species. It is most likely that the highest rates of rediscovery will come from searching for species that have gone missing during the 20th century and have relatively large ranges threatened by habitat loss, rather than from additional effort focused on charismatic missing species.},
	Author = {Fisher, Diana O and Blomberg, Simon P},
	Date-Added = {2011-02-18 12:15:37 +0000},
	Date-Modified = {2011-02-18 12:15:37 +0000},
	Doi = {10.1098/rspb.2010.1579},
	Journal = {Proc Biol Sci},
	Journal-Full = {Proceedings. Biological sciences / The Royal Society},
	Month = {Sep},
	Pmid = {20880890},
	Pst = {aheadofprint},
	Title = {Correlates of rediscovery and the detectability of extinction in mammals},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{GEB:GEB560,
	Abstract = {ABSTRACT
Aim  We investigate the relationship between local and regional richness in marine fouling assemblages using an expanded and globally replicated approach by incorporating two dimensions of diversity (taxonomic and functional) and different successional stages.Location  Global.Methods  In eight different biogeographic regions (Australia, Brazil, Chile, England, Italy, Japan, Portugal and Sweden) 68 polyvinylchloride (PVC) panels (15 × 15 × 0.3 cm) were deployed for colonization. Communities colonizing panels were analysed by measuring percentage cover at each of four different successional ages: 2, 4, 6 and 8 months. Local richness was assessed as the average number of species and functional groups (FGs) per panel and regional richness was evaluated as the estimated (Jack2) asymptote of the sample-accumulation curves for species and FG on experimental panels.Results  We found that the shape of the relationship between local and regional richness depended on successional stage and the type of richness considered, i.e. taxonomic or functional richness. Hardly any relationship was detectable between local taxonomic richness and regional taxonomic richness at any successional stage. In contrast, the relation between local functional and regional functional richness shows a unimodal pattern of change during succession, passing through the stages `independent', `unsaturated rising', `saturated rising' and once again `independent'.Main conclusions  The relationship between local and regional richness, whether taxonomic or functional, frequently displays independence of the two scales, particularly in early and late phases of the successional process.},
	Author = {Canning-Clode, Jo{\~a}o and Maloney, Kelly O. and McMahon, Sean M. and Wahl, Martin},
	Date-Added = {2011-02-18 09:50:20 +0000},
	Date-Modified = {2011-02-18 09:50:20 +0000},
	Doi = {10.1111/j.1466-8238.2010.00560.x},
	Issn = {1466-8238},
	Journal = {Global Ecology and Biogeography},
	Keywords = {Fouling assemblages, functional richness, jackknife estimator, spatial scales, species richness, saturation, succession},
	Number = {6},
	Pages = {875--885},
	Publisher = {Blackwell Publishing Ltd},
	Title = {Expanded view of the local--regional richness relationship by incorporating functional richness and time: a large-scale perspective},
	Url = {http://dx.doi.org/10.1111/j.1466-8238.2010.00560.x},
	Volume = {19},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2010.00560.x}}

@article{Fuller.McDonald-Madden.ea.2010.a,
	Abstract = {Protected areas vary enormously in their contribution to conserving biodiversity, and the inefficiency of protected area systems is widely acknowledged. However, conservation plans focus overwhelmingly on adding new sites to current protected area estates. Here we show that the conservation performance of a protected area system can be radically improved, without extra expenditure, by replacing a small number of protected areas with new ones that achieve more for conservation. Replacing the least cost-effective 1\% of Australia's 6,990 strictly protected areas could increase the number of vegetation types that have 15\% or more of their original extent protected from 18 to 54, of a maximum possible of 58. Moreover, it increases markedly the area that can be protected, with no increase in overall spending. This new paradigm for protected area system expansion could yield huge improvements to global conservation at a time when competition for land is increasingly intense.},
	Author = {Fuller, Richard A and McDonald-Madden, Eve and Wilson, Kerrie A and Carwardine, Josie and Grantham, Hedley S and Watson, James E M and Klein, Carissa J and Green, David C and Possingham, Hugh P},
	Date-Added = {2011-02-10 10:11:18 +0000},
	Date-Modified = {2011-02-10 10:11:18 +0000},
	Doi = {10.1038/nature09180},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Australia; Biodiversity; Conservation of Natural Resources; Cost-Benefit Analysis; Ecosystem; Forestry; Trees},
	Month = {Jul},
	Number = {7304},
	Pages = {365-7},
	Pmid = {20592729},
	Pst = {ppublish},
	Title = {Replacing underperforming protected areas achieves better conservation outcomes},
	Volume = {466},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Tittensor.Mora.ea.2010.a,
	Abstract = {Global patterns of species richness and their structuring forces have fascinated biologists since Darwin and provide critical context for contemporary studies in ecology, evolution and conservation. Anthropogenic impacts and the need for systematic conservation planning have further motivated the analysis of diversity patterns and processes at regional to global scales. Whereas land diversity patterns and their predictors are known for numerous taxa, our understanding of global marine diversity has been more limited, with recent findings revealing some striking contrasts to widely held terrestrial paradigms. Here we examine global patterns and predictors of species richness across 13 major species groups ranging from zooplankton to marine mammals. Two major patterns emerged: coastal species showed maximum diversity in the Western Pacific, whereas oceanic groups consistently peaked across broad mid-latitudinal bands in all oceans. Spatial regression analyses revealed sea surface temperature as the only environmental predictor highly related to diversity across all 13 taxa. Habitat availability and historical factors were also important for coastal species, whereas other predictors had less significance. Areas of high species richness were disproportionately concentrated in regions with medium or higher human impacts. Our findings indicate a fundamental role of temperature or kinetic energy in structuring cross-taxon marine biodiversity, and indicate that changes in ocean temperature, in conjunction with other human impacts, may ultimately rearrange the global distribution of life in the ocean.},
	Author = {Tittensor, Derek P and Mora, Camilo and Jetz, Walter and Lotze, Heike K and Ricard, Daniel and Berghe, Edward Vanden and Worm, Boris},
	Date-Added = {2011-02-10 10:10:42 +0000},
	Date-Modified = {2011-02-10 10:10:42 +0000},
	Doi = {10.1038/nature09329},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Biodiversity; Ecosystem; Humans; Linear Models; Marine Biology; Models, Biological; Temperature},
	Month = {Aug},
	Number = {7310},
	Pages = {1098-101},
	Pmid = {20668450},
	Pst = {ppublish},
	Title = {Global patterns and predictors of marine biodiversity across taxa},
	Volume = {466},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Revell.2009.a,
	Abstract = {Phylogenetic methods for the analysis of species data are widely used in evolutionary studies. However, preliminary data transformations and data reduction procedures (such as a size-correction and principal components analysis, PCA) are often performed without first correcting for nonindependence among the observations for species. In the present short comment and attached R and MATLAB code, I provide an overview of statistically correct procedures for phylogenetic size-correction and PCA. I also show that ignoring phylogeny in preliminary transformations can result in significantly elevated variance and type I error in our statistical estimators, even if subsequent analysis of the transformed data is performed using phylogenetic methods. This means that ignoring phylogeny during preliminary data transformations can possibly lead to spurious results in phylogenetic statistical analyses of species data.},
	Author = {Revell, Liam J},
	Date-Added = {2011-02-10 10:05:01 +0000},
	Date-Modified = {2011-02-10 10:05:01 +0000},
	Doi = {10.1111/j.1558-5646.2009.00804.x},
	Journal = {Evolution},
	Journal-Full = {Evolution; international journal of organic evolution},
	Mesh = {Least-Squares Analysis; Phylogeny; Principal Component Analysis; Species Specificity},
	Month = {Dec},
	Number = {12},
	Pages = {3258-68},
	Pmid = {19663993},
	Pst = {ppublish},
	Title = {Size-correction and principal components for interspecific comparative studies},
	Volume = {63},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{springerlink:10.1007/BF02180186,
	Abstract = {The bipinnaria larva of the shelf-dwelling asteroidLuidia sarsi Duben and Koren, 1845, can attain (exceptionally) a length of 35 mm; metamorphosis to the adult benthic phase usually occurs well before this size is reached. A seastar rudiment develops at the oral end of the bipinnaria and, under normal circumstances, it detaches itself from its larval body before reaching a diameter of 5 mm. Midwater trawl samples taken from the surface to 1650 m in the Porcupine Seabight during 1978 and 1979, however, includedL. sarsi larvae with post-larval rudiments of 15 mm diameter and greater. It is shown that the bipinnariae and attached post-larvae both continued to grow until a point was reached when it appeared that the young sea-star could no longer be sustained by the bipinnaria. There is evidence that the largest post-larvae had absorbed the bipinnaria tissue and this, it is concluded, is the final stage before enforced settlement. From the estimated growth rate it is likely that many specimens had been in the plankton for &gt;1 yr, giving this species a capability for long-distance dispersal.},
	Author = {Domanski, P.},
	Date-Added = {2011-02-09 10:02:59 +0000},
	Date-Modified = {2011-02-09 10:03:43 +0000},
	Issn = {0025-3162},
	Issue = {2},
	Journal = {Marine Biology},
	Keyword = {Biomedical and Life Sciences},
	Note = {10.1007/BF02180186},
	Pages = {189-195},
	Publisher = {Springer Berlin / Heidelberg},
	Title = {Giant larvae: Prolonged planktonic larval phase in the asteroid \textit{Luidia sarsi}},
	Url = {http://dx.doi.org/10.1007/BF02180186},
	Volume = {80},
	Year = {1984},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF02180186}}

@unpublished{Rabosky.Glor..a,
	Author = {Rabosky, Daniel L. and Glor, Richard E.},
	Date-Added = {2011-02-08 11:01:48 +0000},
	Date-Modified = {2011-02-08 11:02:20 +0000},
	Title = {Equilibrium speciation dynamics in a model adaptive radiation of island lizards},
	Bdsk-File-1 = { }}

@article{Pillar.Duarte.2010.a,
	Abstract = {It is well known that species evolutionary history plays a crucial role in community assembly. Here, we offer a formal analytical framework to integrate in metacommunity analysis the species' phylogeny with their functional traits and abundances. We define phylogenetic structure of a community as phylogenetically weighted species composition. This is used to reveal patterns of phylogenetic community variation and to measure and test by specified null models the phylogenetic signal at the metacommunity level, which we distinguish from phylogenetic signal at the species pool level. The former indicates that communities more similar in their phylogenetic structure are also similar in their average trait values, which may indicate species' niche conservation for the given traits. We apply this framework to an example from grassland communities and find that traits with significant phylogenetic signal at the metacommunity level exhibit ecological filtering along the resource gradient, but since both mechanisms act independently on traits, niche conservatism is not supported.},
	Author = {Pillar, Val{\'e}rio D and Duarte, Leandro d S},
	Date-Added = {2011-02-08 10:59:02 +0000},
	Date-Modified = {2011-02-08 10:59:15 +0000},
	Doi = {10.1111/j.1461-0248.2010.01456.x},
	Journal = {Ecology letters},
	Journal-Full = {Ecology letters},
	Mesh = {Models, Genetic; Phylogeny; Poaceae; Species Specificity},
	Month = {May},
	Number = {5},
	Pages = {587-96},
	Pmid = {20337699},
	Pst = {ppublish},
	Title = {A framework for metacommunity analysis of phylogenetic structure},
	Volume = {13},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Lemey.Rambaut.ea.2010.a,
	Abstract = {Research aimed at understanding the geographic context of evolutionary histories is burgeoning across biological disciplines. Recent endeavors attempt to interpret contemporaneous genetic variation in the light of increasingly detailed geographical and environmental observations. Such interest has promoted the development of phylogeographic inference techniques that explicitly aim to integrate such heterogeneous data. One promising development involves reconstructing phylogeographic history on a continuous landscape. Here, we present a Bayesian statistical approach to infer continuous phylogeographic diffusion using random walk models while simultaneously reconstructing the evolutionary history in time from molecular sequence data. Moreover, by accommodating branch-specific variation in dispersal rates, we relax the most restrictive assumption of the standard Brownian diffusion process and demonstrate increased statistical efficiency in spatial reconstructions of overdispersed random walks by analyzing both simulated and real viral genetic data. We further illustrate how drawing inference about summary statistics from a fully specified stochastic process over both sequence evolution and spatial movement reveals important characteristics of a rabies epidemic. Together with recent advances in discrete phylogeographic inference, the continuous model developments furnish a flexible statistical framework for biogeographical reconstructions that is easily expanded upon to accommodate various landscape genetic features.},
	Author = {Lemey, Philippe and Rambaut, Andrew and Welch, John J and Suchard, Marc A},
	Date-Added = {2011-02-08 10:58:26 +0000},
	Date-Modified = {2011-02-08 10:58:34 +0000},
	Doi = {10.1093/molbev/msq067},
	Journal = {Molecular Biology and Evolution},
	Journal-Full = {Molecular biology and evolution},
	Mesh = {Animals; Bayes Theorem; Biological Evolution; Disease Outbreaks; Geography; Models, Genetic; Phylogeny; Rabies; Raccoons; Stochastic Processes; Time Factors; United States},
	Month = {Aug},
	Number = {8},
	Pages = {1877-85},
	Pmc = {PMC2915639},
	Pmid = {20203288},
	Pst = {ppublish},
	Title = {Phylogeography takes a relaxed random walk in continuous space and time},
	Volume = {27},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Morlon.Schwilk.ea.2011.a,
	Abstract = {Ecology Letters (2011) 14: 141-149 ABSTRACT: Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas.},
	Author = {Morlon, H{\'e}l{\`e}ne and Schwilk, Dylan W and Bryant, Jessica A and Marquet, Pablo A and Rebelo, Anthony G and Tauss, Catherine and Bohannan, Brendan J M and Green, Jessica L},
	Date-Added = {2011-02-08 10:56:47 +0000},
	Date-Modified = {2011-02-08 10:57:00 +0000},
	Doi = {10.1111/j.1461-0248.2010.01563.x},
	Journal = {Ecology Letters},
	Journal-Full = {Ecology letters},
	Month = {Feb},
	Number = {2},
	Pages = {141-149},
	Pmid = {21166972},
	Pst = {ppublish},
	Title = {Spatial patterns of phylogenetic diversity},
	Volume = {14},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{Cooper.Freckleton.ea.2011.a,
	Abstract = {Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.},
	Author = {Cooper, Natalie and Freckleton, Rob P and Jetz, Walter},
	Date-Added = {2011-02-08 10:37:03 +0000},
	Date-Modified = {2011-04-20 13:26:40 +0100},
	Doi = {10.1098/rspb.2010.2207},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	Journal-Full = {Proceedings. Biological sciences / The Royal Society},
	Month = {Jan},
	Number = {1},
	Pages = {1 - 12},
	Pmid = {21208967},
	Pst = {aheadofprint},
	Title = {Phylogenetic conservatism of environmental niches in mammals},
	Volume = {111},
	Year = {2011},
	Bdsk-File-1 = { }}

@article{FitzJohn.2010.a,
	Abstract = {Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80\% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.},
	Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
	Author = {FitzJohn, Richard G.},
	Date-Added = {2011-02-08 10:24:33 +0000},
	Date-Modified = {2011-02-08 10:24:33 +0000},
	Doi = {DOI 10.1093/sysbio/syq053},
	Isi = {000283686000002},
	Isi-Recid = {193099422},
	Isi-Ref-Recids = {161666750 182984991 130318075 105011007 176326920 145845813 171770109 135511857 160320221 161942040 67535675 43930323 184957211 163150343 142610603 89674039 103859677 174106902 97260513 125286234 116218403 94357582 98852141 175141814 19956626 162235200 183189534 159220147 152202322 174659715 66690949 145646200 87408719 153760425 155163261 86050888 160037864 142667086 162232797 151685349 175141761 151244319 184957213 172295169 193099427 190634715 103730521 175389783 44724432 26721855 144790677 193099428 59576515},
	Journal = {Systematic Biology},
	Keywords = {Birth-death process; Cope's rule; extinction; macroevolution; speciation},
	Month = dec,
	Number = {6},
	Pages = {619-633},
	Publisher = {OXFORD UNIV PRESS},
	Times-Cited = {1},
	Title = {Quantitative Traits and Diversification},
	Volume = {59},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000283686000002}}

@article{Maddison.Midford.ea.2007.a,
	Abstract = {Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from I to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values. [Birth-death process; branching process; cladogenesis; extinction; key innovation; macroevolution; phylogeny; speciation; speciose; statistical inference.]},
	Address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA},
	Author = {Maddison, Wayne P. and Midford, Peter E. and Otto, Sarah P.},
	Date-Added = {2011-02-08 10:23:41 +0000},
	Date-Modified = {2011-02-08 10:23:41 +0000},
	Doi = {DOI 10.1080/10635150701607033},
	Isi = {000250959000001},
	Isi-Recid = {159220147},
	Isi-Ref-Recids = {120517146 104155531 96136935 159220148 127935555 43930323 103859677 110562597 318386 110444512 152202322 72714421 84640812 113906264 159220149 159220150 66690949 143260236 87408719 87271066 112176434 86050888 105408080 142667086 159220151 90629508 143260234 103730521 44724432 85835724 144790677 101100726},
	Journal = {Systematic Biology},
	Month = oct,
	Number = {5},
	Pages = {701-710},
	Publisher = {TAYLOR \& FRANCIS INC},
	Times-Cited = {46},
	Title = {Estimating a binary character's effect on speciation and extinction},
	Volume = {56},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000250959000001}}

@article{Malcolm.Markham.ea.2002.a,
	Abstract = {Aim Greenhouse-induced warming and resulting shifts in climatic zones may exceed the migration capabilities of some species. We used fourteen combinations of General Circulation Models (GCMs) and Global Vegetation Models (GVMs) to investigate possible migration rates required under CO2 -doubled climatic forcing.

Location Global.

Methods Migration distances were calculated between grid cells of future biome type x and nearest same-biome-type cells in the current climate. In 'base-case' calculations, we assumed that 2 x CO2 climate forcing would occur in 100 years, we used ten biome types and we measured migration distances as straight-line distances ignoring water barriers and human development. In sensitivity analyses, we investigated different time periods of 2 x CO2 climate forcing, more narrowly defined biomes and barriers because of water bodies and human development.

Results In the base-case calculations, average migration rates varied significantly according to the GVM used (BIOME3 vs. MAPSS), the age of the GCM (older- vs. newer-generation GCMs), and whether or not GCMs included sulphate cooling or CO2 fertilization effects. However, high migration rates (greater than or equal to 1000 m year(-1)) were relatively common in all models, consisting on average of 17\% grid cells for BIOME3 and 21\% for MAPSS. Migration rates were much higher in boreal and temperate biomes than in tropical biomes. Doubling of the time period of 2 x CO2 forcing reduced these areas of high migration rates to c . 12\% of grid cells for both BIOME3 and MAPSS. However, to obtain migration rates in the Boreal biome that were similar in magnitude to those observed for spruce when it followed the retreating North American Glacier, a radical increase in the period of warming was required, from 100 to >1000 years. A reduction in biome area by an order of magnitude increased migration rates by one to three orders of magnitude, depending on the GVM. Large water bodies and human development had regionally important effects in increasing migration rates.

Main conclusions In conclusion, evidence from coupled GCMs and GVMs suggests that global warming may require migration rates much faster than those observed during post-glacial times and hence has the potential to reduce biodiversity by selecting for highly mobile and opportunistic species. Several poorly understood factors that are expected to influence the magnitude of any such reduction are discussed, including intrinsic migrational capabilities, barriers to migration, the role of outlier populations in increasing migration rates, the role of climate in setting range limits and variation in species range sizes.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DG, OXON, ENGLAND},
	Author = {Malcolm, J R and Markham, A and Neilson, R P and Garaci, M},
	Date-Added = {2011-02-08 10:16:26 +0000},
	Date-Modified = {2011-02-08 10:16:33 +0000},
	Isi = {000177026400001},
	Isi-Recid = {125780252},
	Isi-Ref-Recids = {98339412 116281874 103871397 99607512 99326200 106152477 104949129 106208535 103230041 99297672 75382861 77954141 59169850 103944401 70848727 80512383 106465831 55513814 67189707 91109564 53876376 113028446 98339421 54835773 99636636 74878726 79668556 108613754 97496795 68391995 62902517 76479372 107566014 125780253 164343124 104194261 112024201 96741484 73804978 114535092 63040355 87729485 91378093 125780254 77654043 125780255 57499447 101659790 78130873 125780256 106443551 61422591 89208311 101380653 47057238 98121665 98980864 88314343 112081014 16650119 111464055 105063640 106035762 125780257},
	Journal = {Journal of Biogeography},
	Keywords = {global warming; plant migration; biomes; greenhouse effect; biodiversity},
	Month = jul,
	Number = {7},
	Pages = {835-849},
	Publisher = {BLACKWELL PUBLISHING LTD},
	Times-Cited = {84},
	Title = {Estimated migration rates under scenarios of global climate change},
	Volume = {29},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000177026400001}}

@article{DYER.1995.a,
	Abstract = {Significant shifts in plant species ranges are anticipated next century if climate warms due to greenhouse gas emissions. The magnitude of the projected warming is considerable; the rate at which it is predicted to occur is unprecedented. There is genuine reason for concern that the extent of the range shifts will exceed the dispersal abilities of many plant species, especially in the context of extensive habitat fragmentation. This study attempts to assess explicitly the influence of two factors - mechanism of dispersal and land use configuration - on the ability of plant species to migrate in response to climatic warming. Computer models were developed to simulate dispersal at the time interval of a generation for wind-dispersed and bird-dispersed tree species. These models were applied to three study areas in the eastern United States, each consisting of two 1:250 000 USGS land use land cover quadrangles, which had been reclassified according to probabilities of successful colonization. The study areas reflected the continuum of human impact on the landscape, from areas in intensive agriculture to heavily forested areas. The fastest modeled migration rate observed was 81 m/yr for the wind-dispersed species and 136 m/yr far the bird-dispersed species. Average migration rates were significantly lower. The wind-dispersed species was especially sensitive to habitat isolation and fragmentation. Significant variations in average bird-dispersed migration rates occurred with modest differences in the land use pattern within a landscape; no single predictor of bird-dispersed migration success emerged. Model results indicate that many species may be unable to migrate as range limits shift with a climatic warming, resulting in long-term climatic disequilibrium.},
	Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
	Author = {Dyer, J M},
	Date-Added = {2011-02-08 10:15:17 +0000},
	Date-Modified = {2011-02-08 10:15:33 +0000},
	Isi = {A1995QV04700017},
	Isi-Recid = {91109564},
	Isi-Ref-Recids = {30305185 74315843 38097023 91109565 91109566 43858111 80512383 67189707 79168566 89307642 46457368 68617364 67252530 71540267 66654014 332816 55769769 48211114 71002430 60248784 1802808 60279243 2886783 70342351 71156329 77654043 66156968 60683542 73618342 412414 68134466 48853137 58540362 53732346 70731222 81631087 59391380},
	Journal = {Ecological Modelling},
	Keywords = {CLIMATE; FOREST ECOSYSTEMS; MIGRATION},
	Month = may,
	Number = {1-3},
	Pages = {199-219},
	Publisher = {ELSEVIER SCIENCE BV},
	Times-Cited = {36},
	Title = {ASSESSMENT OF CLIMATIC WARMING USING A MODEL OF FOREST SPECIES MIGRATION},
	Volume = {79},
	Year = {1995},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1995QV04700017}}

@article{Cornwallis.West.ea.2010.a,
	Annote = {10.1038/nature09335},
	Author = {Cornwallis, Charlie K. and West, Stuart A. and Davis, Katie E. and Griffin, Ashleigh S.},
	Date = {2010/08/19/print},
	Date-Added = {2011-02-08 10:01:44 +0000},
	Date-Modified = {2011-02-08 10:01:44 +0000},
	Day = {19},
	Isbn = {0028-0836},
	Journal = {Nature},
	L3 = {http://www.nature.com/nature/journal/v466/n7309/abs/nature09335.html#supplementary-information},
	M3 = {10.1038/nature09335},
	Month = {08},
	Number = {7309},
	Pages = {969--972},
	Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	Title = {Promiscuity and the evolutionary transition to complex societies},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nature09335},
	Volume = {466},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature09335}}

@article{Forest.Grenyer.ea.2007.a,
	Abstract = {One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots(1). However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change(2). Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa(3,4). PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD5-9. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot - the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use(10), we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.},
	Address = {{MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}},
	Author = {Forest, Felix and Grenyer, Richard and Rouget, Mathieu and Davies, T. Jonathan and Cowling, Richard M. and Faith, Daniel P. and Balmford, Andrew and Manning, John C. and Proches, Serban and van der Bank, Michelle and Reeves, Gail and Hedderson, Terry A. J. and Savolainen, Vincent},
	Date-Added = {2011-01-27 16:56:01 +0000},
	Date-Modified = {2011-01-27 17:09:53 +0000},
	Doi = {DOI 10.1038/nature05587},
	Isi = {000244205200043},
	Isi-Recid = {154402909},
	Isi-Ref-Recids = {129269784 154402950 150968889 111019872 154402951 126205407 133377368 76811901 79838892 152758883 127213685 125651409 147698104 132472175 88158174 129789678 125844854 154402952 113913990 114052789 117728918 149771696 120584782 168902123 124090639 103143847 142670653 74302138 94636978 149214049},
	Journal = {Nature},
	Month = feb,
	Number = {7129},
	Pages = {757-760},
	Publisher = {NATURE PUBLISHING GROUP},
	Times-Cited = {95},
	Title = {Preserving the evolutionary potential of floras in biodiversity hotspots},
	Volume = {445},
	Year = {2007},
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000244205200043}}

@article{Kisel.McInnes.ea.2011.a,
	Author = {Yael Kisel and Lynsey McInnes and Nicola H Toomey and C David L Orme},
	Date-Added = {2011-01-27 10:56:37 +0000},
	Date-Modified = {2011-01-27 10:58:03 +0000},
	Journal = {Philosophical Transactions of the Royal Society B-Biological Sciences},
	Title = {How diversification rates and diversity limits combine to create large-scale species-area relationships},
	Year = {{in press}}}

@article{Olalla-Tarraga.Bini.ea.2010.a,
	Address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
	Author = {Olalla-Tarraga, Miguel A. and Bini, Luis M. and Diniz-Filho, Jose A. F. and Rodriguez, Miguel A.},
	Date-Added = {2011-01-25 10:41:09 +0000},
	Date-Modified = {2011-01-25 10:45:15 +0000},
	Doi = {DOI 10.1111/j.1600-0587.2010.06244.x},
	Isi = {000279073000018},
	Isi-Recid = {189795785},
	Isi-Ref-Recids = {189795853 142098609 160874722 116692102 127654732 124609553 130013503 127500670 9931337 142270887 117605384 146264940 91999521 146443 84358732 132292401 184732694 157586174 107655117 126365074 128357124 47642260 47642261 127500623 84822622 160732265 93800874 148756287 154045994 183990557 157564274 12739598 123833634 158662023 157601009 183312661 149839642 176719432 151430581 7339789 160545047 122926161 151985163 154045990},
	Journal = {Ecography},
	Month = apr,
	Number = {2},
	Pages = {362-368},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {1},
	Title = {Cross-species and assemblage-based approaches to Bergmann's rule and the biogeography of body size in Plethodon salamanders of eastern North America},
	Volume = {33},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000279073000018}}

@book{Mayr.1942.a,
	Author = {Mayr, Ernst Walter},
	Date-Added = {2011-01-25 10:31:43 +0000},
	Date-Modified = {2011-01-25 10:49:23 +0000},
	Title = {Systematics and the Origin of Species},
	Year = {1942}}

@article{Weir.Wheatcroft.2010.a,
	Abstract = {We ask whether rates of evolution in traits important for reproductive isolation vary across a latitudinal gradient, by quantifying evolutionary rates of two traits important for pre-mating isolation‚{\"A}{\^\i}avian syllable diversity and song length. We analyse over 2500 songs from 116 pairs of closely related New World passerine bird taxa to show that evolutionary rates for the two main groups of passerines‚{\"A}{\^\i}oscines and suboscines‚{\"A}{\^\i}doubled with latitude in both groups for song length. For syllable diversity, oscines (who transmit song culturally) evolved more than 20 times faster at high latitudes than in low latitudes, whereas suboscines (whose songs are innate in most species and who possess very simple song with few syllable types) show no clear latitudinal gradient in rate. Evolutionary rates in oscines and suboscines were similar at tropical latitudes for syllable complexity as well as for song length. These results suggest that evolutionary rates in traits important to reproductive isolation and speciation are influenced by latitude and have been fastest, not in the tropics where species diversity is highest, but towards the poles.},
	Author = {Weir, Jason T. and Wheatcroft, David},
	Date-Added = {2011-01-24 11:26:20 +0000},
	Date-Modified = {2011-01-24 11:27:02 +0000},
	Doi = {10.1098/rspb.2010.2037},
	Eprint = {http://rspb.royalsocietypublishing.org/content/early/2010/11/08/rspb.2010.2037.full.pdf+html},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	Title = {{A latitudinal gradient in rates of evolution of avian syllable diversity and song length}},
	Url = {http://rspb.royalsocietypublishing.org/content/early/2010/11/08/rspb.2010.2037.abstract},
	Year = {2010},
	Bdsk-Url-1 = {http://rspb.royalsocietypublishing.org/content/early/2010/11/08/rspb.2010.2037.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2010.2037}}

@electronic{r-forge.a,
	Date-Added = {2011-01-16 15:03:35 +0000},
	Date-Modified = {2011-02-08 10:04:17 +0000},
	Title = {R Forge},
	Url = {http://r-forge.r-project.org},
	Bdsk-Url-1 = {http://r-forge.r-project.org}}

@book{Gaston.2003.a,
	Author = {Gaston, Kevin J.},
	Date-Added = {2011-01-15 17:01:32 +0000},
	Date-Modified = {2011-01-15 17:03:41 +0000},
	Publisher = {Oxford University Press},
	Series = {{Oxford Series in Ecology and Evolution}},
	Title = {The structure and dynamics of geographic ranges},
	Year = {2003}}

@article{Safi.Pettorelli.2010.a,
	Abstract = {Aim

Extinction risk is non-randomly distributed across phylogeny and space and is influenced by environmental conditions. We quantified the relative contribution of these factors to extinction risk to unveil the underlying macroecological processes and derive predictive models.

Location

Global.

Methods

Based on the IUCN global assessments, we divided 192 carnivore species into two dichotomous classes representing different levels of extinction risk. We used spatial proximity, phylogenetic relationship and environmental variables together with phylogenetic eigenvector regression and spatial eigenvector filters to model and predict threat status.

Results

Our full models explained between 57\% and 96\% of the variance in extinction risk. Phylogeny and spatial proximity roughly explained between 21\% and 70\% of the total variation in all analyses, while the explanatory power of environmental conditions was relatively weaker (up to 15\%). Phylogeny and spatial proximity contributed equally to the explained variance in the lower threat level, while spatial proximity was the most important factor in the models of the higher threat level. Prediction of threat status achieved 97\% correct assignments.

Main conclusions

Our approach differs fundamentally from current studies of extinction risk because it does not necessarily rely on life-history information. We clearly show that instead of treating phylogenetic inertia and spatial signal as statistical nuisances, space and phylogeny should be viewed as very useful in explaining a wide range of phenomena in comparative studies.},
	Address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
	Author = {Safi, Kamran and Pettorelli, Nathalie},
	Date-Added = {2011-01-14 14:21:42 +0000},
	Date-Modified = {2011-01-14 14:28:12 +0000},
	Doi = {DOI 10.1111/j.1466-8238.2010.00523.x},
	Isi = {000276490400006},
	Isi-Recid = {187997311},
	Isi-Ref-Recids = {187997312 161666750 187997313 53977871 155066183 127725468 99083011 79665303 129635153 162235422 149555681 129084272 135798305 145845813 157747567 75700942 43397840 172659403 161424033 107655117 143048500 159135186 83197285 135604077 175404022 160732265 12696007 152836347 152891894 75043716 187997314 156727663 187997315 187997316 187032947 187746852 161468904 108801745 122298013 144470456 125765862 158707766 160372671 183414250 132981403 158227694 157261187 116955607 114485286 187997317 150714805 132624207 149283914 133093237 187997318 91702663 84478843 116219079},
	Journal = {Global Ecology and Biogeography},
	Keywords = {Carnivora; conservation; eigenvector; extinction risk; phylogenetic signal; predictive model; spatial signal},
	Month = may,
	Number = {3},
	Pages = {352-362},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {1},
	Title = {Phylogenetic, spatial and environmental components of extinction risk in carnivores},
	Volume = {19},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000276490400006}}

@article{Diniz.De-Santana.ea.1998.a,
	Abstract = {We propose a new method to estimate and correct for phylogenetic inertia in comparative data analysis. The method, called phylogenetic eigenvector regression (PVR) starts by performing a principal coordinate analysis on a pairwise phylogenetic distance matrix between species. Traits under analysis are regressed on eigenvectors retained by a broken-stick model in such a way that estimated values express phylogenetic trends in data and residuals express independent evolution of each species. This partitioning is similar to that realized by the spatial autoregressive method, but the method proposed here overcomes the problem of low statistical performance that occurs with autoregressive method when phylogenetic correlation is low or when sample size is too small to detect it. Also, PVR is easier to perform with large samples because it is based on well-known techniques of multivariate and regression analyses. We evaluated the performance of PVR and compared it with the autoregressive method using real datasets and simulations. A detailed worked example using body size evolution of Carnivora mammals indicated that phylogenetic inertia in this trait is elevated and similarly estimated by both methods. In this example, Type I error at alpha = 0.05 of PVR was equal to 0.048, but an increase in the number of eigenvectors used in the regression increases the error. Also, similarity between PVR and the autoregressive method, defined by correlation between their residuals, decreased by overestimating the number of eigenvalues necessary to express the phylogenetic distance matrix. To evaluate the influence of cladogram topology on the distribution of eigenvalues extracted from the double-centered phylogenetic distance matrix, we analyzed 100 randomly generated cladograms (up Ito 100 species). Multiple linear regression of log transformed variables indicated that the number of eigenvalues extracted by the broken-stick model can be fully explained by cladogram topology. Therefore, the broken-stick model is an adequate criterion for determining the correct number of eigenvectors to be used by PVR. We also simulated distinct levels of phylogenetic inertia by producing a trend across 10, 25, and 50 species arranged in "comblike" cladograms and then adding random vectors with increased residual variances around this trend. In doing so, we provide an evaluation of the performance of both methods with data generated under different evolutionary models than tested previously. The results showed that both PVR and autoregressive method are efficient in detecting inertia in data when sample size is relatively high (more than 25 species) and when phylogenetic inertia is high. However, PVR is more efficient at smaller sample sizes and when level of phylogenetic inertia is low. These conclusions were also supported by the analysis of 10 real datasets regarding body size evolution in different animal clades. We concluded that PVR can be a useful alternative to an autoregressive method in comparative data analysis.},
	Address = {{810 E 10TH STREET, LAWRENCE, KS 66044 USA}},
	Author = {Diniz-Filho, Jos{\'e} Alexandre Felizola and de Sant'ana, Carlos Eduardo Ramos and Bini, Luis Mauricio},
	Date-Added = {2011-01-14 14:05:59 +0000},
	Date-Modified = {2011-01-14 14:08:50 +0000},
	Isi = {000076931100001},
	Isi-Recid = {107655117},
	Isi-Ref-Recids = {98848631 68958032 75931632 91999521 55916243 57561095 99677784 98866181 50437306 98866233 81185375 88261843 94400351 54497548 67535675 107655118 84822622 80759959 94222226 99676099 81631248 74123377 77771533 12696007 107655119 93800763 97260513 76254733 75043716 82131803 54485308 43397839 89558005 85495376 12931118 9098352 57396665 90871560 107655120 76996702 76218624 85835721 98053151 88083507 92471149 107655121 99676097 94842174 95729221 85463423 51222887 61150140 97898754 94930392 92133321 86763569 98866260 86191804 21732903 96577781 107655122 98053157 75537460 23697344 75570316 98967530 90496259 50428468 75215107 88873222 89651333 107491343},
	Journal = {Evolution},
	Keywords = {body size; comparative methods; multiple regression; phylogenetic autocorrelation; phylogenetic inertia; principal coordinate analysis.},
	Month = oct,
	Number = {5},
	Pages = {1247-1262},
	Publisher = {SOC STUDY EVOLUTION},
	Times-Cited = {125},
	Title = {An eigenvector method for estimating phylogenetic inertia},
	Volume = {52},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000076931100001}}

@article{Freckleton.Cooper.ea.2011.a,
	Author = {Rob P. Freckleton and Natalie Cooper and Walter Jetz},
	Date-Added = {2011-01-14 14:02:51 +0000},
	Date-Modified = {2011-01-24 11:02:29 +0000},
	Journal = {American Naturalist},
	Title = {Comparative methods as a statistical fix: the dangers of ignoring evolution},
	Year = {{in press}},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Freckleton.Jetz.2009.a,
	Abstract = {Variation in traits across species or populations is the outcome of both environmental and historical factors. Trait variation is therefore a function of both the phylogenetic and spatial context of species. Here we introduce a method that, within a single framework, estimates the relative roles of spatial and phylogenetic variations in comparative data. The approach requires traits measured across phylogenetic units, e. g. species, the spatial occurrences of those units and a phylogeny connecting them. The method modifies the expected variance of phylogenetically independent contrasts to include both spatial and phylogenetic effects. We illustrate this approach by analysing cross-species variation in body mass, geographical range size and species-typical environmental temperature in three orders of mammals (carnivores, artiodactyls and primates). These species attributes contain highly disparate levels of phylogenetic and spatial signals, with the strongest phylogenetic autocorrelation in body size and spatial dependence in environmental temperatures and geographical range size showing mixed effects. The proposed method successfully captures these differences and in its simplest form estimates a single parameter that quantifies the relative effects of space and phylogeny. We discuss how the method may be extended to explore a range of models of evolution and spatial dependence.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Freckleton, Robert P. and Jetz, Walter},
	Date-Added = {2011-01-14 13:54:09 +0000},
	Date-Modified = {2011-01-14 13:54:09 +0000},
	Doi = {DOI 10.1098/rspb.2008.0905},
	Isi = {000262004900004},
	Isi-Recid = {175404022},
	Isi-Ref-Recids = {155497115 130358354 116692102 110292786 155066183 142270887 129554126 79665303 25426255 126148750 92634749 145412919 153988796 99135675 68749332 43397840 132292401 128357124 159559572 107655117 159135186 130897517 67535677 162265497 23729589 175404023 127500623 129803248 153597006 80759959 71141655 74066850 102791328 75043716 118078912 76254733 155954250 126077027 84575528 99712627 142400107 126360964 114141899 125667014 152891902 76996702 99676097 149555761 157601031 126110725 112336304 105408080 132981403 172457483 100359553 145764956 92133321 92133314 58800826 103374780 132777551 175404024 35089716 68725179 132624207 175404025 129083412 91702663 148326927},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {comparative method; spatial analysis; mammals},
	Month = jan,
	Number = {1654},
	Pages = {21-30},
	Publisher = {ROYAL SOC},
	Times-Cited = {13},
	Title = {Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data},
	Volume = {276},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000262004900004}}

@article{Rangel.Diniz-Filho.ea.2010.a,
	Abstract = {SAM (Spatial Analysis in Macroecology) is a freeware application that offers a comprehensive array of spatial statistical methods, focused primarily on surface pattern spatial analysis. SAM is a compact, but powerful stand-alone software, with a user-friendly, menu-driven graphical interface. The methods available in SAM are the most commonly used in macroecology and geographical ecology, and range from simple tools for exploratory graphical analysis (e.g. mapping and graphing) and descriptive statistics of spatial patterns (e.g. autocorrelation metrics), to advanced spatial regression models (e.g. autoregression and eigenvector filtering). Download of the software, along with the user manual, can be downloaded online at the SAM website: < http://www.ecoevol.ufg.br > (permanent URL at < http://purl.oclc.org/sam/>).},
	Address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
	Author = {Rangel, Thiago F. and Diniz-Filho, Jose Alexandre F. and Bini, Luis Mauricio},
	Date-Added = {2011-01-14 11:14:37 +0000},
	Date-Modified = {2011-01-14 12:09:40 +0000},
	Doi = {DOI 10.1111/j.1600-0587.2009.06299.x},
	Isi = {000275205200004},
	Isi-Recid = {187135424},
	Isi-Ref-Recids = {104859609 187135425 180385296 136767862 135833069 126148750 159645002 184295750 163070898 143048500 159135186 83356433 149708427 129304868 152891894 132777450 128357126 84575528 108604025 151430581 115660668 148889886 150224627 107080476 176477373 39465413},
	Journal = {Ecography},
	Month = feb,
	Number = {1},
	Pages = {46-50},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {2},
	Title = {SAM: a comprehensive application for Spatial Analysis in Macroecology},
	Volume = {33},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000275205200004}}

@article{Kier.Kreft.ea.2009.a,
	Abstract = {Endemism and species richness are highly relevant to the global prioritization of conservation efforts in which oceanic islands have remained relatively neglected. When compared to mainland areas, oceanic islands in general are known for their high percentage of endemic species but only moderate levels of species richness, prompting the question of their relative conservation value. Here we quantify geographic patterns of endemism-scaled richness (``endemism richness'') of vascular plants across 90 terrestrial biogeographic regions, including islands, worldwide and evaluate their congruence with terrestrial vertebrates. Endemism richness of plants and vertebrates is strongly related, and values on islands exceed those of mainland regions by a factor of 9.5 and 8.1 for plants and vertebrates, respectively. Comparisons of different measures of past and future human impact and land cover change further reveal marked differences between mainland and island regions. While island and mainland regions suffered equally from past habitat loss, we find the human impact index, a measure of current threat, to be significantly higher on islands. Projected land-cover changes for the year 2100 indicate that land-use-driven changes on islands might strongly increase in the future. Given their conservation risks, smaller land areas, and high levels of endemism richness, islands may offer particularly high returns for species conservation efforts and therefore warrant a high priority in global biodiversity conservation in this century.},
	Author = {Kier, Gerold and Kreft, Holger and Lee, Tien Ming and Jetz, Walter and Ibisch, Pierre L. and Nowicki, Christoph and Mutke, Jens and Barthlott, Wilhelm},
	Date-Added = {2011-01-13 11:33:08 +0000},
	Date-Modified = {2011-01-13 11:33:38 +0000},
	Doi = {10.1073/pnas.0810306106},
	Eprint = {http://www.pnas.org/content/106/23/9322.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {23},
	Pages = {9322-9327},
	Title = {{A global assessment of endemism and species richness across island and mainland regions}},
	Url = {http://www.pnas.org/content/106/23/9322.abstract},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/106/23/9322.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0810306106}}

@article{Meiri.Dayan.ea.2009.a,
	Abstract = {Evolutionary biologists have long been fascinated by both the ways in which species respond to ecological conditions at the edges of their geographic ranges and the way that species' body sizes evolve across their ranges. Surprisingly, though, the relationship between these two phenomena is rarely studied. Here, we examine whether carnivore body size changes from the interior of their geographic range towards the range edges. We find that within species, body size often varies strongly with distance from the range edge. However, there is no general tendency across species for size to be either larger or smaller towards the edge. There is some evidence that the smallest guild members increase in size towards their range edges, but results for the largest guild members are equivocal. Whether individuals vary in relation to the distance from the range edges often depends on the way edge and interior are defined. Neither geographic range size nor absolute body size influences the tendency of size to vary with distance from the range edge. Therefore, we suggest that the frequent significant association between body size and the position of individuals along the edge-core continuum reflects the prevalence of geographic size variation and that the distance to range edge per se does not influence size evolution in a consistent way.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Meiri, Shai and Dayan, Tamar and Simberloff, Daniel and Grenyer, Richard},
	Date-Added = {2011-01-13 10:54:20 +0000},
	Date-Modified = {2011-01-13 10:54:20 +0000},
	Doi = {DOI 10.1098/rspb.2008.1318},
	Isi = {000264351900011},
	Isi-Recid = {178308341},
	Isi-Ref-Recids = {126806292 139090834 112490276 125462354 136748473 38443340 26745890 93034315 53297234 145845813 34458220 113234871 125716018 127394165 106859608 157318543 93544696 114888072 151552388 9815839 129803248 146642580 178308360 101190259 147901006 25054407 152836347 178308361 124801262 33995251 80509444 148416763 162592968 133671746 127716079 44873788 8143328 20666009 151639051 143230338 144689511 158662064 143184294 146683005 128858516 158662027 144478586 159699770 58453401 71579166 118261409 59161627 160758209 152202313 124318114 152260864 126133086 53951954 130064675 81896920 77869211 22842001 78023876 151452219},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {abundance; Bergmann's rule; body size; Carnivora; range edge},
	Month = apr,
	Number = {1661},
	Pages = {1469-1476},
	Publisher = {ROYAL SOC},
	Times-Cited = {1},
	Title = {Life on the edge: carnivore body size variation is all over the place},
	Volume = {276},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000264351900011}}

@article{Hadfield.Nakagawa.2010.a,
	Abstract = {Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.},
	Address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
	Author = {Hadfield, J. D. and Nakagawa, S.},
	Date-Added = {2011-01-12 11:25:42 +0000},
	Date-Modified = {2011-01-12 11:35:22 +0000},
	Doi = {DOI 10.1111/j.1420-9101.2009.01915.x},
	Isi = {000273949900005},
	Isi-Recid = {186343799},
	Isi-Ref-Recids = {161039951 153595067 5618152 155066183 75103925 32479674 148842032 132864869 40699272 160728134 32096585 107655117 115354206 115425173 152517753 150381302 145965797 162265497 54497548 131246339 50845813 127500623 121125961 114497756 157432224 54212083 50704154 129446390 186343800 160449240 97260513 18098686 129517725 28886402 175381555 133291106 128981719 71361698 155954250 149595491 123342061 122929944 128735929 178284112 119891024 128420639 632122 105935354 76996702 118692123 98053151 99676097 851180 81394232 121740597 174791494 147758606 163094599 54881303 86050888 112336304 150702338 137186922 152835190 20584945 30350646 65464539 177087215 99790860 40043759 143260305 156234392 30332517 107450343 186343801 91835824 128452218 153595072 62972501 145965805 160449250 123712108 186343802},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {comparative method; meta-analysis; pedigree; phylogeny; quantitative genetics},
	Month = mar,
	Number = {3},
	Pages = {494-508},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {4},
	Title = {General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters},
	Volume = {23},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000273949900005}}

@article{Jetz.Sekercioglu.ea.2008.a,
	Abstract = {Traits such as clutch size vary markedly across species and environmental gradients but have usually been investigated from either a comparative or a geographic perspective, respectively. We analyzed the global variation in clutch size across 5,290 bird species, excluding brood parasites and pelagic species. We integrated intrinsic (morphological, behavioural), extrinsic (environmental), and phylogenetic effects in a combined model that predicts up to 68\% of the interspecific variation in clutch size. We then applied the same species-level model to predict mean clutch size across 2,521 assemblages worldwide and found that it explains the observed eco-geographic pattern very well. Clutches are consistently largest in cavity nesters and in species occupying seasonal environments, highlighting the importance of offspring and adult mortality that is jointly expressed in intrinsic and extrinsic correlates. The findings offer a conceptual bridge between macroecology and comparative biology and provide a global and integrative understanding of the eco-geographic and cross-species variation in a core life-history trait.},
	Address = {{185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA}},
	Author = {Jetz, Walter and Sekercioglu, Cagan H. and Boehning-Gaese, Katrin},
	Date-Added = {2011-01-11 10:46:51 +0000},
	Date-Modified = {2011-01-11 16:48:20 +0000},
	Doi = {DOI 10.1371/journal.pbio.0060303},
	Isi = {000261913700008},
	Isi-Recid = {175401655},
	Isi-Ref-Recids = {44977840 125762207 117455537 155306307 156266695 123764304 35517287 143146022 160732265 135262913 102064843 157503094 156727663 126077027 95947297 60984419 175401656 1980801 98607973 134927081 79054833 172566533 81766136 1981076 126110725 163165149 92625999 175401657 99288127 39504092 126602322 113680949 53542344 113680947 146976966 61350537 142477172 128732904 75537462 128357016 175401658 46691757 108807834 29235347 142102215 148326927},
	Journal = {Plos Biology},
	Month = dec,
	Number = {12},
	Pages = {2650-2657},
	Publisher = {PUBLIC LIBRARY SCIENCE},
	Times-Cited = {10},
	Title = {The Worldwide Variation in Avian Clutch Size across Species and Space},
	Volume = {6},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000261913700008}}

@article{Gaston.Chown.ea.2008.a,
	Abstract = {The development of a more synthetic approach to understanding spatial patterns in biogeography, particularly of the way in which these patterns interact, constitutes a major challenge for the field. Here we propose some key elements of such a synthesis for what can broadly be termed 'ecogeographical rules', that is spatial patterns in biological traits. These include understanding: (1) the different kinds of patterns (intraspecific, interspecific and assemblage), and the distinctions between them; (2) the unifying role that geographical ranges play in linking the patterns together; (3) that this unification can be obscured by the methodological assumptions made in documenting some patterns (e.g. assuming that intraspecific variation does not significantly influence interspecific and assemblage patterns in traits); (4) the implications of other methodological issues for the nature of observed patterns (e.g. how ranges are located on positional or environmental axes for interspecific patterns); (5) the need for further development of models linking different types of traits; (6) the nature of the generality of documented patterns at all levels, and particularly the difference between the frequency with which patterns are documented in the literature and the variety of extant species; and (7) the constraints that the form of intraspecific patterns place on interspecific and assemblage patterns, and that interspecific patterns place on assemblage patterns.},
	Address = {{9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}},
	Author = {Gaston, Kevin J. and Chown, Steven L. and Evans, Karl L.},
	Date-Added = {2011-01-11 10:26:59 +0000},
	Date-Modified = {2011-01-15 16:59:16 +0000},
	Doi = {DOI 10.1111/j.1365-2699.2007.01772.x},
	Isi = {000253148300011},
	Isi-Recid = {160732265},
	Isi-Ref-Recids = {94643944 88040490 114203276 114845123 89992923 3972243 157666187 88828710 142091793 144370522 15865465 130013503 127654732 116692102 129105059 94732668 40717611 132848226 124471159 9931337 60779323 97019357 99083011 112490276 117605384 120338806 142270887 120163903 146264940 152993968 24189190 160732266 144689492 117455537 123764309 128368731 91999521 98458438 53297234 16888546 135833036 126308175 160732267 110749415 123764304 123573846 116471883 145412919 131293542 124311824 156050411 110292880 125716018 55215022 149194379 146905391 145780538 149722666 69770009 151548901 150702345 147231137 96776585 75547181 84358732 4970909 27894499 135285575 129804068 148352402 83879538 47317513 143562954 119250580 145905601 143146022 146421004 151430611 151290894 145780567 46697799 71562303 9815839 114326496 152269829 129803248 130473225 156828233 119282909 98567995 104155514 130254191 114924076 117111000 109030704 103871395 120885184 92383162 150191450 160732268 126027034 144641661 94842329 160732269 160732270 75043716 132777450 149839634 151985164 91546563 91370343 147880617 145790625 46605181 152728033 133803689 135574468 145764980 129044241 126360983 121576088 110281508 144766692 135530429 127844660 91066445 101944204 63764344 91786951 18542171 101245271 120729166 126077027 23112584 9890620 133392261 40717613 16871320 109326149 146273062 160732271 128708942 143729358 128251033 29644016 69186882 136033581 128816288 134422860 126716252 53732525 151847362 146264947 132245977 73123355 1980801 2195559 149713542 85224575 109030702 133207866 87634005 49393586 57047892 135968612 152402623 98903174 151639041 54697091 85820375 61702630 147396420 146272992 64135271 113927665 142409780 135267073 136362717 4259023 136065046 20666009 134168040 143184295 143230338 128858516 143562971 150740198 122115595 132777537 121571986 85786615 57561087 35401088 148098786 95155716 149839642 145723116 157585004 55555924 160732272 143037155 134091174 104595771 155809329 43333102 145895946 160732273 91823803 142663313 155663431 152552688 49481211 121521770 129835427 128251058 113333630 62587353 126602322 144050395 148929558 131655879 40199338 84664421 136124856 15237487 120856170 104652308 152260864 124318114 108372009 133698624 146140474 137234059 151336138 96776584 43526051 81099398 2195882 160732274 152299871 145905652 68295209 132203242 111942703 79052069 151904467 315166 6169312 144075272 98460499 110920398 135833133 123443319 119622699 125737136 131176811 113357064 149366517 144766694 129083412 127067444 121813524 132777533 151548886 86875669 157550195 86620984 130254190},
	Journal = {Journal of Biogeography},
	Keywords = {areography; ecogeographical rules; environmental gradients; geographical range; latitudinal gradients; macroecology; macrophysiology; spatial gradients},
	Month = mar,
	Number = {3},
	Pages = {483-500},
	Publisher = {BLACKWELL PUBLISHING},
	Read = {0},
	Times-Cited = {45},
	Title = {Ecogeographical rules: elements of a synthesis},
	Type = {Proceedings Paper},
	Volume = {35},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000253148300011}}

@book{Legendre.Legendre.1998.a,
	Author = {Pierre Legendre and Louis Legendre},
	Date-Added = {2011-01-11 10:22:25 +0000},
	Date-Modified = {2011-01-11 10:25:23 +0000},
	Edition = {2nd},
	Publisher = {Elsevier},
	Series = {Developments in Environmental Modelling 20},
	Title = {Numerical Ecology},
	Year = {1998}}

@article{Pigot.Phillimore.ea.2010.a,
	Abstract = {Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth--death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth--death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.},
	Author = {Pigot, Alex L. and Phillimore, Albert B. and Owens, Ian P. F. and Orme, C. David L.},
	Date-Added = {2010-11-04 17:37:58 +0000},
	Date-Modified = {2011-01-25 16:11:15 +0000},
	Doi = {10.1093/sysbio/syq058},
	Eprint = {http://sysbio.oxfordjournals.org/content/59/6/660.full.pdf+html},
	Journal = {Systematic Biology},
	Number = {6},
	Pages = {660-673},
	Title = {{The Shape and Temporal Dynamics of Phylogenetic Trees Arising from Geographic Speciation}},
	Url = {http://sysbio.oxfordjournals.org/content/59/6/660.abstract},
	Volume = {59},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/content/59/6/660.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syq058}}

@article{Johnson.Omland.2004.a,
	Abstract = {Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from a complete set of competing models. Model selection is widely accepted and well developed in certain fields, most notably in molecular systematics and mark-recapture analysis. However, it is now gaining support in several other areas, from molecular evolution to landscape ecology. Here, we outline the steps of model selection and highlight several ways that it is now being implemented. By adopting this approach, researchers in ecology and evolution will find a valuable alternative to traditional null hypothesis testing, especially when more than one hypothesis is plausible.},
	Address = {84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND},
	Author = {Johnson, JB and Omland, KS},
	Date-Added = {2010-10-27 09:15:58 +0100},
	Date-Modified = {2010-10-27 09:15:58 +0100},
	Doi = {DOI 10.1016/j.tree.2003.10.013},
	Isi = {000188931400011},
	Isi-Recid = {133392261},
	Isi-Ref-Recids = {25770136 117289316 115612953 114285507 127269358 104767004 123716197 111281263 11739040 123155055 114643399 127269360 121027692 90565227 120776056 115396809 67748941 131586169 122589970 108297614 128832985 122737542 99996694 103223082 123699535 128031345 100640946 111652279 127468982 92527897 125589058 78803085 119763853 123172204 113186583 123297349 106208526 111462125 120277568 121637803 133392262 121157036 122552135 121999857 114314330 33870047 124339865 125044484 92745162 122723309 112942208 120277599 104992635 115260259 127645177 95661814 105377765 120150715 128967147 125557583 124364530 114463996 113090854 124641761 114094447 114895769 123729300 114463999},
	Journal = {Trends In Ecology \& Evolution},
	Month = feb,
	Number = {2},
	Pages = {101-108},
	Publisher = {ELSEVIER SCIENCE LONDON},
	Times-Cited = {572},
	Title = {Model selection in ecology and evolution},
	Volume = {19},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000188931400011}}

@article{Vamosi.Vamosi.2010.a,
	Abstract = {Elucidating factors associated with diversification have been attempted in lineages as diverse as birds, mammals and angiosperms, yet has met with limited success. In flowering plants, the ambiguity of associations between traits and diversification has sparked debate since Darwin's description of angiosperm diversification as an 'abominable mystery'. Recent work has found that diversification is often diversity- dependent, suggesting that species richness depends on geographical area available more than on traits or the time available to accumulate species. Here, we undertake phylogenetic generalized least squares analyses that jointly examine the effects of age, ecoregion area and four ecological traits on diversification in 409 angiosperm families. Area explained the most variation, dwarfing the effect of traits and age, suggesting that diversity-dependent diversification is controlled by ecological limits. Within the context of area, however, traits associated with biotic pollination (zygomorphy) exhibited the greatest effect, possibly through the evolution of specialization.},
	Author = {Jana C. Vamosi and Steven M. Vamosi},
	Date-Added = {2010-08-18 10:24:24 +0100},
	Date-Modified = {2010-08-18 10:25:32 +0100},
	Journal = {Ecology Letters},
	Title = {Key innovations within a geographical context in flowering plants: towards resolving Darwin's abominable mystery},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Baselga.2010.a,
	Abstract = {Aim

Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns.

Innovation

I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns.

Main conclusion

Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Baselga, Andres},
	Date-Added = {2010-05-26 11:10:00 +0100},
	Date-Modified = {2010-05-26 11:10:00 +0100},
	Doi = {DOI 10.1111/j.1466-8238.2009.00490.x},
	Isi = {000272573200012},
	Isi-Recid = {185288017},
	Isi-Ref-Recids = {150035229 172332062 160867097 159115287 161503353 159644994 185288018 179670869 123261390 159644995 154140024 123261388 143694295 56035266 119282909 78849614 112011126 2635925 159018012 175914720 129210415 96776544 122706012 113305462 156899484 118224424 159180605 141996022 132334346 86025611 48685 3099140 156266687 154708831 127706092 157034158 175396142 127026968 6124932 112490241 96136931 53980563 81800612},
	Journal = {Global Ecology and Biogeography},
	Keywords = {Beta diversity; Cerambycidae; Europe; nestedness; similarity measures; spatial turnover},
	Month = jan,
	Number = {1},
	Pages = {134-143},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {2},
	Title = {Partitioning the turnover and nestedness components of beta diversity},
	Volume = {19},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-File-3 = { },
	Bdsk-File-4 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000272573200012}}

@article{Midgley.Davies.ea.2010.a,
	Abstract = {BioMove simulates plant species' geographic range shifts in response to climate, habitat structure and disturbance, at annual time steps. This spatially explicit approach integrates species' bioclimatic suitability and population-level demographic rates with simulation of landscape-level processes (dispersal, disturbance, species' response to dynamic dominant vegetation structure). Species population dynamics are simulated through matrix modelling that includes scaling demographic rates by climatic suitability. Dispersal functions simulate population spread. User-specified plant functional types (PFTs) provide vegetation structure that determines resource competition and disturbance. PFTs respond annually through dispersal, inter-PFT competition and demographic shifts. BioMove provides a rich framework for dynamic range simulations.},
	Author = {Guy F. Midgley and Ian D. Davies and C{\'e}cile H. Albert and Res Altwegg and Lee Hannah and Gregory O. Hughes and Lydia R. O'Halloran and Changwan Seo and James H. Thorne and Wilfried Thuiller},
	Date = {2010 %@ 1600-0587},
	Date-Added = {2010-05-25 11:14:36 +0100},
	Date-Modified = {2010-05-25 11:14:57 +0100},
	Journal = {Ecography},
	Number = {9999},
	Refer1 = {10.1111/j.1600-0587.2009.06000.x},
	Title = {BioMove - an integrated platform simulating the dynamic response of species to environmental change},
	Url = {http://dx.doi.org/10.1111/j.1600-0587.2009.06000.x},
	Volume = {9999},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1600-0587.2009.06000.x}}

@article{RaymondB.Huey05142010,
	Author = {Huey, Raymond B. and Losos, Jonathan B. and Moritz, Craig},
	Date-Added = {2010-05-24 10:28:06 +0100},
	Date-Modified = {2010-05-24 10:28:06 +0100},
	Doi = {10.1126/science.1190374},
	Eprint = {http://www.sciencemag.org/cgi/reprint/328/5980/832.pdf},
	Journal = {Science},
	Number = {5980},
	Pages = {832-833},
	Title = {{Are Lizards Toast?}},
	Url = {http://www.sciencemag.org},
	Volume = {328},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1190374}}

@article{Sinervo.Mendez-de-la-Cruz.ea.2010.a,
	Abstract = {It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12\% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4\% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39\% worldwide, and species extinctions may reach 20\%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.},
	Author = {Sinervo, Barry and M{\'e}ndez-de-la-Cruz, Fausto and Miles, Donald B and Heulin, Benoit and Bastiaans, Elizabeth and Villagr{\'a}n-Santa Cruz, Maricela and Lara-Resendiz, Rafael and Mart{\'\i}nez-M{\'e}ndez, Norberto and Calder{\'o}n-Espinosa, Martha Luc{\'\i}a and Meza-L{\'a}zaro, Rubi Nelsi and Gadsden, H{\'e}ctor and Avila, Luciano Javier and Morando, Mariana and De la Riva, Ignacio J and Victoriano Sepulveda, Pedro and Rocha, Carlos Frederico Duarte and Ibarg{\"u}engoyt{\'\i}a, Nora and Aguilar Puntriano, C{\'e}sar and Massot, Manuel and Lepetz, Virginie and Oksanen, Tuula A and Chapple, David G and Bauer, Aaron M and Branch, William R and Clobert, Jean and Sites, Jr, Jack W},
	Date-Added = {2010-05-24 10:26:07 +0100},
	Date-Modified = {2010-05-24 10:26:07 +0100},
	Doi = {10.1126/science.1184695},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Month = {May},
	Number = {5980},
	Pages = {894-9},
	Pmid = {20466932},
	Pst = {ppublish},
	Title = {Erosion of lizard diversity by climate change and altered thermal niches},
	Volume = {328},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Triantis.Mylonas.ea.2008.a,
	Abstract = {The species2013area relationship (SAR) between different biological provinces is one of the most interesting, but least explored aspects of the well-known species2013area pattern. Following the usage that a biological province is a region whose species have for the most part evolved within it, rather than immigrating from somewhere else, we propose that islands can be considered equivalent to biological provinces for single island endemic species (SIEs). Hence, analyses of the relationships between numbers of SIEs and island area can be used as model systems to explore the form of inter-provincial SARs. We analyzed 13 different data sets derived from 11 sources, using the power (log2013log) model. Eleven of the SIE2013area relationships were statistically significant, explaining high proportions of the variance in SIE numbers (R2 0.5720130.95). The z-values (slopes) of the statistically significant SIE2013area relationships ranged from 0.47 to 1.13, with a mean value of 0.80 (SD$\pm$0.24). All the island systems in which SIE represent &gt;50% of species exhibited z-values for the SARs of native species higher than those deemed typical of archipelagic SARs. The SIE2013area slopes are quite similar to those previously calculated for inter-provincial SARs, indicating that, when speciation becomes the dominant process adding to the species richness of assemblages, high z-values should be anticipated, regardless of the biogeographical scale of the study system.},
	Author = {Kostas A. Triantis and Moisis Mylonas and Robert J. Whittaker},
	Date = {2008 %@ 1600-0587},
	Date-Added = {2010-05-24 10:19:51 +0100},
	Date-Modified = {2010-05-24 10:20:44 +0100},
	Journal = {Ecography},
	Number = {3},
	Pages = {401-407},
	Refer1 = {10.1111/j.0906-7590.2007.05323.x},
	Title = {Evolutionary species-area curves as revealed by single-island endemics: insights for the inter-provincial species-area relationship},
	Url = {http://dx.doi.org/10.1111/j.0906-7590.2007.05323.x},
	Volume = {31},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.0906-7590.2007.05323.x}}

@article{Schielzeth2010,
	Abstract = {1. Linear regression models are an important statistical tool in evolutionary and ecological studies. Unfortunately, these models often yield some uninterpretable estimates and hypothesis tests, especially when models contain interactions or polynomial terms. Furthermore, the standard errors for treatment groups, although often of interest for including in a publication, are not directly available in a standard linear model. 2. Centring and standardization of input variables are simple means to improve the interpretability of regression coefficients. Further, refitting the model with a slightly modified model structure allows extracting the appropriate standard errors for treatment groups directly from the model. 3. Centring will make main effects biologically interpretable even when involved in interactions and thus avoids the potential misinterpretation of main effects. This also applies to the estimation of linear effects in the presence of polynomials. Categorical input variables can also be centred and this sometimes assists interpretation. 4. Standardization (z-transformation) of input variables results in the estimation of standardized slopes or standardized partial regression coefficients. Standardized slopes are comparable in magnitude within models as well as between studies. They have some advantages over partial correlation coefficients and are often the more interesting standardized effect size. 5. The thoughtful removal of intercepts or main effects allows extracting treatment means or treatment slopes and their appropriate standard errors directly from a linear model. This provides a simple alternative to the more complicated calculation of standard errors from contrasts and main effects. 6. The simple methods presented here put the focus on parameter estimation (point estimates as well as confidence intervals) rather than on significance thresholds. They allow fitting complex, but meaningful models that can be concisely presented and interpreted. The presented methods can also be applied to generalised linear models (GLM) and linear mixed models.},
	Author = {Schielzeth, Holger},
	Date-Added = {2010-04-28 16:56:32 +0100},
	Date-Modified = {2010-04-28 16:56:32 +0100},
	Doi = {10.1111/j.2041-210X.2010.00012.x},
	Issn = {2041-210X},
	Journal = {Methods in Ecology and Evolution},
	Number = {9999},
	Title = {Simple means to improve the interpretability of regression coefficients},
	Url = {http://dx.doi.org/10.1111/j.2041-210X.2010.00012.x},
	Volume = {9999},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.2041-210X.2010.00012.x}}

@article{Zuur2010,
	Abstract = {1.?While teaching statistics to ecologists, the lead authors of this paper have noticed common statistical problems. If a random sample of their work (including scientific papers) produced before doing these courses were selected, half would probably contain violations of the underlying assumptions of the statistical techniques employed. 2.?Some violations have little impact on the results or ecological conclusions; yet others increase type I or type II errors, potentially resulting in wrong ecological conclusions. Most of these violations can be avoided by applying better data exploration. These problems are especially troublesome in applied ecology, where management and policy decisions are often at stake. 3.?Here, we provide a protocol for data exploration; discuss current tools to detect outliers, heterogeneity of variance, collinearity, dependence of observations, problems with interactions, double zeros in multivariate analysis, zero inflation in generalized linear modelling, and the correct type of relationships between dependent and independent variables; and provide advice on how to address these problems when they arise. We also address misconceptions about normality, and provide advice on data transformations. 4.?Data exploration avoids type I and type II errors, among other problems, thereby reducing the chance of making wrong ecological conclusions and poor recommendations. It is therefore essential for good quality management and policy based on statistical analyses.},
	Author = {Zuur, Alain F. and Ieno, Elena N. and Elphick, Chris S.},
	Date-Added = {2010-04-28 16:50:59 +0100},
	Date-Modified = {2010-04-28 16:50:59 +0100},
	Doi = {10.1111/j.2041-210X.2009.00001.x},
	Issn = {2041-210X},
	Journal = {Methods in Ecology and Evolution},
	Number = {1},
	Pages = {3--14},
	Title = {A protocol for data exploration to avoid common statistical problems},
	Url = {http://dx.doi.org/10.1111/j.2041-210X.2009.00001.x},
	Volume = {1},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.2041-210X.2009.00001.x}}

@article{Pigot.Owens.ea.2010.a,
	Author = {Pigot, Alex L. and Owens, Ian P. F. and Orme, C. David L.},
	Date-Added = {2010-04-13 13:52:18 +0100},
	Date-Modified = {2010-11-30 10:14:25 +0000},
	Journal = {Ecology Letters},
	Number = {6},
	Pages = {705 - 15},
	Title = {The environmental limits to geographic range expansion in birds},
	Volume = {13},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-File-3 = { },
	Bdsk-File-4 = { },
	Bdsk-File-5 = { }}

@article{Orme.Toomey.ea.2010.a,
	Author = {Orme, C. David L. and Toomey, Nicola H. and Cardillo, Marcel and Owens, Ian P. F. and Gittleman, John L. and Davies, T. Jonathan and Thomas, Rosie G. P. and Brummitt, Neil and Chase, Mark W and Purvis, Andy},
	Date-Added = {2010-04-10 20:37:17 +0100},
	Date-Modified = {2010-04-10 20:40:02 +0100},
	Title = {The phylogenetic species-area relationship},
	Year = {in prep}}

@book{Brummitt.2001.a,
	Author = {Brummitt, R K},
	Date-Added = {2010-04-10 18:07:19 +0100},
	Date-Modified = {2010-04-10 18:09:28 +0100},
	Editor = {International Working Group on Taxonomic Databases For Plant Sciences (TDWG)},
	Number = {2},
	Publisher = {Hunt Institute for Botanical Documentation Carnegie Mellon University, Pittsburgh},
	Series = {Plant Taxonomic Database Standards},
	Title = {World Geographical Scheme for Recording Plant Distributions Edition 2.},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Ronquist.1997.a,
	Abstract = {Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have different effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known.},
	Address = {NATL MUSEUM NATURAL HISTORY NHB 163, WASHINGTON, DC 20560},
	Author = {Ronquist, F},
	Date-Added = {2010-04-10 18:04:05 +0100},
	Date-Modified = {2010-04-10 18:04:05 +0100},
	Isi = {A1997WZ11000009},
	Isi-Recid = {100468614},
	Isi-Ref-Recids = {84223297 82339475 73091833 14249622 45758850 89254100 96919530 41786014 100468615 75324573 79837298 83672312 8143328 72813012 91685795 88132716 100468616 96921155 88307087 94330249 74452102 68103263 94842292},
	Journal = {Systematic Biology},
	Keywords = {Cladistic biogeography; comparative phylogeography; dispersal; extinction; historical biogeography; optimization; vicariance; widespread species},
	Month = mar,
	Number = {1},
	Pages = {195-203},
	Publisher = {SOC SYSTEMATIC BIOLOGISTS},
	Times-Cited = {397},
	Title = {Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography},
	Volume = {46},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WZ11000009}}

@article{Meiri.2010.a,
	Abstract = {Body shape and body size are hugely important for the understanding of multiple ecological phenomena. In order to study and compare sizes across taxa and to understand the ecological significance of shape differences, there is a need for ways to 'translate' different size measurements to a common metric. Body mass is the most useful such common index for size across taxa. Based on a large (&gt;900 species in 28 families) dataset of lizard and amphisbaenian weights, I generate equations to estimate weights from the common size index used in lizard morphometrics (snout2013vent length). I then use a species-level phylogenetic hypothesis to examine the ecological factors that affect the variation in weight2013length relationships. Legless and leg-reduced lizards are characterized by shallower allometric slopes, and thus long-bodied legless species are lighter than legged lizards of comparable length. Among legged species, the foraging strategy strongly influences the weights, with sit-and-wait species being bulkier at comparable lengths than active foraging species. Environmental productivity (positively related to mass) and activity times (diurnal species being heavier) are only significant when using non-phylogenetic models. The need for effective locomotion is a major factor affecting lizard shape. Previously used allometric equations are inaccurate.},
	Author = {Meiri, Shai},
	Date-Added = {2010-03-11 10:27:24 +0000},
	Date-Modified = {2010-03-11 10:28:32 +0000},
	Journal = {Journal of Zoology},
	Title = {Length-weight allometries in lizards},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{Phillimore.Price.2008.a,
	Abstract = {A characteristic signature of adaptive radiation is a slowing of the rate of speciation toward the present. On the basis of molecular phylogenies, studies of single clades have frequently found evidence for a slowdown in diversification rate and have interpreted this as evidence for density dependent speciation. However, we demonstrated via simulation that large clades are expected to show stronger slowdowns than small clades, even if the probability of speciation and extinction remains constant through time. This is a consequence of exponential growth: clades, which, by chance, diversify at above the average rate early in their history, will tend to be large. They will also tend to regress back to the average diversification rate later on, and therefore show a slowdown. We conducted a meta-analysis of the distribution of speciation events through time, focusing on sequence-based phylogenies for 45 clades of birds. Thirteen of the 23 clades (57\%) that include more than 20 species show significant slowdowns. The high frequency of slowdowns observed in large clades is even more extreme than expected under a purely stochastic constant-rate model, but is consistent with the adaptive radiation model. Taken together, our data strongly support a model of density-dependent speciation in birds, whereby speciation slows as ecological opportunities and geographical space place limits on clade growth.},
	Address = {185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA},
	Author = {Phillimore, Albert B. and Price, Trevor D.},
	Date-Added = {2010-03-08 15:43:46 +0000},
	Date-Modified = {2010-03-08 15:43:46 +0000},
	Doi = {DOI 10.1371/journal.pbio.0060071},
	Isi = {000254928600010},
	Isi-Recid = {162232797},
	Isi-Ref-Recids = {155497115 115486570 104620852 152767917 148667739 50437306 160320221 162232798 150369836 118447136 102619435 147910945 130685216 89651281 136433706 91009694 148756287 135799612 111425140 103225 151480311 157832440 80791779 153760425 116692088 160172554 155124538 117605548 151244319 159735608 154416728 162232799 24348788 31084069 151244320 87519749 132161485 158698421 159851617 152891850 144579204 120517150 116873340 109948452 104155576 75537462 25007790 89412910 150198030 154881665 949309 133477889 91809311},
	Journal = {Plos Biology},
	Month = mar,
	Number = {3},
	Pages = {483-489},
	Publisher = {PUBLIC LIBRARY SCIENCE},
	Times-Cited = {21},
	Title = {Density-dependent cladogenesis in birds},
	Volume = {6},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000254928600010}}

@article{Rabosky.2009.b,
	Abstract = {Species richness varies dramatically among groups of organisms, yet the causes of this variation remain poorly understood. Variation in species-level diversification rates may partially explain differential species richness among clades, but older clades should also be more diverse, because they will have had more time to accumulate species. Surprisingly, studies that have investigated this question have reached dramatically different conclusions: several claim to find no such age-diversity relationship, whereas a recent and more inclusive study reported that clade age and not diversification rate explains the variation in species richness among animal taxa. Here I address the relationship between clade age and species richness using a model-based approach that controls for variation in diversification rates among clades. I find that species richness is effectively independent of clade age in four of five data sets. Even extreme among-clade variation in diversification rates cannot account for the absence of a positive age-diversity relationship in angiosperms, birds, and teleost fishes. I consider two alternative explanations for these results and find that a clade volatility model positing correlated speciation-extinction dynamics does not underlie these patterns. Rather, ecological limits on clade growth, such as geographic area, appear to mediate temporal declines in diversification within higher taxa.},
	Address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA},
	Author = {Rabosky, Daniel L.},
	Date-Added = {2010-03-08 15:33:10 +0000},
	Date-Modified = {2010-03-08 15:33:10 +0000},
	Doi = {DOI 10.1086/597378},
	Isi = {000264812800011},
	Isi-Recid = {178768513},
	Isi-Ref-Recids = {9176865 85902891 42089680 127935555 135511857 133377368 145864215 150369836 147910945 89674039 142749465 159735607 130685216 559267 84031319 130094744 162235200 117770535 111425140 8934350 19464611 122062632 174659715 155194014 87630012 99631610 143260236 158698420 119968552 80791779 87408719 151429453 112080936 110178480 142667086 135194361 162232797 151685349 160572884 117605548 172295169 172938889 159424374 151244319 24348788 56091527 159851617 157632187 132161485 152891850 32540426 144579204 94204180 32408725 35170674 104155576 75537460 1982903 129108949 71680231 159068487 40512834 24280877 108201948 21067437 19848696 54185376 150198030 142230433},
	Journal = {American Naturalist},
	Keywords = {diversification; macroevolution; phylogeny; speciation; clade age; species richness},
	Month = may,
	Number = {5},
	Pages = {662-674},
	Publisher = {UNIV CHICAGO PRESS},
	Times-Cited = {6},
	Title = {Ecological Limits on Clade Diversification in Higher Taxa},
	Volume = {173},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000264812800011}}

@article{Hurlbert.Jetz.2010.a,
	Abstract = {Abstract: One of the primary ecological hypotheses put forward to explain patterns of biodiversity is known as the more-individuals hypothesis of species-energy theory. This hypothesis suggests that the number of species increases along the global energy gradient primarily as a result of an increase in the total number of individuals that can be supported along that gradient. Implicit in this hypothesis is that species richness should scale with energy in the same way in which it scales with area in species-area relationships. We developed a novel framework for thinking about the interaction of area and energy, and we provide the first global test of this equivalence assumption using a data set on terrestrial breeding birds. We found that (1) species-energy slopes are typically greater than species-area slopes, (2) the magnitude of species-area and species-energy slopes varies strongly across the globe, and (3) the degree to which area and energy interact to determine species richness depends on the way mean values of species occupancy change along the energy gradient. Our results indicate that the increase in richness along global productivity gradients cannot be explained by more individuals alone, and we discuss other mechanisms by which increased productivity might facilitate species coexistence.},
	Author = {Hurlbert, Allen H and Jetz, Walter},
	Date-Added = {2010-03-07 13:27:13 +0000},
	Date-Modified = {2010-03-07 13:27:13 +0000},
	Doi = {10.1086/650723},
	Journal = {Am Nat},
	Journal-Full = {The American naturalist},
	Month = {Feb},
	Pmid = {20184428},
	Pst = {aheadofprint},
	Title = {More than "More Individuals": The Nonequivalence of Area and Energy in the Scaling of Species Richness},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Hutchinson.MacArthur.1959.a,
	Author = {Hutchinson, George Evelyn and MacArthur, Robert H.},
	Date-Added = {2010-03-04 12:02:40 +0000},
	Date-Modified = {2010-03-04 12:48:34 +0000},
	Doi = {10.1086/282063},
	Eprint = {http://www.journals.uchicago.edu/doi/pdf/10.1086/282063},
	Journal = {The American Naturalist},
	Number = {869},
	Pages = {117},
	Title = {A Theoretical Ecological Model of Size Distributions Among Species of Animals},
	Url = {http://www.journals.uchicago.edu/doi/abs/10.1086/282063},
	Volume = {93},
	Year = {1959},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.journals.uchicago.edu/doi/abs/10.1086/282063},
	Bdsk-Url-2 = {http://dx.doi.org/10.1086/282063}}

@article{Jablonski.Roy.2003.a,
	Abstract = {The notion of a positive relation between geographical range and speciation rate or speciation probability may go back to Darwin, but a negative relation between these parameters is equally plausible. Here, we test these alternatives in fossil and living molluscan taxa. Late Cretaceous gastropod genera exhibit a strong negative relation between the geographical ranges of constituent species and speciation rate per species per million years; this result is robust to sampling biases against small-bodied taxa and is not attributable to phylogenetic effects. They also exhibit weak inverse or non-significant relations between geographical range and (i) the total number of species produced over the 18 million year timeframe, and (ii) the number of species in a single timeplane. Sister-group comparisons using extant molluscan species also show a non-significant relation between median geographical range and species richness of genera. These results support the view that the factors promoting broad geographical ranges also tend to damp speciation rates. They also demonstrate that a strong inverse relation between per-species speciation rate and geographical range need not be reflected in analyses conducted within a single timeplane, underscoring the inadequacy of treating net speciation as a proxy for raw per-taxon rates.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Jablonski, D and Roy, K},
	Date-Added = {2010-03-03 19:34:43 +0000},
	Date-Modified = {2010-03-03 19:34:43 +0000},
	Doi = {DOI 10.1098/rspb.2002.2243},
	Isi = {000181320500010},
	Isi-Recid = {128390187},
	Isi-Ref-Recids = {113345468 109037533 104155516 121717533 82270055 112715 35836472 118397809 108628281 119282909 113776039 104155514 89674039 89712867 34634538 48466185 115424970 107655136 120020537 116698135 121261181 91009694 61451455 128582829 74358992 98852141 63764344 105179914 128582830 128582831 118397916 109501453 112631327 109236251 119924644 8143328 103223104 85964638 109296627 96892012 43566124 56091527 97019345 121941790 120171671 92086885 32540426 88698586 163362035 33461739 104155576 64509608 50287795 58776412 40512767 76207350 23306729 128582832 178652003},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {speciation; geographical range; sister-group comparisons; species richness; molluscs},
	Month = feb,
	Number = {1513},
	Pages = {401-406},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {45},
	Title = {Geographical range and speciation in fossil and living molluscs},
	Volume = {270},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000181320500010}}

@article{Ritchie.2007.a,
	Abstract = {Sexual selection has a reputation as a major cause of speciation, one of the most potent forces driving reproductive isolation. This reputation arises from observations that species differ most in traits involved with mating success and from successful models of sexual selection-driven speciation. But how well proven is the case? Models confirm that the process can occur, but is strongest in conjunction with ecological or niche specialization. Some models also show that strong sexual selection can act against speciation. Studies using the comparative method are equivocal and often inconclusive, but some phylogeographic studies are more convincing. Experimental evolution and genetic or genomic analyses are in their infancy, but look particularly promising for resolving the importance of sexual selection. The case for sexual selection is not as strongly supported as, for example, allopatric speciation. Sexual selection probably contributes most effectively alongside ecological selection or selection for species recognition than as a solitary process.},
	Address = {4139 EL CAMINO WAY, PO BOX 10139, PALO ALTO, CA 94303-0139 USA},
	Author = {Ritchie, Michael G.},
	Date-Added = {2010-03-03 15:55:39 +0000},
	Date-Modified = {2010-03-03 15:55:39 +0000},
	Doi = {DOI 10.1146/annurev.ecolsys.38.091206.095733},
	Isi = {000252359800004},
	Isi-Recid = {160142327},
	Isi-Ref-Recids = {129394831 133723924 116671108 123431444 105774942 90616320 153827940 53977841 144105281 154105358 127391638 69070131 70408993 53977825 105872176 149506401 149194412 68588763 99677793 143540593 700383 110943913 1980546 118188 129702773 115381965 136752473 42138465 101667114 33174 149111428 127481253 119055760 126071472 113914042 107655210 136860346 117985950 132249088 160142328 143310907 74444408 118447143 112739667 69306433 104304293 113356984 151359502 63167656 75111171 120655815 117455554 75163561 127437744 45200083 134049899 108216681 110943916 136752544 122929946 45779432 43382725 148923848 131299108 123301788 124271804 142460324 128732843 94553850 130282738 96678998 105935413 128532907 104304396 70041185 72389413 110178480 120517148 104155555 39797826 127437772 91150253 160142329 107455630 104155544 152998462 87519749 110001256 157632300 144933633 83267995 62264804 71156279 75674118 147932221 125671916 149713537 110341129 142475104 134758453 136535278 109514232 116525913 144105262 130158038 135215426 123431563 37222135 153738774 107808111 111093471 92133271 107352422 134838499 122115591 49380623 151359495 117387809 119259855 96241740 54752395 146298930 136962796 129944161},
	Journal = {Annual Review of Ecology Evolution and Systematics},
	Keywords = {reproductive isolation; sexual conflict; comparative method; experimental evolution; genomics},
	Pages = {79-102},
	Publisher = {ANNUAL REVIEWS},
	Times-Cited = {34},
	Title = {Sexual selection and speciation},
	Volume = {38},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000252359800004}}

@article{Mayhew.2007.a,
	Abstract = {Over half of all described species are insects, but until recently our understanding of the reasons for this diversity was based on very little macroevolutionary evidence. Here I summarize the hypotheses that have been posed, tests of these hypotheses and their results, and hence identify gaps in knowledge for future researchers to pursue. I focus on inferences from the following sources: (i) the fossil record, normally at family level, and (ii) insect phylogenies, sometimes combined with: (iii) the species richness of insect higher taxa, and (iv) current extinction risks.

There is evidence that the species richness of insects has been enhanced by: (i) their relative age, giving time for diversification to take place; (ii) low extinction rates. There is little evidence that rates of origination have generally been high or that there are limits on numbers of species. However, the evidence on macroevolutionary rates is not yet so extensive or coherent as to present unequivocal messages.

As regards morphological, ecological, or behavioural hypotheses, there is evidence that diversity has been enhanced by (iii) flight or properties resulting from it like enhanced dispersal, (iv) wing folding, and (v) complete metamorphosis. However, in all these cases the evidence is somewhat equivocal, either because of statistical issues or because evidence from different sources is conflicting.

There is extensive evidence that diversity is affected by (vi) the ecological niche. Comparative studies indicate that phytophagy generally increases net diversification rates, and reduces extinction risk. However, niche specialization is also associated with an increase in extinction risk. Small body size (vii) is often associated with low extinction risk in comparative studies, but as yet there is no solid evidence that it consistently enhances net rates of diversification. Mouthpart diversity (viii) has generally increased over time in the insects, but cannot explain the apparent great increase in diversity seen in the Cretaceous and Tertiary. Sexual selection and sexual conflict (ix) are two processes that are widespread in insects, and there is comparative evidence linking both to increased diversification. Although some comparative evidence links tropical distributions (x) to increased rates of diversification, the extent to which latitudinal richness gradients are unusual in insects is equivocal.

There is little to no direct evidence from fossils and phylogenies that insect diversity has generally been affected by (i) sensory- or neuro-sophistication, (ii) population size or density, (iii) generation time or fecundity, (iv) the presence of an exoskeleton or cuticle, (v) segmentation or appendage diversity, (vi) adaptability or genetic versatility, though all of these remain plausible hypotheses awaiting further tests. The data suggest that the insect body ground plan itself had no direct effect on insect diversity.

Thus, whilst studies to date have given substantial understanding, substantial gaps still remain. Future challenges include: (i) interpreting conflicting messages from different sources of data; (ii) rating the importance of different hypotheses that are statistically supported; (iii) linking specific proximate to specific ultimate explanations and vice versa; and (iv) understanding how different ultimate hypotheses might be dependent on each other.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Mayhew, Peter J.},
	Date-Added = {2010-03-03 14:33:26 +0000},
	Date-Modified = {2010-03-03 14:33:26 +0000},
	Doi = {DOI 10.1111/j.1469-185X.2007.00018.x},
	Isi = {000247904200005},
	Isi-Recid = {157154245},
	Isi-Ref-Recids = {124134013 126077025 116671108 126763941 107746724 109079337 116186501 151875722 121779862 102919842 90856089 151194265 144773414 132292353 39575425 116189719 110749415 6083181 82382131 125453788 88086417 100388577 94636974 87270963 135511857 84358732 107222689 114793149 133207853 133377368 127935581 108228229 113293298 106348601 120819361 145679168 110224187 157154246 133148681 57880907 119208496 106191437 146304724 104389623 108971389 76958285 119282909 124836990 142466792 153661082 142749465 143587569 82749589 75914963 96939431 88086439 145640154 135219806 89651281 44406036 80118056 133803689 44328383 125469556 221292 128447859 142103879 105131166 104106882 130121879 148622747 120655815 118261344 141991244 126017533 142988388 129328611 132151201 113550633 87283847 134090197 84031319 103222859 115645151 42144939 151521458 97528793 39531614 81839792 131164262 124749327 157154247 127935551 128113896 66690949 99631610 143260236 146871415 128692889 99631614 80791779 119968552 87408719 97486130 146943109 81063208 118224424 125430245 72478124 46769609 142490974 134723386 99631616 24348788 56091527 134840452 131121223 119659019 115753600 33470601 127047301 142493738 88018521 144516167 87283818 127935537 104155576 143886829 111967696 40512834 67781233 116219007 145350146 113555877 132624207 87271014 133684292 64427761 124318038 125800969 42946248 74249932 120539761 125453786 85596076 87198459 132203247 1982272 86135699 50287854 119419411 157154248 147097716 949309 69534315},
	Journal = {Biological Reviews},
	Keywords = {co-evolution; dispersal evolution; diversity; extinction; flight; herbivory; macroevolution; phytophagy; speciation; species richness},
	Month = aug,
	Number = {3},
	Pages = {425-454},
	Publisher = {BLACKWELL PUBLISHING},
	Times-Cited = {6},
	Title = {Why are there so many insect species? Perspectives from fossils and phylogenies},
	Volume = {82},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000247904200005}}

@article{Thomas.2010.a,
	Abstract = {Aim A major issue in ecology, biogeography, conservation biology and invasion biology is the extent to which climate, and hence climate change, contributes to the positions of species' range boundaries. Thirty years of rapid climate warming provides an excellent opportunity to test the hypothesis that climate acts as a major constraint on range boundaries, treating anthropogenic climate change as a large-scale experiment.Location  UK and global data, and literature.Methods  This article analyses the frequencies with which species have responded to climate change by shifting their range boundaries. It does not consider abundance or other changes.Results  For the majority of species, boundaries shifted in a direction that is concordant with being a response to climate change; 84% of all species have expanded in a polewards direction as the climate has warmed (for the best data available), which represents an excess of 68% of species after taking account of the fact that some species may shift in this direction for non-climatic reasons. Other data sets also show an excess of animal range boundaries expanding in the expected direction.Main conclusions  Climate is likely to contribute to the majority of terrestrial and freshwater range boundaries. This generalization excludes species that are endemic to specific islands, lakes, rivers and geological outcrops, although these local endemics are not immune from the effects of climate change. The observed shifts associated with recent climate change are likely to have been brought about through both direct and indirect (changes to species' interactions) effects of climate; indirect effects are discussed in relation to laboratory experiments and invasive species. Recent observations of range boundary shifts are consistent with the hypothesis that climate contributes to, but is not the sole determinant of, the position of the range boundaries of the majority of terrestrial animal species.},
	Author = {Chris D. Thomas},
	Date-Added = {2010-02-24 12:17:05 +0000},
	Date-Modified = {2010-02-24 12:17:59 +0000},
	Journal = {Diversity and Distributions},
	Title = {Climate, climate change and range boundaries},
	Year = {2010}}

@article{Van-Bocxlaer.Loader.ea.2010.a,
	Abstract = {Recent studies have identified range expansion as a potential driver of speciation. Yet it remains poorly understood how, under identical extrinsic settings, differential tendencies for geographic movement of taxa originate and subsequently affect diversification. We identified multiple traits that predict large distributional ranges in extant species of toads (Bufonidae) and used statistical methods to define and phylogenetically reconstruct an optimal range-expansion phenotype. Our results indicate that lineage-specific range-shifting abilities increased through an accumulation of adaptive traits that culminated in such a phenotype. This initiated the episode of global colonization and triggered the major radiation of toads. Evolution toward a range-expansion phenotype might be crucial to understanding both ancient widespread radiations and the evolutionary background of contemporary invasive species such as the cane toad.
},
	Author = {Van Bocxlaer, Ines and Loader, Simon P. and Roelants, Kim and Biju, S. D. and Menegon, Michele and Bossuyt, Franky},
	Date-Added = {2010-02-23 11:06:02 +0000},
	Date-Modified = {2010-02-23 11:06:25 +0000},
	Doi = {10.1126/science.1181707},
	Eprint = {http://www.sciencemag.org/cgi/reprint/327/5966/679.pdf},
	Journal = {Science},
	Number = {5966},
	Pages = {679-682},
	Title = {{Gradual Adaptation Toward a Range-Expansion Phenotype Initiated the Global Radiation of Toads}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/327/5966/679},
	Volume = {327},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/327/5966/679},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1181707}}

@article{Ricklefs.2000.a,
	Address = {P O BOX 88, OSNEY MEAD, OXFORD OX2 0NE, OXON, ENGLAND},
	Author = {Ricklefs, Robert E.},
	Date-Added = {2010-02-05 11:19:19 +0000},
	Date-Modified = {2010-02-05 15:53:12 +0000},
	Isi = {000166798000017},
	Isi-Recid = {118557568},
	Isi-Ref-Recids = {98980858 87630329 78849522 32575492 104155514 111942753 91494678 114245042 109651130 111913709 32626255 67495966 61209000 111047790 112959333 91924375 90158638 83197234 109685989 68295209 40842835 71442233 56924797},
	Journal = {Journal of Animal Ecology},
	Month = nov,
	Number = {6},
	Pages = {1111-1116},
	Publisher = {BLACKWELL SCIENCE LTD},
	Times-Cited = {12},
	Title = {The relationship between local and regional species richness in birds of the Caribbean Basin},
	Volume = {69},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000166798000017}}

@article{Ricklefs.2010.a,
	Abstract = {The population component of a species' niche corresponds to the distribution of individuals across environments within a region. As evolutionary clades of species diversify, they presumably fill niche space, and, consequently, the rate of increase in species numbers slows. Total niche space and species numbers appear to be relatively stable over long periods, and so an increase in the species richness of one clade must be balanced by decrease in others. However, in several analyses, the total population niche space occupied per clade is independent of the number of species, suggesting that species in more diverse clades overlap more in niche space. This overlap appears to be accommodated by variation in the populations of each species, including their absence, within suitable niche space. I suggest that the uneven filling of niche space results from localized outcomes of the dynamic coevolutionary interactions of populations with their pathogens or other antagonists. Furthermore, I speculate that relationships with pathogens might constrain diversification if pathogen diversity increased with host diversity and resulted in more frequent host switching and emergent disease. Many indirect observations are consistent with these scenarios. However, the postulated influence of pathogens on the filling of niche space and diversification of clades primarily highlights our lack of knowledge concerning the space and time dimensions of coevolutionary interactions and their influence on population distribution and species diversification.},
	Author = {Ricklefs, Robert E},
	Date-Added = {2010-02-02 16:52:51 +0000},
	Date-Modified = {2010-02-02 16:53:12 +0000},
	Doi = {10.1073/pnas.0913626107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {Jan},
	Pmid = {20080597},
	Title = {Evolutionary diversification, coevolution between populations and their antagonists, and the filling of niche space},
	Year = {2010},
	Bdsk-File-1 = { }}

@article{McPeek.2008.a,
	Abstract = {Clades diversify in an ecological context, but most macroevolutionary models do not directly encapsulate ecological mechanisms that influence speciation and extinction. A data set of 245 chordate, arthropod, mollusk, and magnoliophyte phylogenies had a majority of clades that showed rapid lineage accumulation early with a slowing more recently, whereas a small but significant minority showed accelerated lineage accumulation in their recent histories. Previous analyses have demonstrated that macroevolutionary birth-death models can replicate the pattern of slowing lineage accumulation only by a strong decrease in speciation rate with increasing species richness and extinction rate held extremely low or absent. In contrast, the metacommunity model presented here could generate the full range of patterns seen in the real phylogenies by simply manipulating the degree of ecological differentiation of new species at the time of speciation. Specifically, the metacommunity model predicts that clades showing decelerating lineage accumulation rates are those that have diversified by ecological modes of speciation, whereas clades showing accelerating lineage accumulation rates are those that have diversified primarily by modes of speciation that generate little or no ecological diversification. A number of testable predictions that integrate data from molecular systematics, community ecology, and biogeography are also discussed.},
	Address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA},
	Author = {McPeek, Mark A.},
	Date-Added = {2010-01-31 18:30:49 +0000},
	Date-Modified = {2010-01-31 18:30:49 +0000},
	Doi = {DOI 10.1086/593137},
	Isi = {000261235500003},
	Isi-Recid = {174659715},
	Isi-Ref-Recids = {110001272 98982906 106499516 126763941 70642979 102825412 91999521 118519437 151624209 135340891 89107817 133425205 118012549 122437807 103315099 135511857 145983636 118188 143230308 119924611 96020553 118292149 158968921 137183068 147910945 89674039 144671337 47282511 126022333 32408723 130685216 89651281 82131803 98866124 111573674 106231789 121261181 119924612 96696148 143232092 133477883 66475620 146903789 85212467 115911711 114094445 148756287 87135898 131085467 90752083 150894677 132784741 145111896 11002466 136963102 70029652 39077 150894693 146742288 162030554 114518949 154099697 155194014 172637817 99631610 133364294 87408719 119968552 87271066 80791779 153760425 131678200 135194361 133983053 174659716 174659717 36726093 160572884 174659718 108208900 117605548 172295169 151244319 127725613 108134958 24348788 56091527 77904793 151359526 151244320 75561128 86191804 61209000 103223044 35390727 144579204 116873340 102111786 35170674 104155576 38225604 131980585 1982903 57274 133590558 133278303 159068487 160773895 112705269 153537671 135799539 128967147 143230305 119659066 54185376 127725576 150198030 137134365 114508121 146140451},
	Journal = {American Naturalist},
	Keywords = {clade diversification; extinction; macroevolution; metacommunity; phylogenetic rates; speciation},
	Month = dec,
	Number = {6},
	Pages = {E270-E284},
	Publisher = {UNIV CHICAGO PRESS},
	Times-Cited = {13},
	Title = {The Ecological Dynamics of Clade Diversification and Community Assembly},
	Volume = {172},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000261235500003}}

@article{Chesson.2000.a,
	Abstract = {The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence, in which species diversity slowly decays over time, have focused almost exclusively on equalizing mechanisms. These models would be more robust if they also included stabilizing mechanisms, which arise in many and varied ways but need not be adequate for full stability of a system. Models of unstable coexistence invite a broader view of diversity maintenance incorporating species turnover. },
	Author = {Chesson, Peter},
	Date-Added = {2010-01-31 17:50:17 +0000},
	Date-Modified = {2010-02-01 09:55:53 +0000},
	Doi = {10.1146/annurev.ecolsys.31.1.343},
	Eprint = {http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.31.1.343},
	Journal = {Annual Review of Ecology and Systematics},
	Number = {1},
	Pages = {343 - 366},
	Title = {Mechanisms of maintainance of species diversity},
	Url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.31.1.343},
	Volume = {31},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.31.1.343},
	Bdsk-Url-2 = {http://dx.doi.org/10.1146/annurev.ecolsys.31.1.343}}

@article{Rabosky.McCune.2010.a,
	Annote = {Species selection as a potential driver of macroevolutionary trends has been relegated to a largely philosophical position in modern evolutionary biology. Fundamentally, species selection is the outcome of heritable differences in speciation and extinction rates among lineages when the causal basis of those rate differences can be decoupled from genotypic (within-population) fitnesses. Here, we discuss the rapidly growing literature on variation in species diversification rates as inferred from molecular phylogenies. We argue that modern studies of diversification rates demonstrate that species selection is an important process influencing both the evolution of biological diversity and distributions of phenotypic traits within higher taxa. Explicit recognition of multi-level selection refocuses our attention on the mechanisms by which traits influence speciation and extinction rates.},
	Author = {Rabosky, Daniel L. and McCune, Amy R.},
	Date = {2010/02/01},
	Date-Added = {2010-01-29 15:42:59 +0000},
	Date-Modified = {2010-01-29 15:42:59 +0000},
	Id = {S0169-5347(09)00232-8 DOI - 10.1016/j.tree.2009.07.002},
	Isbn = {0169-5347},
	Month = {02},
	Number = {2},
	Pages = {68--74},
	Title = {Reinventing species selection with molecular phylogenies},
	Ty = {ABST},
	Url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534709002328},
	Volume = {25},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0169534709002328}}

@article{Loarie.2009.a,
	Abstract = {The ranges of plants and animals are moving in response to recent changes in climate(1). As temperatures rise, ecosystems with 'nowhere to go', such as mountains, are considered to be more threatened(2,3). However, species survival may depend as much on keeping pace with moving climates as the climate's ultimate persistence(4,5). Here we present a new index of the velocity of temperature change (km yr(-1)), derived from spatial gradients (degrees C km(-1)) and multimodel ensemble forecasts of rates of temperature increase (degrees C yr(-1)) in the twenty-first century. This index represents the instantaneous local velocity along Earth's surface needed to maintain constant temperatures, and has a global mean of 0.42 km yr(-1) (A1B emission scenario). Owing to topographic effects, the velocity of temperature change is lowest in mountainous biomes such as tropical and subtropical coniferous forests (0.08 km yr(-1)), temperate coniferous forest, and montane grasslands. Velocities are highest in flooded grasslands (1.26 km yr(-1)), mangroves and deserts. High velocities suggest that the climates of only 8\% of global protected areas have residence times exceeding 100 years. Small protected areas exacerbate the problem in Mediterranean-type and temperate coniferous forest biomes. Large protected areas may mitigate the problem in desert biomes. These results indicate management strategies for minimizing biodiversity loss from climate change. Montane landscapes may effectively shelter many species into the next century. Elsewhere, reduced emissions, a much expanded network of protected areas(6), or efforts to increase species movement may be necessary(7).},
	Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Loarie, Scott R. and Duffy, Philip B. and Hamilton, Healy and Asner, Gregory P. and Field, Christopher B. and Ackerly, David D.},
	Date-Added = {2010-01-08 14:22:44 +0000},
	Date-Modified = {2010-01-08 14:23:15 +0000},
	Doi = {DOI 10.1038/nature08649},
	Isi = {000272996000046},
	Isi-Recid = {185604446},
	Isi-Ref-Recids = {161434811 150782089 106208535 103230041 173302027 175196851 151919834 171918549 148243617 171770065 162524676 172758400 163126447 175663731 125780252 177647499 145780569 173302028 135691093 158874712 122306281 152154559 127580979 149676359 101380937 129365616 144745203 162177523 154582239 67019680 155760046},
	Journal = {Nature},
	Month = dec,
	Number = {7276},
	Pages = {1052-U111},
	Publisher = {NATURE PUBLISHING GROUP},
	Times-Cited = {0},
	Title = {The velocity of climate change},
	Volume = {462},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000272996000046}}

@article{Venditti.2009.a,
	Author = {Venditti, Chris and Meade, Andrew and Pagel, Mark},
	Date-Added = {2009-12-14 09:54:54 +0000},
	Date-Modified = {2009-12-14 09:59:33 +0000},
	Journal = {Nature},
	Title = {Phylogenies reveal new interpretation of speciation and the Red Queen},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Soberon.Nakamura.2009.a,
	Abstract = {Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue that conceptual clarity is enhanced by adopting restricted definitions of ‚{\"A}{\'u}niche‚{\"A}{\`u} that enable operational definitions of basic concepts like fundamental, potential, and realized niches and potential and actual distributional areas. We apply these definitions to the question of niche conservatism, addressing what it is that is conserved and showing with a quantitative example how niche change can be measured. In this example, we display the extremely irregular structure of niche space, arguing that it is an important factor in understanding niche evolution. Many cases of apparently successful models of distributions ignore biotic factors: we suggest explanations to account for this paradox. Finally, relating the probability of observing a species to ecological factors, we address the issue of what objects are actually calculated by different niche modeling algorithms and stress the fact that methods that use only presence data calculate very different quantities than methods that use absence data. We conclude that the results of niche modeling exercises can be interpreted much better if the ecological and mathematical assumptions of the modeling process are made explicit.
},
	Author = {Sober{\'o}n, Jorge and Nakamura, Miguel},
	Date-Added = {2009-12-03 13:48:57 +0000},
	Date-Modified = {2009-12-03 13:50:47 +0000},
	Doi = {10.1073/pnas.0901637106},
	Eprint = {http://www.pnas.org/content/106/suppl.2/19644.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {Supplement 2},
	Pages = {19644-19650},
	Title = {{Niches and distributional areas: Concepts, methods, and assumptions}},
	Url = {http://www.pnas.org/content/106/suppl.2/19644.abstract},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/106/suppl.2/19644.abstract}}

@article{Gromping.2007.a,
	Abstract = {Assigning shares of "relative importance" to each of a set of regressors is one of the key goals of researchers applying linear regression, particularly in sciences that work with observational data.. Although the topic is quite old, advances in computational capabilities have led to increased applications of computer-intensive methods like averaging over orderings that enable a reasonable decomposition of the model variance. This article serves two purposes: to reconcile the large and somewhat fragmented body of recent literature on relative importance and to investigate the theoretical and empirical properties of the key competitors for decomposition of model variance.},
	Address = {1429 DUKE ST, ALEXANDRIA, VA 22314 USA},
	Author = {Gr{\"o}mping, Ulrike},
	Date-Added = {2009-11-19 14:44:04 +0000},
	Date-Modified = {2009-11-19 14:44:41 +0000},
	Doi = {DOI 10.1198/000313007X188252},
	Isi = {000245762200006},
	Isi-Recid = {155679810},
	Isi-Ref-Recids = {51455923 130680702 155679811 96023209 135101899 85359740 75700942 96667103 132784381 56062019 14284964 127026564 73381044 155679812 155679813 155679814 155679815 155679816 155679817 6525104 120285229 135101871 135101888 64382593 68628118 61750894 135101879 43142946 122677283 114960615 37946463 115494295 96023212 155679818 155679819 78480844 67552086 19352417 155679820 155679821},
	Journal = {American Statistician},
	Keywords = {averaging over orderings; linear model; proportional marginal variance decomposition (PMVD); sequential sums of squares},
	Month = may,
	Number = {2},
	Pages = {139-147},
	Publisher = {AMER STATISTICAL ASSOC},
	Times-Cited = {10},
	Title = {Estimators of relative importance in linear regression based on variance decomposition},
	Volume = {61},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000245762200006}}

@article{Gromping.2006.a,
	Abstract = {Relative importance is a topic that has seen a lot of interest in recent years, particularly in applied work. The R package relaimpo implements six different metrics for assessing relative importance of regressors in the linear model, two of which are recommended averaging over orderings of regressors and a newly proposed metric (Feldman 2005) called pmvd. Apart from delivering the metrics themselves, relaimpo also provides ( exploratory) bootstrap confidence intervals. This paper offers a brief tutorial introduction to the package. The methods and relaimpo's functionality are illustrated using the data set swiss that is generally available in R. The paper targets readers who have a basic understanding of multiple linear regression. For the background of more advanced aspects, references are provided.},
	Address = {UCLA DEPT STATISTICS, 8130 MATH SCIENCES BLDG, BOX 951554, LOS ANGELES, CA 90095-1554 USA},
	Author = {Gr{\"o}mping, Ulrike},
	Date-Added = {2009-11-19 14:43:40 +0000},
	Date-Modified = {2009-11-19 14:45:17 +0000},
	Isi = {000241807900001},
	Isi-Recid = {153014249},
	Isi-Ref-Recids = {150035229 51455923 96023209 85359740 75700942 96667103 14284964 114681711 153014250 153014251 128924249 153014252 151282641 6525104 135101871 43142946 96023212 90352543 153014253},
	Journal = {Journal of Statistical Software},
	Keywords = {relative importance; hierarchical partitioning; linear model; relaimpo; hier.part; variance decomposition; R-2},
	Month = oct,
	Number = {1},
	Publisher = {JOURNAL OF STATISTICAL SOFTWARE},
	Times-Cited = {0},
	Title = {Relative importance for linear regression in R: The package relaimpo},
	Volume = {17},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000241807900001}}

@article{Dutilleul.1993.a,
	Abstract = {Clifford, Richardson, and Hemon (1989, Biometrics 45, 123-134) presented modified tests of association between two spatially autocorrelated processes, for lattice and non-lattice data. These tests are built on the sample covariance and on the sample correlation coefficient; they require the estimation of an effective sample size that takes into account the spatial structure of both processes. Clifford et al. developed their method on the basis of an approximation of the variance of the sample correlation coefficient and assessed it by Monte Carlo simulations for lattice and non-lattice networks of moderate to large size.

In the present paper, the variance of the sample covariance is computed for a finite number of locations, under the multinormality assumption, and the mathematical derivation of the definition of effective sample size is given. The theoretically expected number of degrees of freedom for the modified t test with renewed modifications is compared with that computed on the basis of equation (2.9) of Clifford et al. (1989). The largest differences are observed for small numbers of locations and high autocorrelation, in particular when the latter is present with opposite sign in the two processes. Basic references that were missing in Clifford et al. (1989) are given and inherent ambiguities are discussed.},
	Address = {808 17TH ST NW SUITE 200, WASHINGTON, DC 20006-3910},
	Author = {Dutilleul, Pierre},
	Date-Added = {2009-11-17 12:04:31 +0000},
	Date-Modified = {2011-01-16 22:54:53 +0000},
	Isi = {A1993LB23000029},
	Isi-Recid = {83356433},
	Isi-Ref-Recids = {72501720 83356434 52338797 742754 742843 72126739 43397840 68749332 76432668 77408092 56679125 70582440 74066850 72481265 44517585 83356435},
	Journal = {Biometrics},
	Keywords = {CORRELATION ANALYSIS; EFFECTIVE SAMPLE SIZE; MODIFIED T-TEST; SPATIAL AUTOCORRELATION},
	Month = mar,
	Number = {1},
	Pages = {305-314},
	Publisher = {INTERNATIONAL BIOMETRIC SOC},
	Times-Cited = {194},
	Title = {Modifying the t-test for assessing the correlation between two spatial processes},
	Type = {Letter},
	Volume = {49},
	Year = {1993},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1993LB23000029}}

@article{Farris.Albert.ea.1996.a,
	Abstract = {Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data A. new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor-joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch-swapping, yet is better able to screen out poorly-supported groups. (C) 1996 The Willi Hennig Society.},
	Address = {24-28 OVAL RD, LONDON, ENGLAND NW1 7DX},
	Author = {Farris, JS and Albert, VA and Kallersjo, M and Lipscomb, D and Kluge, AG},
	Date-Added = {2009-11-10 10:56:10 +0000},
	Date-Modified = {2009-11-10 10:56:10 +0000},
	Isi = {A1996WG86200001},
	Isi-Recid = {99267367},
	Isi-Ref-Recids = {84275476 80794978 94553816 66253883 99267368 84503979 80930633 48244145 21673693 22623839 99267369 35954665 18034917 56562694 99267370 90379737 88546944 82308359 86189008 44188367 84503987 78469861 90123997 97572506 88296200 80703233 69982665 65596522 81959125 67464899 83009475},
	Journal = {Cladistics-The International Journal of the Willi Hennig Society},
	Month = jun,
	Number = {2},
	Pages = {99-124},
	Publisher = {ACADEMIC PRESS LTD},
	Times-Cited = {739},
	Title = {Parsimony jackknifing outperforms neighbor-joining},
	Volume = {12},
	Year = {1996},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1996WG86200001}}

@article{Erwin.1998.a,
	Abstract = {The evolutionary consequences of mass extinctions depend as much on the processes of survival and recovery following these biotic crises as on the patterns of extinction themselves. Paleontologists are currently documenting biotic recoveries from six major mass extinctions and several smaller biotic crises. Although the immediate responses are remarkably similar after each event, with low-diversity assemblages dominated by widespread, eurytopic species, the recovery response in the long-term is more varied. Lineages that survive the extinction can lack the resilience for recovery, whereas others vanish from the fossil record seemingly to return from the dead after several million years.},
	Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
	Author = {Erwin, Douglas H.},
	Date-Added = {2009-11-10 10:55:20 +0000},
	Date-Modified = {2009-11-10 10:55:37 +0000},
	Isi = {000075606400004},
	Isi-Recid = {106788311},
	Isi-Ref-Recids = {106788312 106788313 91802654 93400026 105803270 106788314 104072334 85884286 64284725 70760674 106788316 93400028 97346333 106788317 85656348 106788318 91009694 104072335 106788319 164076976 106788321 106788322 99238906 102480485 106788323 80650493 106788324 100539014 92073015 81116738 102919846 106788325 78279520 101757755 97001665 89712903 101522639 95406955 101512350},
	Journal = {Trends In Ecology \& Evolution},
	Month = sep,
	Number = {9},
	Pages = {344-349},
	Publisher = {ELSEVIER SCI LTD},
	Times-Cited = {87},
	Title = {The end and the beginning: recoveries from mass extinctions},
	Volume = {13},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000075606400004}}

@article{Erwin.2000.a,
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Erwin, D},
	Date-Added = {2009-11-10 10:54:15 +0000},
	Date-Modified = {2009-11-10 10:54:38 +0000},
	Isi = {000085870900025},
	Isi-Recid = {114094387},
	Isi-Ref-Recids = {109822141 102919842 107262015 106788311 114094388 114094389 104072335 114094390 53634409 51076275},
	Journal = {Nature},
	Month = mar,
	Number = {6774},
	Pages = {129-130},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Times-Cited = {19},
	Title = {Life's downs and ups},
	Type = {Editorial Material},
	Volume = {404},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000085870900025}}

@article{Eeckhaut.McHugh.ea.2000.a,
	Abstract = {Myzostomids are obligate symbiotic invertebrates associated with echinoderms with a fossil record that extends to the Ordovician period. Due to their long history as host-specific symbionts, myzostomids have acquired a unique anatomy that obscures their phylogenetic affinities to other metazoans: they are incompletely segmented, parenchymous, acoelomate organisms with chaetae and a trochophore larva. Today, they are most often classified within annelids either as an aberrant family of polychaetes or as a separate class. We inferred the phylogenetic position of the Myzostomida by analysing the DNA sequences of two slowly evolving nuclear genes: the small subunit ribosomal RNA and elongation factor-la. All our analyses congruently indicated that myzostomids are not annelids but suggested instead that they are more closely related to flatworms than to any trochozoan taxon. These results, together with recent analyses of the myzostomidan ultrastructure, have significant implications for understanding the evolution of metazoan body plans, as major characters (segmentation, coeloms, chaetae and trochophore larvae) might have been independently lost or gained in different animal phyla.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Eeckhaut, I and McHugh, D and Mardulyn, P and Tiedemann, R and Monteyne, D and Jangoux, M and Milinkovitch, MC},
	Date-Added = {2009-11-10 10:53:46 +0000},
	Date-Modified = {2009-11-10 10:53:46 +0000},
	Isi = {000088677300002},
	Isi-Recid = {116194908},
	Isi-Ref-Recids = {56558559 49218176 108698691 108698671 103606282 92283261 100467489 12145218 116194909 101903315 116194910 116194911 99457381 77339836 59277392 56562694 36391001 64799777 108698702 89396980 84646461 90553169 57684838 98430803 95184070 116194912 71636482 80934069 100468577 22547332 82982423 97854255 63336861 97335933 69760203 95498817 83784748 104806353 87648932 116194913 116194914 116194915 106761987 116194916 96240931 83672312 63950472 108698661 51215768 106172530 98622437 112176428 63336858 100719897 103606281 116194918 95661814 114293889 48678186 89412910 108508448 73773010 25069525 98929022 74329936 91858287 93361778 98430800 108698696 116194919 107189372},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {Metazoa; Myzostomida; Annelida; evolution; molecular phylogeny; symbiosis},
	Month = jul,
	Number = {1451},
	Pages = {1383-1392},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {46},
	Title = {Myzostomida: a link between trochozoans and flatworms?},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000088677300002}}

@article{Edgecombe.Wilson.ea.2000.a,
	Abstract = {Morphological, developmental, ultrastructural, and gene order characters are catalogued for the same set of arthropod terminals as we have scored in a recent study of histone H3 and U2 snRNA sequences (D. J. Colgan et al., 1998, Aust. J. Zool. 46, 419-437). We examine the implications of separate and simultaneous analyses of sequence and non-sequence data for arthropod relationships. The most parsimonious trees based on 211 non-sequence characters (273 apomorphic states) support traditional higher taxa as clades, including Mandibulata, Crustacea, Atelocerata, Myriapoda, and Hexapoda. Combined analysis of morphology with histone H3 and U2 sequences with equal character weights differs from the morphological results alone in supporting Progoneata + Hexapoda (= Labiophora) in favor of a monophyletic Myriapoda, resolves the entognathous hexapods as a grade, and supports pycnogonids as sister group to Euchelicerata (rather than as basal euarthropods). Monophyly of Chelicerata (including pycnogonids), Mandibulata, Crustacea, Progoneata, Chilopoda, and Hexapoda is maintained under a range of transition/transversion and third codon weights, whereas Atelocerata and Myriapoda/labiophora do not withstand all sensitivity analyses. (C) 2000 The Willi Hennig Society.},
	Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
	Author = {Edgecombe, GD and Wilson, GDF and Colgan, DJ and Gray, MR and Cassis, G},
	Date-Added = {2009-11-10 10:53:21 +0000},
	Date-Modified = {2009-11-10 10:53:21 +0000},
	Isi = {000087505700001},
	Isi-Recid = {115270458},
	Isi-Ref-Recids = {100558925 96534594 110788647 99797658 50442745 23742918 65433146 51513611 90752102 115270459 49193022 53782410 39575423 81550275 87135906 48426013 88663248 108780932 104710452 91999499 97649757 47806496 106550043 115270460 92283261 115270461 115270462 11951495 18233889 109098693 54634783 109590359 51080036 25495734 55403160 109434908 63965702 79987016 85956725 106880317 115270463 82431250 108780943 87566598 95671527 107189375 57213208 99802445 115270464 67908238 44433740 115270465 109590360 109590357 81959074 99582790 18572413 16878681 52064209 92283268 103606190 61577939 115270466 26716842 20131774 91999500 96103849 81568559 99637217 106172598 94202994 101628275 57213346 43516708 44157144 44406036 81568593 115270467 3311807 111999990 103905870 95139478 115270468 4506571 59787593 66521988 80417452 110788657 115270469 27083238 106426055 28574224 105872841 93963351 103905865 43840108 41877376 81550281 26711023 108780951 42375713 79532715 106550045 64183596 63193107 42917440 115270470 115270471 49228267 74563390 100874231 115270472 32879825 115270473 98557303 55833371 9854700 12701830 13711348 22069184 4959031 65469207 35064986 44515402 47673345 81568630 88255522 32611821 15723482 163592474 109706590 103905904 77225634 95671564 91376397 103905866 58635514 108698719 91943339 95812073 99797670 115270475 93203068 93601646 74966912 70450243 41877393 73394095 98069416 95228616 105637688 115270476 99802447 101891901 108698680 98161473 57213230 48816535 46239870 103606281 94349491 18319550 50268141 35065051 107863716 106550047 106550042 91108264 42325693 63467292 108340273 115270477 107863733 115270478 25364757 56558580 71321392 12701831 70409056 115270479 105872839 72005416 70450707 79497786 827600 6665821 115270480 23683 108698713 44433735 94349532 38656291 52436434 84361160 74272126 114092940 83638287 106880322 2594761 2043043 4934395 45181264 103232910 92405300 88161709 115270481 87315084 113473272 74563388 81568585 108854556 109434916 115270482 110788626 115270483 103640339 38315439 58862419 109706596 105872842 93866270 84646419 115270484 106119056 107025989 83817599 100468556 111073163 112217103 115270485 95593785 105179932 81568656 56916002 108780963 99177547 90243796 98061987 115270486 89502329 92862645 105872840},
	Journal = {Cladistics},
	Month = jun,
	Number = {2},
	Pages = {155-203},
	Publisher = {ACADEMIC PRESS LTD},
	Times-Cited = {75},
	Title = {Arthropod cladistics: Combined analysis of histone H3 and U2 snRNA sequences and morphology},
	Volume = {16},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000087505700001}}

@article{Diaz-Uriarte.Garland.1998.a,
	Abstract = {We examined Type I error rates of Felsenstein's (1985; Am. Nat. 125:1-15) comparative method of phylogenetically independent contrasts when branch lengths are in error and the model of evolution is not Brownian motion. We used seven evolutionary models, six of which depart strongly from Brownian motion, to simulate the evolution of two continuously valued characters along two different phylogenies (15 and 49 species). First, we examined the performance of independent contrasts when branch lengths are distorted systematically, for example, by taking the square root of each branch segment. These distortions often caused inflated Type I error rates, but performance was almost always restored when branch length transformations were used. Next, we investigated effects of random errors in branch lengths. After the data were simulated, we added errors to the branch lengths and then used the altered phylogenies to estimate character correlations. Errors in the branches could be of two types: fixed, where branch lengths are either shortened or lengthened by a fixed fraction; or variable, where the error is a normal variate with mean zero and the variance is scaled to the length of the branch (so that expected error relative to branch length is constant for the whole tree). Thus, the error added is unrelated to the microevolutionary model. Without branch length checks and transformations, independent contrasts tended to yield extremely inflated and highly variable Type I error rates. Type I error rates were reduced, however, when branch lengths were checked and transformed as proposed by Garland ct al. (1992; Syst. Biol. 41:18-32), and almost never exceeded twice the nominal P-value at alpha = 0.05. Our results also indicate that, if branch length transformations are applied, then the appropriate degrees of freedom for testing the significance of a correlation coefficient should, in general, be reduced to account fur estimation of the best branch length transformation. These results extend those reported in Diaz-Uriarte and Garland (1996; Syst. Biol. 45:27-47), and show that, even with errors in branch lengths and evolutionary models different from Brownian motion, independent contrasts are a robust method for testing hypotheses of correlated evolution.},
	Address = {ONE GUNPOWDER SQUARE, LONDON EC4A 3DE, ENGLAND},
	Author = {Diaz-Uriarte, R and Garland, T},
	Date-Added = {2009-11-10 10:52:51 +0000},
	Date-Modified = {2009-11-10 10:52:51 +0000},
	Isi = {000077592700009},
	Isi-Recid = {108228217},
	Isi-Ref-Recids = {106822152 98848631 64134651 41197076 95243159 54497548 80759959 84822622 80535801 92204032 89170746 108228218 108228219 108228220 71141655 75043716 86717196 88319323 99676097 98053151 106209247 94842174 76218624 88083507 108228221 85463423 105408080 85105165 100359553 86763569 85938648 95821558 98068978 64284742 94715312 42937627 95661814 95243164 107331443 53877170},
	Journal = {Systematic Biology},
	Month = dec,
	Number = {4},
	Pages = {654-672},
	Publisher = {TAYLOR \& FRANCIS LTD},
	Times-Cited = {116},
	Title = {Effects of branch length errors on the performance of phylogenetically independent contrasts},
	Volume = {47},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000077592700009}}

@article{Dial.Marzluff.1988.a,
	Address = {2010 MASSACHUSETTS AVE, NW, STE 400, WASHINGTON, DC 20036},
	Author = {Dial, Kenneth P. and Marzluff, John M.},
	Date-Added = {2009-11-10 10:51:48 +0000},
	Date-Modified = {2009-11-10 10:52:22 +0000},
	Isi = {A1988Q291900033},
	Isi-Recid = {67019755},
	Isi-Ref-Recids = {37128985 46496408 67019756 67019757 57283149 47426144 46457368 62514303 33750399 5395222 5395238 39233987 56629303 39531614 60384717 54147084 50798003 49732765 67019758 39021248 22842001 24280889 22842046 31335351},
	Journal = {Ecology},
	Month = oct,
	Number = {5},
	Pages = {1620-1624},
	Publisher = {ECOLOGICAL SOC AMER},
	Times-Cited = {96},
	Title = {ARE THE SMALLEST ORGANISMS THE MOST DIVERSE},
	Type = {Note},
	Volume = {69},
	Year = {1988},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1988Q291900033}}

@article{Dewdney.1998.a,
	Abstract = {When a community of species is sampled, nonappearing species are not those with abundances that fall shy of some arbitrary mark, the "veil line" proposed by E. F. Preston in 1948 (Ecology 29, 254-283). Instead, they follow a hypergeometric distribution, which has no resemblance to the veil line. There is therefore no justification for the truncation of distributions proposed to describe the abundances of species in natural communities. The mistake of the veil line points to the need for a general theory of sampling. If a community has a distribution g of species abundances and if samples taken of the community tend to follow distribution f, what is the relationship of f to g7 The seeds of such a theory are available in the work of E. C. Pielou. Using the Poisson distribution as a close approximation to the hypergeometric, one may immediately write and (in most cases) solve the transformation from g to f. The transformation appears to preserve distribution formulas to within constants and parameters, providing yet another reason to rule out the use of truncation. Well beyond this application, the theory provides a foundation for rethinking the sampling process and its implications for ecology. (C) 1998 Academic Press.},
	Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	Author = {Dewdney, AK},
	Date-Added = {2009-11-10 10:51:20 +0000},
	Date-Modified = {2009-11-10 10:51:20 +0000},
	Isi = {000077463200008},
	Isi-Recid = {108057419},
	Isi-Ref-Recids = {108057420 108057421 5159109 318402 62557398 72322471 108057422 28454599 29159828 34407447 318440 8121949 10159310 108057423},
	Journal = {Theoretical Population Biology},
	Month = dec,
	Number = {3},
	Pages = {294-302},
	Publisher = {ACADEMIC PRESS INC},
	Times-Cited = {23},
	Title = {A general theory of the sampling process with applications to the "veil line"},
	Volume = {54},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000077463200008}}

@article{Queiroz.2002.a,
	Abstract = {Key innovations have often been invoked to explain the exceptional diversification of particular groups. However, there are few convincing examples of traits that are repeatedly and consistently associated with increased diversification. The paucity of such cases may reflect the contingent nature of the diversifying effect of key traits. These contingencies can be viewed as statistical interactions between the trait and at least three kinds of factors: (1) other taxa, (2) other traits of the group itself, and (3) the physical environment. I describe tentative examples in each of these categories: (1) a dampening of the diversification of clades with image-forming eyes by groups that earlier evolved such eyes, (2) an effect of growth form (woody or herbaceous) on the diversifying effect of biotic seed dispersal in angiosperms, and (3) an effect of atmospheric CO2 level on the diversifying effect of C-4 photosynthesis in monocots. These examples suggest the need for more complex analyses of the relationship between possible key traits and diversification. They also suggest that radiations may be predictable given certain circumstances, thus supporting a view of evolution as both predictable and contingent. Ironically, a certain degree of predictability may be critical to arguments for evolutionary contingency.},
	Address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA},
	Author = {de Queiroz, A},
	Date-Added = {2009-11-10 10:49:58 +0000},
	Date-Modified = {2009-11-10 10:49:58 +0000},
	Doi = {DOI 10.1080/10635150290155980},
	Isi = {000180254400011},
	Isi-Recid = {127935581},
	Isi-Ref-Recids = {105011007 106499516 99881344 52542194 101702900 113633113 75608885 91999521 74019025 49323634 101964595 75503682 83556609 113293298 110894175 107239160 115424934 116119080 102811322 85463323 75349743 84369610 77591703 81491460 78027514 78027556 109396824 48803797 112908714 6610338 48635239 105179093 32408723 70472434 100218248 75914963 82749589 37956979 89651281 82131803 96136971 68713462 94357582 100719918 113337781 103413128 34531073 98852141 111148612 110659408 122195135 1493818 78840624 99005090 67597379 48346579 121272324 104514688 113629636 5345168 66690949 92625540 104155591 109791275 70574697 89334657 87679912 94357585 41877393 67710763 105135479 127935542 70681647 24348788 31594492 115753600 90871598 77461694 66876807 58490899 120885366 87283818 94204180 50619856 116873340 112515732 1982903 73091861 120206396 66890434 93609185 34591807 118081744 55161434 90087049 83463696 95282935 97934644 87933937},
	Journal = {Systematic Biology},
	Keywords = {biotic seed dispersal; contingency; C-4 photosynthesis; diversification; eyes; key innovation; key trait; predictability},
	Month = dec,
	Number = {6},
	Pages = {917-929},
	Publisher = {TAYLOR \& FRANCIS INC},
	Times-Cited = {24},
	Title = {Contingent predictability in evolution: Key traits and diversification},
	Type = {Proceedings Paper},
	Volume = {51},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000180254400011}}

@article{Demetrius.2000.a,
	Abstract = {Directionality theory, a dynamic theory of evolution that integrates population genetics with demography, is based on the concept of evolutionary entropy, a measure of the variability in the age of reproducing individuals in a population. The main tenets of the theory are three principles relating the response to the ecological constraints a population experiences, with trends in entropy as the population evolves under mutation and natural selection. (i) Stationary size or fluctuations around a stationary size (bounded growth): a unidirectional increase in entropy; (ii) prolonged episodes of exponential growth (unbounded growth), large population size: a unidirectional decrease in entropy; and (iii) prolonged episodes of exponential growth (unbounded growth), small population size: random, non-directional change in entropy.

We invoke these principles, together with an allometric relationship between entropy, and the morphometric variable body size, to provide evolutionary explanations of three empirical patterns pertaining to trends in body size, namely (i) Cope's rule, the tendency towards size increase within phyletic lineages; (ii) the island rule, which pertains to changes in body size that occur as species migrate from mainland populations to colonize island habitats; and (iii) Bergmann's rule, the tendency towards size increase with increasing latitude. The observation that these ecotypic patterns can be explained in terms of the directionality principles for entropy underscores the significance of evolutionary entropy as a unifying concept in forging a link between micro-evolution, the dynamics of gene frequency change, and macro-evolution, dynamic changes in morphometric variables.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Demetrius, L},
	Date-Added = {2009-11-10 10:49:12 +0000},
	Date-Modified = {2009-11-10 10:49:12 +0000},
	Isi = {000166088300005},
	Isi-Recid = {118081751},
	Isi-Ref-Recids = {5618152 18306088 67415910 118081752 63492693 28413015 118081753 85040241 26367823 48734055 79198568 100286514 116741469 118081754 102005703 33174 9815839 24882227 65563349 7268970 98852141 100286518 7885641 12748497 54697091 61433301 4259023 22696661 20666009 100368462 50798003 118081756 38106546 22842001 50904151 27243773 99847899},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {Cope's rule; the island rule; Bergmann size clines; evolutionary entropy},
	Month = dec,
	Number = {1460},
	Pages = {2385-2391},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {21},
	Title = {Directionality theory and the evolution of body size},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000166088300005}}

@article{Davidson.Peterson.ea.1995.a,
	Abstract = {An argument is proposed to explain the origin of large metazoans, based on the regulatory processes that underlie the morphogenetic organization of pattern in modern animals. Genetic regulatory systems similar to those used in modern, indirectly developing marine invertebrates are considered to indicate the Precambrian regulatory platform on which were erected innovations that underlie the development of macroscopic body plans. Those systems are genetic regulatory programs that produce groups of unspecified ''set-aside cells'' and hierarchical regulatory programs that initially define regions of morphogenetic space in terms of domains of transcription factor expression, These ideas affect interpretation of the development of arthropods and chordates as well as interpretation of the role of the genes of the homeotic complex in embryogenesis.},
	Address = {1333 H ST NW, WASHINGTON, DC 20005},
	Author = {Davidson, Eric H. and Peterson, Kevin J. and Cameron, R Andrew},
	Date-Added = {2009-11-10 10:48:01 +0000},
	Date-Modified = {2009-11-10 10:48:53 +0000},
	Isi = {A1995TF89900028},
	Isi-Recid = {93601567},
	Isi-Ref-Recids = {86534204 73950889 63975313 4265274 86056794 84584161 20139891 74019025 93601588 62200616 71881701 84588728 90592065 80279576 82844137 79556518 88581210 93601589 88326760 88581207 71937656 77167320 84217609 93601590 86256470 90534017 93601591 88947335 82113566 25744167 88947336 93601592 70472434 48765515 90553169 90631309 90779042 68826996 77614413 6653400 80257871 23688510 87878513 16358661 86607118 8677163 81874553 20241103 72801122 90592040 80216215 93601593 82113557 85149706 90752113 56224198 79944889 92412156 93601594 89455961 61370661 93601595 72801126 87230050 47146617 47779247 93601596 93601597 89633321 93601598 82382080 57406258 36281449 50526000 315166 93601599 86257565 93601600 84646419 84959049 82844129 89527020 90305460},
	Journal = {Science},
	Month = nov,
	Number = {5240},
	Pages = {1319-1325},
	Publisher = {AMER ASSOC ADVAN SCIENCE},
	Times-Cited = {248},
	Title = {ORIGIN OF BILATERIAN BODY PLANS - EVOLUTION OF DEVELOPMENTAL REGULATORY MECHANISMS},
	Volume = {270},
	Year = {1995},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1995TF89900028}}

@article{Cracraft.1985.a,
	Address = {2345 TOWER GROVE AVENUE, ST LOUIS, MO 63110},
	Author = {Cracraft, Joel},
	Date-Added = {2009-11-10 10:46:34 +0000},
	Date-Modified = {2009-11-10 10:46:54 +0000},
	Isi = {A1985AUG3600007},
	Isi-Recid = {57426533},
	Isi-Ref-Recids = {38443336 37751938 3523009 54624720 15531621 38186006 34842979 57426534 55428929 788736 48385448 55195076 28109986 13928864 42089680 36506401 29662283 8944117 41364100 16654374 18879062 57426535 49217787 46195736 44482855 52265475 44724469 48579746 18086499 52154836 28454597 57426536 700501 20508511 32984322 33679032 34834981 39568805 25715300 39692546 29750155 56035266 6533059 33174 680993 45469493 26857947 37017392 21875529 41786014 47146602 29384281 49366070 47449175 47449183 42089614 37500807 19722404 23610716 35836477 20222395 43793880 17273882 13378667 56091552 43475229 54830227 36281344 5395238 48426057 25186229 57426537 43224155 53634328 12060543 47146605 47146607 20015348 6538917 20251548 36416352 45779432 43382725 29358413 36867331 37649221 47202289 8944113 7714486 12332807 19464611 11002466 8934350 21209385 14833701 42321165 8143328 17154446 29530008 47118871 24256594 2044305 31162102 27706603 42769807 48579752 48579750 27243751 11818459 50754755 43153812 52121585 28676186 44326996 11566955 34348043 49366071 48782274 22048163 21879825 57426538 24348788 31084070 31084071 21656688 45244890 44406137 30294895 57426539 41578651 31809080 24280804 46395821 38630820 35136250 32540426 25986670 15813749 20311414 30304607 43289206 27389642 24809795 48954510 43988638 32408725 35170674 38225604 53634409 47761649 24809815 1981700 8976291 21118850 29600474 43570149 38380623 53634332 40512834 43988695 26721855 35291605 16684028 13241409 16334856 20015343 23306729 53732588 47337422 41662800 47557867 57426540 40852341 50242538 25714886 21067437 18756314 42089684 47761652 20311410 27243773 32262328 32771645 14249717 39568797 49483653 29829813 49380623 34761578 37888177 22881351 37304236 41680252 34532798 32551348 57426541 57426422 46129967 32193114 24642440 57426542},
	Journal = {Annals of the Missouri Botanical Garden},
	Number = {4},
	Pages = {794-822},
	Publisher = {MISSOURI BOTANICAL GARDEN},
	Times-Cited = {69},
	Title = {BIOLOGICAL DIVERSIFICATION AND ITS CAUSES},
	Volume = {72},
	Year = {1985},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1985AUG3600007}}

@article{Cossins.1998.a,
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON, ENGLAND N1 9XW},
	Author = {Cossins, A},
	Date-Added = {2009-11-10 10:45:45 +0000},
	Date-Modified = {2009-11-10 10:45:45 +0000},
	Isi = {000077204000021},
	Isi-Recid = {107791967},
	Isi-Ref-Recids = {85354827 91667933 103079678 85275756 7878091 107791968 24764385 100211178 104052475},
	Journal = {Nature},
	Month = nov,
	Number = {6709},
	Pages = {309-310},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Times-Cited = {9},
	Title = {Cryptic clues revealed},
	Type = {Editorial Material},
	Volume = {396},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000077204000021}}

@article{Cook.Smith.ea.2001.a,
	Abstract = {The arthropods are the most speciose, and among the most morphologically diverse, of the animal phyla, Their evolution has been the subject of intense research for well over a century, yet the relationships among the four extant arthropod subphyla - chelicerates, crustaceans, hexapods, and myriapods - are still not fully resolved. Morphological taxonomies have often placed hexapods and myriapods together (the Atelocerata) [1, 2], but recent molecular studies have generally supported a hexapod/crustacean clade [2-9], A cluster of regulatory genes, the Hox genes, control segment identity in arthropods, and comparisons of the sequences and functions of Hox genes can reveal evolutionary relationships [10], We used Hox gene sequences from a range of arthropod taxa, including new data from a basal hexapod and a myriapod, to estimate a phylogeny of the arthropods. Our data support the hypothesis that insects and crustaceans form a single clade within the arthropods to the exclusion of myriapods, They also suggest that myriapods are more closely allied to the chelicerates than to this insect/crustacean clade.},
	Address = {1100 MASSACHUSETTES AVE,, CAMBRIDGE, MA 02138 USA},
	Author = {Cook, CE and Smith, ML and Telford, MJ and Bastianello, A and Akam, M},
	Date-Added = {2009-11-10 10:45:17 +0000},
	Date-Modified = {2009-11-10 10:45:17 +0000},
	Isi = {000168765100017},
	Isi-Recid = {119962132},
	Isi-Ref-Recids = {114844844 84275377 81550275 91999499 104710452 74019025 115424967 110642526 115270458 91999500 115270487 94202994 103223082 99996694 106172542 101891901 97209324 101085100 76953407 119935439 112864963},
	Journal = {Current Biology},
	Month = may,
	Number = {10},
	Pages = {759-763},
	Publisher = {CELL PRESS},
	Times-Cited = {81},
	Title = {Hox genes and the phylogeny of the arthropods},
	Volume = {11},
	Year = {2001},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000168765100017}}

@article{Cook.1998.a,
	Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
	Author = {Cook, S},
	Date-Added = {2009-11-10 10:44:13 +0000},
	Date-Modified = {2009-11-10 10:44:13 +0000},
	Isi = {000075606400002},
	Isi-Recid = {106788309},
	Isi-Ref-Recids = {97577833 16399926 85585641 101613286 90158734 86191804 92086885 99076487 6538881},
	Journal = {Trends In Ecology \& Evolution},
	Month = sep,
	Number = {9},
	Pages = {340-341},
	Publisher = {ELSEVIER SCI LTD},
	Times-Cited = {4},
	Title = {A diversity of approaches to the study of species richness},
	Type = {Editorial Material},
	Volume = {13},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000075606400002}}

@article{Conway-Morris.1998.a,
	Abstract = {Metazoan phylogeny is in a state of ferment, stirred by the addition of new molecular trees as well as controversial interpretations of molecular 'clocks'. Concerning the latter topic, the clocks recurrently point to divergence times substantially older than the known fossil record. Some attempt reconciliation by appealing to a conveniently cryptic interval prior to the first fossils. This effectively reduces the fossil record to an erratic search-light giving only glimpses into the true evolutionary history. Other options, however, remain open. Molecular clocks may themselves run erratically and what happens in molecular history may not coincide with the emergence of body plans.},
	Address = {34-42 CLEVELAND STREET, LONDON W1P 6LE, ENGLAND},
	Author = {Conway Morris, Simon},
	Date-Added = {2009-11-10 10:42:50 +0000},
	Date-Modified = {2009-11-10 10:43:07 +0000},
	Isi = {000077614100008},
	Isi-Recid = {108152227},
	Isi-Ref-Recids = {100558925 102526379 101441920 103692980 104825784 101964466 104773135 104710452 107863719 105774777 104620858 99287968 104636227 68944967 108152228 101849968 100482929 93859108 95429654 101628275 90553169 90779042 102639204 104900702 102644244 108152229 103757391 87838091 102385751 103606145 105020095 104781916 93859107 104155591 108152230 104155584 90752113 99131722 106704628 102790024 102639203 102791346 101267119 80542874 107159554 105774776 92690259 107039429 105179920 105587154 97846734 106123009 103757390},
	Journal = {Current Opinion In Genetics \& Development},
	Month = dec,
	Number = {6},
	Pages = {662-667},
	Publisher = {CURRENT BIOLOGY LTD},
	Times-Cited = {15},
	Title = {Metazoan phylogenies: falling into place or falling to pieces? A palaeontological perspective},
	Volume = {8},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000077614100008}}

@article{Conway-Morris.1994.a,
	Abstract = {Molecular biology has re-opened the debate on metazoan diversification, including the vexing question of the origin of the major body plans (phyla), In particular, sequence analyses of rRNA have reconfigured significantly metazoan phylogeny, while homeobox genes suggest there could be an underlying similarity of developmental instructions in nominally disparate phyla. Despite this dramatic progress I argue that this renaissance of activity is lop-sided, but can be redressed by palaeontological data, especially from the Cambrian and immediately preceding Vendian. The fossil record complements and amplifies the conclusions derived from molecular biology, notably in the early radiation of cnidarians (Ediacaran faunas) and key steps in the diversification of the protostomes.},
	Address = {BIDDER BUILDING CAMBRIDGE COMMERCIAL PARK COWLEY RD, CAMBRIDGE, CAMBS, ENGLAND CB4 4DL},
	Author = {Conway Morris, Simon},
	Date-Added = {2009-11-10 10:42:12 +0000},
	Date-Modified = {2009-11-10 10:42:27 +0000},
	Isi = {A1994QK89700002},
	Isi-Recid = {90591919},
	Isi-Ref-Recids = {70666460 90591920 90591921 84275377 90591922 85660192 81550275 87838048 36753646 14725743 82113559 81845217 77568500 69813347 90591923 39743966 80326159 80930640 70408867 75904592 84408016 86157884 86816207 87315078 74539309 88947163 87838050 67693537 77833235 87198454 75229552 73458407 84329224 61885115 84425892 85384103 90591924 45927453 90591925 86267799 73846122 64410692 64799777 41111371 83585187 65812682 63904834 71782050 52539850 19547598 70472434 86072660 75158680 79488790 81728588 74544245 78385820 78385818 1437200 72547313 62448054 85149729 88101021 83784748 84765873 82363772 71308899 90591926 35136271 71934412 79781691 84445713 84680472 72817949 82749541 90591927 72817950 82113557 60459637 76505223 85149706 36765348 54689818 70472446 3334463 77960112 81728605 83313299 56224213 83742826 80759982 81653173 70163568 44406029 71047449 79488764 52874073 75903070 82531016 80802020 90591928 47146617 90591929 90591930 77960114 84942020 79538866 80542874 69813324 81728608 85350221 82844152 85616386 83463675 90591931 84657251 90591932 32929736 82652479 83481409 58008794 78763808 14191647 90591933 81422078 80216383 86257565 83009475 80771743 77932808 75224790 83817599 44499498 72632899 87198459 61752577 80440154 78279515 89632517 70539239 82113582},
	Journal = {Development},
	Keywords = {CAMBRIAN; EDIACARAN; EVOLUTION; FOSSIL; METAZOA; PHYLOGENY},
	Pages = {1-13},
	Publisher = {COMPANY OF BIOLOGISTS LTD},
	Times-Cited = {18},
	Title = {WHY MOLECULAR-BIOLOGY NEEDS PALEONTOLOGY},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994QK89700002}}

@book{Wiley.Siegel-Causey.ea.1991.a,
	Author = {Wiley, E O and Siegel-Causey, D and Brooks, D R and Funk, V A},
	Date-Added = {2009-11-10 10:36:36 +0000},
	Date-Modified = {2009-11-10 10:38:35 +0000},
	Publisher = {THE UNIVERSITY OF KANSAS MUSEUM OF NATURAL HISTORY},
	Title = {The Compleat Cladist},
	Year = {1991},
	Bdsk-File-1 = { }}

@article{Cohen.Gawthrop.ea.1998.a,
	Abstract = {Brachiopod and phoronid phylogeny is inferred from SSU rDNA sequences of 28 articulate and nine inarticulate brachiopods, three phoronids, two ectoprocts and various outgroups, using gene trees reconstructed by weighted parsimony, distance and maximum likelihood methods. Of these sequences, 33 from brachiopods, two from phoronids and one each from an ectoproct and a priapulan are newly determined. The brachiopod sequences belong to 31 different genera. and thus survey about 10\% of extant genus-level diversity. Sequences determined in different laboratories and those from closely related taxa agree well, but evidence is presented suggesting that one published phoronid sequence (GenBank accession U12648) is a brachiopod-phoronid chimaera, and this sequence is excluded from the analyses. The chiton, Acanthopleura, is identified as the phenetically proximal outgroup; other selected outgroups were chosen to allow comparison with recent, non-molecular analyses of brachiopod phylogeny. The different outgroups and methods of phylogenetic reconstruction lead to similar results, with differences mainly in the resolution of weakly supported ancient and recent nodes, including the divergence of inarticulate brachiopod sub-phyla, the position of the rhynchonellids in relation to long- and short-looped articulate brachiopod clades and the relationships of some articulate brachiopod genera and species. Attention is drawn to the problem presented by nodes that are strongly supported by non-molecular evidence but receive only low bootstrap resampling support.

Overall, the gene trees agree with morphology-based brachiopod taxonomy, but novel relationships are tentatively suggested for thecideidine and megathyrid brachiopods. Articulate brachiopods are found to be monophyletic in all reconstructions, but monophyly of inarticulate brachiopods and the possible inclusion of phoronids in the inarticulate brachiopod clade are less strongly established. Phoronids are clearly excluded from a sister-group relationship with articulate brachiopods, this proposed relationship being due to the rejected, chimaeric sequence (GenBank U12648). Lineage relative rate tests show no heterogeneity of evolutionary rate among articulate brachiopod sequences, but indicate that inarticulate brachiopod plus phoronid sequences evolve somewhat more slowly. Both brachiopods and phoronids evolve slowly by comparison with other invertebrates. A number of palaeontologically dated times of earliest appearance are used to make upper and lower estimates of the global rate of brachiopod SSU rDNA evolution, and these estimates are used to infer the likely divergence times of other nodes in the gene tree. There is reasonable agreement between most inferred molecular and palaeontological ages. The estimated rates of SSU rDNA sequence evolution suggest that the last common ancestor of brachiopods, chitons and other protostome invertebrates (Lophotrochozoa and Ecdysozoa) lived deep in Precambrian time.

Results of this first DNA-based, taxonomically representative analysis of brachiopod phylogeny are in broad agreement with current morphology-based classification and systematics and are largely consistent with the hypothesis that brachiopod shell ontogeny and morphology are a good guide to phylogeny.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Cohen, BL and Gawthrop, A and Cavalier-Smith, T},
	Date-Added = {2009-11-10 10:23:11 +0000},
	Date-Modified = {2009-11-10 10:23:11 +0000},
	Isi = {000078032500005},
	Isi-Recid = {108512700},
	Isi-Ref-Recids = {83585188 100558925 74762858 85565684 72152451 93859071 98987606 85902891 66253883 74019025 99481735 80440182 96427139 106768849 102663488 104620858 110217431 42481844 83704706 74452094 51321644 53625163 90752121 81959074 81862368 45927453 34936788 45927466 75561117 75312056 17421711 99267367 47837233 101849968 84933676 64799777 100482929 71782050 108512702 107164021 59944112 97831084 90553169 94567622 95324778 94110788 73443113 105315438 57684838 67149904 97351096 97319128 80062222 94005037 5930871 31647708 70507989 72423869 81685793 41807846 95230548 86145800 104620863 81554268 87648933 102663485 108512703 92217475 19835250 108512704 96240931 88736162 52265466 57741903 74316141 99529817 91478429 95324775 91943339 74875578 95812073 89632497 87454950 79022228 82192017 108512705 163386472 94976536 95324777 83704697 89455961 100954981 90591939 80440188 63203468 71712746 81959090 67672876 86933215 89733280 96765984 97209324 108512706 95661814 83481386 23420076 84193413 95230555 108512707 74329936 22647713 3991496 97710271 89334669 80836720 86070100 72632899 15848938 108512708 108512709 91858287 88473221 83108810 87948376 97846734 56566221 88167305 10401450 68654995 92388095 76140524},
	Journal = {Philosophical Transactions of the Royal Society B-Biological Sciences},
	Keywords = {brachiopod; phoronid; SSU rDNA; molecular phylogeny; lophophorate; lophotrochozoa},
	Month = dec,
	Number = {1378},
	Pages = {2039-2061},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {63},
	Title = {Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences},
	Volume = {353},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000078032500005}}

@article{Cohen.2000.a,
	Abstract = {Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, confirm previous indications that in such data, brachiopod and phoronids form a well-supported clade that (on previous evidence) is unambiguously affiliated with protostomes rather than deuterostomes. Within the brachiopod - phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inarticulates is weakly indicated. Brachiopod-phoronid monophyly is reconciled with the most recent Linnaean classification of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell-less forms.

Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true: undermines virtually all morphology-based reconstructions of phylogeny made during the past century or more.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Cohen, BL},
	Date-Added = {2009-11-10 10:22:45 +0000},
	Date-Modified = {2009-11-10 10:22:45 +0000},
	Isi = {000085554900003},
	Isi-Recid = {113921486},
	Isi-Ref-Recids = {107128626 100558925 103849819 74019025 98015777 102663488 104620858 108512700 104620859 110642526 88102462 81959074 45927453 45927466 103232884 52835856 34936788 107960097 111371839 64799777 90553169 95324778 94567622 97319128 5930871 110788657 96240931 95324775 91943339 95812073 83704697 113921488 71712746 81959090 112527614 100771117 89334669 108512708 97710271 108512693 113921489 72632899 83108810 91858297 107189372},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {protostomozoa; deuterostomozoa; Brachiopoda; Phoronida; 18S rDNA; DNA sequence},
	Month = feb,
	Number = {1440},
	Pages = {225-231},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {53},
	Title = {Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.)},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000085554900003}}

@article{Chown.Gaston.1997.a,
	Abstract = {1. Recently, fresh attempts have been made to understand the mechanisms structuring species-body size distributions. Of these, the model developed by Brown, Marquet \& Taper (1993) (BMT), which uses measures of resource acquisition and conversion to determine an optimal body size (M*) for a given assemblage, is potentially the most significant. Here, we examine the novelty of the model and some of its assumptions, and test its empirical predictions.

2. The BMT model is one of a suite of physiological/life-history models examining size at maturity. Such energetic or 'physical' approaches to body size evolution have a considerable modern history and continue to enjoy attention in physiological ecology and life-history theory.

3. Although mortality significantly influences life-history evolution and mostly precludes the evolution of a body size that maximizes reproductive power output, it is excluded from the BMT model. Likewise, the model assumes that power and not efficiency is maximized, although there are conditions where this is not likely to be the case. Furthermore, the BMT model assumes that resource acquisition and conversion are physiologically limited, although the importance of physiological limitation in ecology remains unclear.

4. Additional assumptions of the model include coincidence of the optimum body size of an individual and a species, when in many species this is not the case, and coincidence of the most speciose size class in an assemblage and the optimal body size. Similarly, the probable influence of differences in the scaling of various parameters at the intra- and interspecific levels are not addressed, nor are the impacts of discrepancies between phenotypic and genotypic optima.

5. The measures of resource acquisition and conversion used in the BMT model are not only problematic, but also limit the utility of the model. If the scaling constants and exponents of field metabolic rate minus basal metabolic are used as a measure of resource acquisition beyond maintenance needs, and those for intrinsic rate of increase (r(max)) as a measure of resource conversion, the applicability of the model to other taxa can be extended.

6. Using these measures we show that the model continues to provide a reasonable prediction of M* for the terrestrial mammal assemblages of both North America and Australia. However, when taxonomic inclusiveness is reduced by removing eutherians from the Australian data set and by examining the predictions of the model with regard to diprotodonts only, the model fails to provide reasonable predictions of M*.

7. Given problems with the BMT model, but its clear ability to predict the modal body size of at least two terrestrial mammal assemblages, we suggest that there is considerable scope for exploring the relationships between resource acquisition and conversion at the level of the individual and energy partitioning between individuals in multispecies communities.},
	Address = {P O BOX 88, OSNEY MEAD, OXFORD, OXON, ENGLAND OX2 0NE},
	Author = {Chown, SL and Gaston, KJ},
	Date-Added = {2009-11-10 10:22:07 +0000},
	Date-Modified = {2009-11-10 10:22:07 +0000},
	Isi = {A1997XF36700013},
	Isi-Recid = {100958169},
	Isi-Ref-Recids = {88265256 90158721 89256113 77823412 94380384 93026022 87312641 96699904 88792303 86215462 89395450 92191768 88440266 73741806 63140160 78521178 85211999 96176557 91999521 68352674 70374758 85040241 67019755 86973804 91546524 78849547 79662915 59231757 92017008 30265863 75706840 66426016 71782659 85495583 19464667 89395451 90671900 72497348 77846057 91198315 98567995 82135304 96699863 39344682 63005913 79263088 94635655 89832880 91022171 1745010 47952856 77466733 96699907 5395222 76686457 66311374 89249992 100958170 100958171 83169927 87602704 74962267 82135305 86717196 12739598 99363657 91543608 67479261 80683501 39531614 89249972 89249975 55319350 56891665 67167574 15796050 85463320 50798003 72085013 72479357 43794706 92403197 76947166 91254374 88036208 61065280 80389483 61238314 44850036 72078903 64144936 54497583 78676547 70364022 81322830 46871442 94222218 79909317 92625537},
	Journal = {Functional Ecology},
	Keywords = {energy partitioning; mammal assemblages; physiological constraints},
	Month = jun,
	Number = {3},
	Pages = {365-375},
	Publisher = {BLACKWELL SCIENCE LTD},
	Times-Cited = {39},
	Title = {The species-body size distribution: Energy, fitness and optimality},
	Volume = {11},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997XF36700013}}

@article{Carroll.2000.a,
	Abstract = {New concepts and information from molecular developmental biology, systematics, geology and the fossil record of all groups of organisms, need to be integrated into an expanded evolutionary synthesis. These fields of study show that large-scale evolutionary phenomena cannot be understood solely on the basis of extrapolation from processes observed at the level of modern populations and species. Patterns and rates of evolution are much more varied than had been conceived by Darwin or the evolutionary synthesis, and physical factors of the earth's history have had a significant, but extremely varied, impact on the evolution of life.},
	Address = {84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND},
	Author = {Carroll, RL},
	Date-Added = {2009-11-10 10:21:13 +0000},
	Date-Modified = {2009-11-10 10:21:13 +0000},
	Isi = {000085525100011},
	Isi-Recid = {113933826},
	Isi-Ref-Recids = {106172526 66932529 85902891 105191595 90545788 107976058 92338093 102664218 101702901 106331706 113933827 99331551 108152240 106331817 100971217 75674122 28434441 101628275 110585930 106681284 107997643 80304358 107976038 113933829 70760608 109415849 113933830 87502255 42877193 103580265 113933831 104155591 108698663 102219631 107181869 96522143 106399777 113933832 101620796 109450739 94567618 113933833 108340255 113933834 106287334},
	Journal = {Trends In Ecology \& Evolution},
	Month = jan,
	Number = {1},
	Pages = {27-32},
	Publisher = {ELSEVIER SCIENCE LONDON},
	Times-Cited = {34},
	Title = {Towards a new evolutionary synthesis},
	Volume = {15},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000085525100011}}

@article{Carranza.Baguna.ea.1997.a,
	Abstract = {In most zoological textbooks, Platyhelminthes are depicted as an early-emerging clade forming the likely sister group of all the other Bilateria. Other phylogenetic proposals see them either as the sister group of most of the Protostomia or as group derived from protostome coelomate ancestors by progenesis. The main difficulty in their correct phylogenetic placing is the lack of convincing synapomorphies for all Platyhelminthes, which may indicate that they are polyphyletic. Moreover, their internal phylogenetic relationships are still uncertain. To test these hypotheses, new complete 18S rDNA sequences from 13 species of ''Turbellaria'' have been obtained and compared to published sequences of 2 other ''Turbellaria,'' 3 species of parasitic Platyhelminthes, and several diploblastic and deuterostome and protostome triploblastics. Maximum-parsimony, maximum-likelihood, and neighbour-joining methods were used to infer their phylogeny. The results show the order Catenulida to form an independent early-branching clade and emerge as a potential sister group of the rest of the Bilateria, while the rest of Platyhelminthes (Rhabditophora), which includes the parasites, form a clear monophyletic group closely related to the protostomes. The order Acoela, morphologically considered as candidates to be ancestral, are shown to be fast-clock organisms for the 18S rDNA gene. Hence, long-branching of acoels and insufficient sampling of catenulids and acoels leave their position still unresolved and call for further studies. Within the Rhabditophora, our analyses suggest (1) a close relationship between orders Macrostomida and Polycladida, forming a clear sister group to the rest of orders; (2) that parasitic platyhelminthes appeared early in the evolution of the group and form a sister group to a still-unresolved clade made by Nemertodermatida, Lecithoepitheliata, Prolecithophora, Proseriata, Tricladida, and Rhabdocoela; and (3) that Seriata is paraphyletic.},
	Address = {PO BOX 1897, LAWRENCE, KS 66044-8897},
	Author = {Carranza, S and Baguna, J and Riutort, M},
	Date-Added = {2009-11-10 10:19:56 +0000},
	Date-Modified = {2009-11-10 10:19:56 +0000},
	Isi = {A1997WZ08500003},
	Isi-Recid = {100467451},
	Isi-Ref-Recids = {83585188 100467452 66932529 76491928 83298460 91858307 68800524 74019025 10158843 96464836 100467453 38704976 75229552 94305638 58463631 56038476 56562694 43930323 94202997 64799777 13119336 91999500 83585187 96326917 57557770 98430803 77487239 1437066 27006538 93311628 84164129 41807846 92452292 71308899 93124737 82113557 66195115 86466415 163386472 90277911 86662818 85468831 11029479 50663110 59482683 82531016 80802020 92452287 74648235 85328654 89961570 96464839 63203468 34512939 44694877 58463637 88457912 100467454 27232791 28281355 83638287 76953407 78763808 94567618 86257565 83009475 15711325 72632899 32193114 91858287 93361778 62523217},
	Journal = {Molecular Biology and Evolution},
	Keywords = {18S rDNA; Platyhelminthes; phylogeny; metazoan; monophyletic primitive group},
	Month = may,
	Number = {5},
	Pages = {485-497},
	Publisher = {SOC MOLECULAR BIOLOGY EVOLUTION},
	Times-Cited = {141},
	Title = {Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences},
	Volume = {14},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WZ08500003}}

@article{Cantino.Bryant.ea.1999.a,
	Abstract = {Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species namer, governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.},
	Address = {11 NEW FETTER LANE, LONDON EC4P 4EE, ENGLAND},
	Author = {Cantino, PD and Bryant, HN and De Queiroz, K and Donoghue, MJ and Eriksson, T and Hillis, DM and Lee, MSY},
	Date-Added = {2009-11-10 10:17:58 +0000},
	Date-Modified = {2009-11-10 10:17:58 +0000},
	Isi = {000088185000005},
	Isi-Recid = {114029113},
	Isi-Ref-Recids = {96191804 110970921 103620107 108228213 88319325 6795098 101187173 115923074 105401198 104155495 105401206 81631282 74452094 110464202 114401491 102830025 72005446 85786639 81775262 106497683 93855051 104264435 29451796 107719957 105586838 106231789 105401208 108228232 99038215 97667086 109148683 8978759 8143323 79215590 104079434 106786288 81959110 93201550 105401194 105401197 110761668 87817218 92192406 114315016 99457393},
	Journal = {Systematic Biology},
	Keywords = {phylogenetic nomenclature; species names; binomial nomenclature},
	Month = dec,
	Number = {4},
	Pages = {790-807},
	Publisher = {TAYLOR \& FRANCIS LTD},
	Times-Cited = {75},
	Title = {Species names in phylogenetic nomenclature},
	Volume = {48},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000088185000005}}

@article{Budd.Jensen.2000.a,
	Abstract = {It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable, A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred ill the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversification, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the definition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversification based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversification occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimony and functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversification through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just one of them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and flexibility.},
	Address = {40 WEST 20TH STREET, NEW YORK, NY 10011-4211 USA},
	Author = {Budd, GE and Jensen, S},
	Date-Added = {2009-11-10 09:57:13 +0000},
	Date-Modified = {2009-11-10 09:57:13 +0000},
	Isi = {000087780600003},
	Isi-Recid = {115424967},
	Isi-Ref-Recids = {70666460 109526117 100558925 106172526 45559171 104814191 56038471 108706126 103692980 104825784 60518061 85902891 109450923 111205205 60082398 69763464 106550043 107244502 103673316 80930640 66890426 81568572 33532605 100011242 107352113 99797686 80411995 111712495 107239151 109842172 107239148 114447047 97207269 86816207 100955214 96520101 93293583 85135499 10342036 16567459 32295977 104620859 41573 104636227 62218105 92403193 63965706 105644887 93601567 96924872 77167320 78469870 100196784 107239160 94574960 110705111 109590360 33544362 84425892 110323463 64789555 97844939 109590357 115424968 114994462 87834999 56038476 101307446 90591925 111073144 99331551 57262981 105135435 87198499 81850512 88741078 7349238 100482929 83742837 94942842 110027649 98264287 113604114 63904834 82113566 108847487 106331817 100971217 115424969 19848706 112984368 13882725 22843793 31471638 103535162 70472434 87943094 108847512 94567622 90553169 96191827 84865280 85463379 115424970 90779042 98430803 67892202 103535190 23396709 70932423 115424971 108512694 87868429 97710250 109590362 78385818 5534818 102639204 109905619 44897952 111535071 23688510 112515730 44406041 102959454 110292777 115424972 104155596 114395277 79876943 78425890 49010892 64853610 63500042 107976038 92107502 95218598 110659408 44956075 110292811 106335907 102984604 103748481 109590300 82427128 110042046 101442081 108847502 96924877 99529817 60459637 106704628 108698681 103032998 82113557 108423955 36765348 43185083 76505223 90752113 63585467 106274083 74414924 25069733 91943339 56224213 74875578 102639203 5352553 62430543 63206380 24990891 97790337 67464879 115424974 81631204 83997412 84806552 108642063 101267119 95678808 70472450 18823598 109590366 75903070 50579043 115424975 59482683 88318283 112033063 69048384 94220563 100277150 31413224 48138236 93601596 27022275 47513589 47146617 83017755 94942855 80727789 80197762 50663100 65916992 107781121 98430807 107863716 85757442 23767799 84942020 94683870 95678818 107159554 108847537 74414945 108847483 82033125 98130882 95228658 112515732 88698599 67930747 83637071 114555587 82382080 33998649 96537980 95504988 23683 14169178 108668210 50579041 45962257 83997539 83481409 115424976 18118323 115424977 85255387 91820362 78763808 50095729 94567618 25714886 87838012 91475860 87650247 109450753 94005201 107333648 86257565 106761990 96191811 112984357 113473272 74563388 109434916 91065434 113632057 38348323 98929022 61834368 35808854 72632899 2465295 105179920 56224226 97846734 103757390 780416 49869372 42325677 70256609 89775307 76505246 108478920 46343163},
	Journal = {Biological Reviews},
	Keywords = {Cambrian; Bilateria; functional morphology; plankotrophy; trace fossils; body size; stem groups; phyla; origins; molecular clocks},
	Month = may,
	Number = {2},
	Pages = {253-295},
	Publisher = {CAMBRIDGE UNIV PRESS},
	Times-Cited = {151},
	Title = {A critical reappraisal of the fossil record of the bilaterian phyla},
	Volume = {75},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000087780600003}}

@article{Brown.Nicoletto.1991.b,
	Abstract = {We describe the nonrandom assembly of the North American terrestrial mammalian fauna based on body size and spatial scale.  The frequency distribution of body masses among species for the entire continental fauna was highly modal and right skewed, even on a logarithmic scale; the median size of the 465 species was approximately 45 g.  In contrast, comparable frequency distributions for 24 small patches of relatively homogeneous habitat were essentially uniform, with approximately equal numbers of species in each logarithmic size class; the median sizes of the 19-37 species ranged from approximately 100 to 2,500 g.  Frequency distributions for 21 biomes (large regions of relatively similar vegetation) were intermediate between the continental and local assemblages.  This pattern of assembly indicates that species of modal size (20-250 g) tend not to coexist in local habitat patches and they replace each other more frequently from habitat to habitat across the landscape than species of relatively large or small size.  We hypothesize that three mechanisms are necessary and possibly sufficient to produce this result:  competitive exclusion of species of similar size within local habitats, differential extinction of species of large size with small geographic ranges, and greater specialization of modal-sized species owing to energetic and dietary constraints.},
	Address = {5720 S WOODLAWN AVE, CHICAGO, IL 60637},
	Author = {Brown, James H and Nicoletto, Paul F.},
	Date-Added = {2009-11-10 09:55:32 +0000},
	Date-Modified = {2009-11-10 09:56:08 +0000},
	Isi = {A1991HB55000009},
	Isi-Recid = {78521178},
	Isi-Ref-Recids = {78521179 78521180 72602383 67415910 46068029 60188210 63140160 44632501 55554687 50252106 59647954 23563377 56997848 31689665 68352676 68352674 37338665 53742605 72551876 29212819 37595607 78521181 42664384 78521182 67019755 28454597 57499474 69381330 47426144 53568287 61791890 30280269 9815839 66814376 61487462 45815132 37768995 78521183 60384739 40981494 5395222 5395238 61451462 45410835 54697091 21209385 14833701 50487070 55598194 39531614 66814306 20666009 60938610 78521184 64774445 62438198 39275050 46442149 54705862 39901630 53590699 50798003 67710763 8121949 8122103 78521185 49481211 58504583 61209000 12693285 78521186 19372808 54094855 18300151 55446240 14819621 64190691 33077644 48167536 44738890 78521187 27243773 56889036 51079650 65830055 53980563 71442405},
	Journal = {American Naturalist},
	Month = dec,
	Number = {6},
	Pages = {1478-1512},
	Publisher = {UNIV CHICAGO PRESS},
	Times-Cited = {138},
	Title = {SPATIAL SCALING OF SPECIES COMPOSITION - BODY MASSES OF NORTH-AMERICAN LAND MAMMALS},
	Volume = {138},
	Year = {1991},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1991HB55000009}}

@article{Bromham.Degnan.1999.a,
	Abstract = {Hemichordates were traditionally allied to the chordates, but recent molecular analyses have suggested that hemichordates are a sister group to the echinoderms, a relationship that has important consequences for the interpretation of the evolution of deuterostome body plans. However, the molecular phylogenetic analyses to date have not provided robust support for the hemichordate + echinoderm clade. We use a maximum likelihood framework, including the parametric bootstrap, to reanalyze DNA data from complete mitochondrial genomes and nuclear 18S rRNA. This approach provides the first statistically significant support for the hemichordate + echinoderm clade from molecular data. This grouping implies that the ancestral deuterostome had features that included an adult with a pharynx and a dorsal nerve cord and an indirectly developing dipleurula-like larva.},
	Address = {350 MAIN ST, MALDEN, MA 02148 USA},
	Author = {Bromham, LD and Degnan, BM},
	Date-Added = {2009-11-10 09:55:01 +0000},
	Date-Modified = {2009-11-10 09:55:01 +0000},
	Isi = {000086321600005},
	Isi-Recid = {114446999},
	Isi-Ref-Recids = {107128626 114447000 114447001 107352113 107573363 104620858 82262639 43930323 41575 114447002 82166166 85302247 90553169 57684838 114447003 76473745 92660234 90983278 99457389 99996694 62448054 104806401 110585928 108642063 110697043 101267119 114447004 100719897 114447005 60356538 93007753 113293479 107037147 110071637 104864613 87648946 109450739 83550134 106761990 85801419 88167305 86599948 107189372},
	Journal = {Evolution \& Development},
	Month = {Nov-Dec},
	Number = {3},
	Pages = {166-171},
	Publisher = {BLACKWELL SCIENCE INC},
	Times-Cited = {55},
	Title = {Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate plus echinoderm clade},
	Volume = {1},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000086321600005}}

@article{Bourke.1999.a,
	Abstract = {The broad limits of mature colony size in social insect species are likely to be set by ecological factors. However, any change in colony size has a number of important social consequences. The most fundamental is a change in the expected reproductive potential of workers. If colony size rises, workers experience a fall in their chances of becoming replacement reproductives and, it is shown, increasing selection for mutual inhibition of one another's reproduction (worker policing). As workers' reproductive potential falls, the degree of dimorphism between reproductive and worker castes (morphological skew) can rise. This helps explain why small societies have low morphological skew and tend to be simple in organization, whereas large societies have high morphological skew and tend to be complex. The social consequences of change in colony size may also alter colony size itself in a process of positive feedback. For these reasons, small societies should be characterized by intense, direct conflict over reproduction and caste determination. By contrast, conflict in large societies should predominantly be over brood composition, and members of these societies should be relatively compliant to manipulation of their caste. Colony size therefore deserves fuller recognition as a key determinant, along with kin structure, of social complexity, the reproductive potential of helpers, the degree of caste differentiation, and the nature of within-group conflict.},
	Address = {P O BOX 88, OSNEY MEAD, OXFORD OX2 0NE, OXON, ENGLAND},
	Author = {Bourke, AFG},
	Date-Added = {2009-11-10 09:54:42 +0000},
	Date-Modified = {2009-11-10 09:54:42 +0000},
	Isi = {000079104400004},
	Isi-Recid = {109201163},
	Isi-Ref-Recids = {26321811 77438944 78302500 100388784 23368697 67415910 103174408 92434209 67034428 29560204 105687484 66228666 104304371 101575272 63955647 48229276 91703809 95324615 81612605 92613887 78458969 107293732 103050737 82473608 93114956 65364282 77846004 72115858 60333250 79138649 9786697 67925912 72142551 109201164 86191766 77090727 95474483 27948249 39021373 77527817 91058727 92133293 86389616 89033936 82987176 102563704 80083595 87426412 78858008 95729171 24640222 99676096 79819997 97017520 15121741 103614179 72961762 65371795 65748473 95414843 36578853 56183400 75547201 77442576 76868673 96699896 94602045 88943886 101098846 9584714 80928094 80928087 66948258 86050901 100991042 77334415 75523701 77614339 82582766 102115683 101444726 91703808 109201165 83613225 80797861 94413732 109201166 29376559 75896629 82475740 73656490 78438588 102919806 80407075 74596805 34097299 67034435 27383547 78267280 59813347 5474866 23593182 26277858 76811947},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {complexity; reproductive conflict; social evolution; social insect; worker policing},
	Month = mar,
	Number = {2},
	Pages = {245-257},
	Publisher = {BLACKWELL SCIENCE LTD},
	Times-Cited = {120},
	Title = {Colony size, social complexity and reproductive conflict in social insects},
	Volume = {12},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000079104400004}}

@article{Borchiellini.Manuel.ea.2001.a,
	Abstract = {In order to allow critical evaluation of the interrelationships between the three sponge classes, and to resolve the question of mono- or paraphyly of sponges (Porifera), we used the polymerase chain reaction (PCR) to amplify almost the entire nucleic acid sequence of the 18S rDNA from several hexactinellid, demosponge and calcareous sponge species. The amplification products were cloned, sequenced and then aligned with previously reported sequences from other sponges and nonsponge metazoans and variously distant outgroups, and trees were constructed using both neighbour-joining and maximum parsimony methods. Our results suggest that sponges are paraphyletic, the Calcarea being more related to monophyletic Eumetazoa than to the siliceous sponges (Demospongiae, Hexactinellida). These results have important implications for our understanding of metazoan origins, because they suggest that the common ancestor of Metazoa was a sponge. They also have consequences for basal metazoan classification, implying that the phylum Porifera should be abandoned. Our results support the upgrading of the calcareous sponge class to the phylum level.},
	Address = {P O BOX 88, OSNEY MEAD, OXFORD OX2 0NE, OXON, ENGLAND},
	Author = {Borchiellini, C and Manuel, M and Alivon, E and Boury-Esnault, N and Vacelet, J and Le Parco, Y},
	Date-Added = {2009-11-10 09:53:47 +0000},
	Date-Modified = {2009-11-10 09:53:47 +0000},
	Isi = {000167700700017},
	Isi-Recid = {120756353},
	Isi-Ref-Recids = {115956482 62587169 48496576 112233866 68013409 114623107 105377524 25624419 88126924 111479698 3066386 120756354 22773833 74019025 98015777 75229552 108310867 106822055 113216974 90196006 106122469 1777095 99069435 97335963 2250160 90553169 108980663 98069423 73671495 100468577 664090 1437200 68475057 4970653 109299397 41807846 54262156 95498817 85293030 105466532 95230548 5534824 82363772 71308899 32279551 103757391 49576251 101442081 81735284 92297373 120756356 91943339 19972818 97892230 8244375 49576270 45622205 101540354 120756357 88322889 63203468 33510396 5534832 111479712 45609221 85616386 120756358 71885196 89971854 116904964 93293761 83009475 109692372 93361778 105587154 120756359},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {metazoan origin; new phyla; phylogeny; Porifera; 18S rDNA},
	Month = jan,
	Number = {1},
	Pages = {171-179},
	Publisher = {BLACKWELL SCIENCE LTD},
	Times-Cited = {98},
	Title = {Sponge paraphyly and the origin of Metazoa},
	Volume = {14},
	Year = {2001},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000167700700017}}

@article{Bonnaud.BoucherRodoni.ea.1997.a,
	Abstract = {Sequences of partial mitochondrial cytochrome oxidase III gene (533 bp) were obtained for 17 species of cephalopods, 14 decapods, 2 octopods, and 1 vampyromorph. This study aimed to: (1) compare partial COII and COIII amino acid sequences of three species of cephalopods with other invertebrates in terms of base composition and phylogenetic relationships, Cephalopod sequences are closer to Katharina tunicata sequences than to Mytilus edulis (marine bivalve) and Albinuria turrita (terrestrial gastropod); (2) investigate the phylogenetic relationships among cephalopods. Nucleotides as well as amino acid sequence variations of a COIII fragment were examined with parsimony and distance methods. Our data confirm the monophyly of the Decapoda and of each family. A high hierarchical rank for sepiolids, already suggested by other authors, appears justified. The order Sepioidea comprising five families should be abandoned, with Spirula being excluded. The surprising position of Idiosepius as the sister group of some oegopsids and not of sepioids or sepiolids is confirmed. Vampyroteu this is the sister group of octopods. However, the data do not allow resolution of the phylogenetic relationships between the orders of Decapoda; consequently we suspect a rapid radiation. (C) 1997 Academic Press.},
	Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495},
	Author = {Bonnaud, L and BoucherRodoni, R and Monnerot, M},
	Date-Added = {2009-11-10 09:53:18 +0000},
	Date-Modified = {2009-11-10 09:53:18 +0000},
	Isi = {A1997WN53000004},
	Isi-Recid = {99705455},
	Isi-Ref-Recids = {84765856 87838135 83481404 70864151 99705456 87806193 88720633 94553861 99705457 86662817 69466574 70469987 57496329 88582671 72183949 48456973 79781661 50523439 90457620 79785065 66405788 77195225 69830275 91586849 86638086 82193146 84822639 11518706 78810479 86104604 90277911 85468831 13689845 99705458 89396969 83742846 60493326 99705459 92271142 89412910 88695976 81847509 35113595 91858297 99705460},
	Journal = {Molecular Phylogenetics and Evolution},
	Month = feb,
	Number = {1},
	Pages = {44-54},
	Publisher = {ACADEMIC PRESS INC JNL-COMP SUBSCRIPTIONS},
	Times-Cited = {46},
	Title = {Phylogeny of cephalopods inferred from mitochondrial DNA sequences},
	Volume = {7},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WN53000004}}

@article{Blaxter.De-Ley.ea.1998.a,
	Abstract = {Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale(1,2); interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers(3); and Caenorhabditis elegans is a favourite experimental model system(4). A lack of dearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.},
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON, ENGLAND N1 9XW},
	Author = {Blaxter, ML and De Ley, P and Garey, JR and Liu, LX and Scheldeman, P and Vierstraete, A and Vanfleteren, JR and Mackey, LY and Dorris, M and Frisse, LM and Vida, JT and Thomas, WK},
	Date-Added = {2009-11-10 09:52:43 +0000},
	Date-Modified = {2009-11-10 09:52:43 +0000},
	Isi = {000072373000051},
	Isi-Recid = {104149225},
	Isi-Ref-Recids = {77149831 82624571 94033895 104149286 58480106 86345924 90471069 102108625 100701890 95661814 100558925 98123017 90987209 62176987 92146987 104149287 92242680 71804425 48862332 90791824 93361778 96255350 83638287 104149288 86189008 96748800 89133145 101585232 36391001},
	Journal = {Nature},
	Month = mar,
	Number = {6671},
	Pages = {71-75},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Times-Cited = {572},
	Title = {A molecular evolutionary framework for the phylum Nematoda},
	Volume = {392},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000072373000051}}

@article{Blackburn.Gaston.1994.a,
	Abstract = {Frequency distributions of body size have been reported in the literature for a range of animal higher taxa. However, the reported shapes of these distributions may be biased by species missing from them, specifically by currently undiscovered species. There is a body of evidence that the small-bodied species in a taxon are described later, on average, than the large-bodied. From this, we predict that the means of animal body size frequency distributions should decrease through time, and the skewnesses of the distributions increase. These predictions are shown to be true for body size distributions for five different higher taxa of animals. Thus, any reported body size distribution for a taxon is likely to be systematically biased, even if it includes all the species which are known, if many species are likely to remain undiscovered.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Blackburn, Tim M. and Gaston, Kevin J.},
	Date-Added = {2009-11-10 09:51:25 +0000},
	Date-Modified = {2009-11-10 09:51:59 +0000},
	Isi = {A1994PJ86800012},
	Isi-Recid = {88792303},
	Isi-Ref-Recids = {88792304 88792305 87312641 78521178 85211999 70374758 86519687 62596730 72497346 77846057 88792306 88792307 1745010 5395222 39531614 88792308 50798003 49732765 75537462 45283070 22842046},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Month = sep,
	Number = {1350},
	Pages = {293-297},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {17},
	Title = {ANIMAL BODY-SIZE DISTRIBUTIONS CHANGE AS MORE SPECIES ARE DESCRIBED},
	Volume = {257},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994PJ86800012}}

@article{Berney.Pawlowski.ea.2000.a,
	Abstract = {The phylogenetic position of the Acoela is a key problem in the understanding of metazoan evolution. Recent studies based on 18S ribosomal DNA (rDNA) sequences have placed the Acoela in an extremely basal position as the sister group to all other extant triploblastic animals, suggesting that the phylum Platyhelminthes is polyphyletic. In order to test the results obtained with 18S rDNA, we sequenced elongation factor 1-alpha (EF1a) for the acoel Convoluta roscoffensis and five species of Turbellaria (two polyclads, Leptoplana tremellaris, and Prostheceraeus vittatus, and three triclads, Crenobia alpina, Schmidtea polychroa and Girardia tigrina). Phylogenetic analyses of EF1a sequences show that the acoel sequences branch within the Platyhelminthes, in opposition to the 18S rDNA data. Moreover, comparison of the central variable region of EF1a shows similar sequence signatures between C. roscoffensis and the three triclad species. Although EF1a sequences fail to prove the monophyly of the phylum Platyhelminthes, they do not confirm the early divergence of the Acoela.},
	Address = {PO BOX 1897, LAWRENCE, KS 66044-8897 USA},
	Author = {Berney, C and Pawlowski, J and Zaninetti, L},
	Date-Added = {2009-11-10 09:50:23 +0000},
	Date-Modified = {2009-11-10 09:50:23 +0000},
	Isi = {000087874900005},
	Isi-Recid = {115600851},
	Isi-Ref-Recids = {107128626 101100745 100558925 115600852 100558926 96748814 85660192 106961984 100467451 91858298 38292950 56038476 67748941 99069435 106172598 90553169 86075973 80934069 93311628 69760203 104806353 83784748 84059569 87648932 104806401 108508441 101442081 99953141 88533255 89055569 100467455 101891901 115600854 109236332 63203468 58463637 58463656 101085100 97209324 106460718 110770977 93361778},
	Journal = {Molecular Biology and Evolution},
	Keywords = {elongation factor 1-alpha; molecular phylogeny; Convoluta roscoffensis; Acoela; Platyhelminthes},
	Month = jul,
	Number = {7},
	Pages = {1032-1039},
	Publisher = {SOC MOLECULAR BIOLOGY EVOLUTION},
	Times-Cited = {32},
	Title = {Elongation factor 1-alpha sequences do not support an early divergence of the acoela},
	Volume = {17},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000087874900005}}

@article{Benton.2001.b,
	Abstract = {Life on land today is as much as 25 times as diverse as life in the sea. Paradoxically, this extraordinarily high level of continental biodiversity has been achieved in a shorter time and it occupies a much smaller area of the Earth's surface than does marine biodiversity. Raw palaeontological data suggest very different models for the diversification of life on land and in the sea. The well-studied marine fossil record appears to show evidence for an equilibrium model of diversification, with phases of rapid radiation, followed by plateaux that may indicate times of equilibrium diversity. The continental fossil record shows exponential diversification from the Silurian to the present. These differences appear to be real: the continental fossil record is unlikely to be so poor that all evidence for a high initial equilibrial diversity has been lost. In addition, it is not clear that the apparently equilibrial marine model is correct, since it is founded on studies at familial level. At species level, a logistic family-level curve probably breaks down to an exponential. The rocketing diversification rates of flowering plants, insects, and other land life are evidently hugely different from the more sluggish rates of diversification of life in the sea, perhaps as a result of greater endemism and habitat complexity on land. Copyright (C) 2001 John Wiley \& Sons, Ltd.},
	Address = {BAFFINS LANE CHICHESTER, W SUSSEX PO19 1UD, ENGLAND},
	Author = {Benton, MJ},
	Date-Added = {2009-11-10 09:49:26 +0000},
	Date-Modified = {2009-11-10 09:49:26 +0000},
	Isi = {000171395100003},
	Isi-Recid = {121779862},
	Isi-Ref-Recids = {46132327 90856089 96136965 63500039 102919842 100093617 91966326 86254934 112176410 113633113 102919843 56537391 84764046 85902891 121779864 42089680 95696930 34462741 57426533 65431104 121779865 114094387 54334176 115594583 79022032 78771350 88692179 67540892 121779866 13641258 109132394 64091704 96934517 89674046 68369713 114094445 61159652 84031319 36867331 14833701 45180841 72652600 86215524 79689095 110970845 67818629 64659671 82402085 61062554 21656688 105279918 52835847 92086885 32540426 43867337 45969199 89132581 53634409 38225604 35170674 101522633 114395254 82613655 80829871 87686544 61159310 77442503 50523613 108544590 102013130 69181899 88691862 19848696 102919847 114113938 61159312 54185376 72208896 90306616 37888177 22881351 101332622 49016794 112176408},
	Journal = {Geological Journal},
	Keywords = {biodiversity; diversification; diversity; equilibrium; fossil record; Phanerozoic; terrestrial; marine},
	Month = {Jul-Dec},
	Number = {3-4},
	Pages = {211-230},
	Publisher = {JOHN WILEY \& SONS LTD},
	Times-Cited = {20},
	Title = {Biodiversity on land and in the sea},
	Type = {Proceedings Paper},
	Volume = {36},
	Year = {2001},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000171395100003}}

@article{Benton.2000.a,
	Abstract = {Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings. Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have Rained strong support among some vocal theoreticians and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In practice, phylogenetic nomenclature will be disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.},
	Address = {110 MIDLAND AVE, PORT CHESTER, NY 10573-4930 USA},
	Author = {Benton, MJ},
	Date-Added = {2009-11-10 09:48:00 +0000},
	Date-Modified = {2009-11-10 09:48:00 +0000},
	Isi = {000167453300004},
	Isi-Recid = {118992216},
	Isi-Ref-Recids = {111611612 113623042 101867970 111153212 88319325 96191804 103620107 114029113 101187173 105401206 402220 67641517 102830025 72005445 74452094 81631282 85786639 103898081 39692546 118992217 45381598 76958285 118992218 4442655 13641258 99996690 1813754 105774778 49010892 108228232 97667086 24005006 3020972 81959109 39077 47398792 114401492 112972205 34579443 118992220 83009255 118992221 102730553 81959110 118992222 104155576 112972202 110659444 110761668 6550446 41618698 86231350 99457393 118992224 110253907},
	Journal = {Biological Reviews},
	Keywords = {systematics; classification; phylogeny; clade; cladistics; Linnaeus; PhyloCode; taxonomy; nomenclature},
	Month = nov,
	Number = {4},
	Pages = {633-648},
	Publisher = {CAMBRIDGE UNIV PRESS},
	Times-Cited = {65},
	Title = {Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?},
	Volume = {75},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000167453300004}}

@article{Bell.Mooers.1997.a,
	Abstract = {The diversity of specialized cell types ('complexity') is estimated for a wide range of multicellular organisms. Complexity increases with size, independently of phylogeny. This is interpreted in economic terms as the consequence of a greater degree of cooperative division of labour within larger entities. The late of increase of complexity with size is less in the case of a cooperative division of labour (cell types within bodies) than in the analogous case of a competitive division of labour (species within communities). This is atttributed to the inutility of single specialized cells whose goods must be shared among all the many cells of a large organism. Major groups of organisms differ in complexity at given size: animals are more complex than plants, and phaeophytes are simpler than either. (C) 1997 The Linnean Society of London.},
	Address = {24-28 OVAL RD, LONDON, ENGLAND NW1 7DX},
	Author = {Bell, G and Mooers, AO},
	Date-Added = {2009-11-10 09:47:25 +0000},
	Date-Modified = {2009-11-10 09:47:25 +0000},
	Isi = {A1997WY32400002},
	Isi-Recid = {100388784},
	Isi-Ref-Recids = {15637896 20285499 38943870 100388785 13968546 66847348 1437171 55949340 100388786 83403771 38533377 67415910 12260160 1128269 13198603 100388787 12631039 1893549 100388788 1826441 52440573 2458905 100388789 100388790 1538477 30323154 14166204 100388791 11582723 100388792 99975 16673461 20054898 54497548 32534226 21374946 35211655 21730775 100388793 100388794 80759959 83515422 786037 34507313 30547370 100388795 21971531 70274670 100388796 3331551 75043716 76254733 1964204 100388797 50956304 54252096 1437200 3356132 52168557 44379285 39698905 69434829 85354141 11714217 32004216 54547593 22473560 85466172 62555175 46823998 32261961 36103015 57820399 11966067 4323236 100388798 100388799 15686065 100388800 56977807 2649589 9022320 76218624 28454599 100388801 20749702 11572807 95729171 15633966 50303772 69965006 57740685 38219684 17055118 446331 85105165 80134800 28432773 100388802 80301111 81298664 8121949 8122103 60469465 92213623 85938648 100388803 54334225 25306245 27232780 92086885 13585967 28220129 100388804 46970007 38943837 41411297 689418 100388805 6802594 17196900 34543724 100388806 100388807 4941847 100388808 433301 42045370 890657 33444951 6189075 33560480 15134209 50095715 70956577 71836569 100388809 16906502 30225480 88519244},
	Journal = {Biological Journal of the Linnean Society},
	Keywords = {development; differentiation; histology; complexity; evolution; economic biology; division of labour; allometry},
	Month = mar,
	Number = {3},
	Pages = {345-363},
	Publisher = {ACADEMIC PRESS LTD},
	Times-Cited = {45},
	Title = {Size and complexity among multicellular organisms},
	Volume = {60},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WY32400002}}

@article{Balavoine.Adoutte.1998.a,
	Address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA},
	Author = {Balavoine, G and Adoutte, A},
	Date-Added = {2009-11-10 09:45:35 +0000},
	Date-Modified = {2009-11-10 09:45:35 +0000},
	Isi = {000073159600034},
	Isi-Recid = {104825784},
	Isi-Ref-Recids = {100558925 69813324 101849968 62218105 104825785 90553169 91858287 93361778 100558926 98430800 90277911 78804507 83997484 93293583 97846734 103692980 100482929 87838004},
	Journal = {Science},
	Month = apr,
	Number = {5362},
	Pages = {397-398},
	Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
	Times-Cited = {48},
	Title = {One or three Cambrian radiations?},
	Volume = {280},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000073159600034}}

@article{Ayala.Rzhetsky.ea.1998.a,
	Abstract = {The time of origin of the animal phyla is controversial, Abundant fossils from the major animal phyla are found in the Cambrian, starting 544 million years ago. Many paleontologists hold that these phyla originated in the late Neoproterozoic, during the 160 million years preceding the Cambrian fossil explosion. We have analyzed 18 protein-coding gene loci and estimated that protostomes (arthropods, annelids, and mollusks) diverged from deuterostomes (echinoderms and chordates) about 670 million years ago, and chordates from echinoderms about 600 million years ago. Both estimates are consistent with paleontological estimates. A published analysis of seven gene loci that concludes that the corresponding divergence times are 1,200 and 1,000 million years ago is shown to be flawed because it extrapolates from slow-evolving vertebrate rates to faster-evolving invertebrate rates, as well as in other ways.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Ayala, FJ and Rzhetsky, A and Ayala, FJ},
	Date-Added = {2009-11-10 09:44:44 +0000},
	Date-Modified = {2009-11-10 09:44:44 +0000},
	Isi = {000071606000032},
	Isi-Recid = {103692980},
	Isi-Ref-Recids = {32400060 23420076 68713173 75986072 82113569 71664652 81163146 93293748 69763464 82113557 52539850 21525451 90277911 47513589 58483959 69813342 97846734 101441920 97799209 60031286 80216430 89412910 54432866 36112364 52276181 103692981 85384143 74892596 92572039 63203468 11852521 103692982 95817177 81959074 101620619 34985305 103692983 98641052 101441933 42937627},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = jan,
	Number = {2},
	Pages = {606-611},
	Publisher = {NATL ACAD SCIENCES},
	Times-Cited = {212},
	Title = {Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates},
	Volume = {95},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000071606000032}}

@article{Ayala.1999.a,
	Abstract = {The hypothesis of the molecular clock proposes that molecular evolution occurs at rates that persist through time and across lineages, for a given gene. The neutral theory of molecular evolution predicts that the clock will be a Poisson process, with equal mean and variance. Experimental data have shown that the variance is typically larger than the mean. Hypotheses have been advanced to account for the hypervariance of molecular evolution. Four recent papers show that none of the predictive hypotheses that have been proposed can be generally maintained. The conclusion is that molecular evolution is dependent on the fickle process of natural selection. But it is a time-dependent process, so that accumulation of empirical data often yields an approximate clock, as a consequence of the expected convergence of large numbers. (C) 1999 John Wiley \& Sons, Inc.},
	Address = {BIDDER BUILDING CAMBRIDGE COMMERCIAL PARK COWLEY RD, CAMBRIDGE, CAMBS, ENGLAND CB4 4DL},
	Author = {Ayala, FJ},
	Date-Added = {2009-11-10 09:43:49 +0000},
	Date-Modified = {2009-11-10 09:43:49 +0000},
	Isi = {000078407900009},
	Isi-Recid = {108706126},
	Isi-Ref-Recids = {101441920 60031286 97799209 13119336 87838000 104885024 80216430 66001077 32193123 86891675 108706127 14888862 50517071 25250638 101620619 105466536 61431238 22051570 85394438 105554801 11852521},
	Journal = {Bioessays},
	Month = jan,
	Number = {1},
	Pages = {71-75},
	Publisher = {COMPANY OF BIOLOGISTS LTD},
	Times-Cited = {61},
	Title = {Molecular clock mirages},
	Volume = {21},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000078407900009}}

@article{Avise.Wollenberg.1997.a,
	Abstract = {A recent criticism that al-re biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage, Two analytical approaches are employed to rapture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive lies are related aspects of phylogeny and jointly illuminate biotic discontinuity.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418},
	Author = {Avise, JC and Wollenberg, K},
	Date-Added = {2009-11-10 09:42:31 +0000},
	Date-Modified = {2009-11-10 09:42:31 +0000},
	Isi = {A1997XM42800010},
	Isi-Recid = {101441918},
	Isi-Ref-Recids = {78864416 64135285 91629493 95484151 70128752 52646105 66340994 87198102 101441958 75811222 94940567 93855052 48307227 57406171 98458343 28109986 65103879 52265475 71437920 112715 67641517 72005445 118188 94041655 58066701 93870751 39692546 71851181 71664678 93855051 101441959 77869348 69309958 13641258 97984312 99457395 48322904 93773006 77365478 67350484 70956609 52079755 68770962 93855053 91802658 93690517 86092052 95504916 1980729 8143328 65103876 67641522 90983281 93216599 61431238 62224536 40943499 73533264 84822614 71032549 87135892 67093400 71851198 93216552 79343115 38630820 34432 87135865 77365476 24286337 50218399 55777166 69788601 71999591 77365489 82262577 72007749 53925082 72005448 2250122 74899812 94977589},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {allelic genealogies; gene trees; lineages; mitochondrial DNA; phylogeography},
	Month = jul,
	Number = {15},
	Pages = {7748-7755},
	Publisher = {NATL ACAD SCIENCES},
	Times-Cited = {138},
	Title = {Phylogenetics and the origin of species},
	Type = {Proceedings Paper},
	Volume = {94},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997XM42800010}}

@article{Avise.Johns.1999.a,
	Abstract = {With respect to conveying useful comparative information, current biological classifications are seriously flawed because they fail to (i) standardize criteria for taxonomic ranking and (ii) equilibrate assignments of taxonomic rank across disparate kinds of organisms. In principle, these problems could be rectified by adopting a universal taxonomic yardstick based on absolute dates of the nodes in evolutionary trees. BS using procedures of temporal banding described herein, a simple philosophy of biological classification is proposed that would retain a manageable number of categorical ranks yet apply them in standardized fashion to time-dated phylogenies. The phylogenetic know ledge required for a time-standardized nomenclature arguably mag. emerge in the foreseeable future from,ast increases in multilocus DNA sequence information (coupled with continued attention to phylogeny estimation from traditional systematic data). By someday encapsulating time-dated phylogenies in a familiar Set modified hierarchical ranking scheme, a temporal-banding approach would improve the comparative information content of biological classifications.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Avise, JC and Johns, GC},
	Date-Added = {2009-11-10 09:42:08 +0000},
	Date-Modified = {2009-11-10 09:42:08 +0000},
	Isi = {000081056000045},
	Isi-Recid = {110653595},
	Isi-Ref-Recids = {86326780 95484151 87198102 101441918 109525895 105860347 101187173 33968837 102495425 85786639 94305638 95817179 79838892 108956328 107192159 105010942 106172656 108381586 105900 13641258 97351096 105390374 107691195 26818756 104900702 108228232 101620619 9321919 106586174 76174543 73783125 110653596 64158877 109995661 34579443 96451476 75537460 6550446 74302138 109822096 79161658 25556906 25365139 11852521},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {systematics; taxonomy; molecular clocks; comparative biology},
	Month = jun,
	Number = {13},
	Pages = {7358-7363},
	Publisher = {NATL ACAD SCIENCES},
	Times-Cited = {73},
	Title = {Proposal for a standardized temporal scheme of biological classification for extant species},
	Volume = {96},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000081056000045}}

@article{Apakupakul.Siddall.ea.1999.a,
	Abstract = {The evolutionary patterns of divergence of seven euhirudinean families were investigated by cladistic analysis of 33 euhirudinean species. Oligochaetes, Acanthobdella peledina, and branchiobdellidans were included as outgroup taxa. Cladistic analysis employed 1.8 kb of nuclear 18S ribosomal DNA and 651 bp of mitochondrial cytochrome c oxidase subunit I in addition to morphological data. The use of two molecular data sets, one nuclear gene and one mitochondrial gene, as well as morphological data combined historical information evolving under a variety of different constraints and therefore was less susceptible to the biases that could confound the use of only one type of data. Results suggest that the nuclear 18S rDNA gene yields a meaningful historical signal for determining higher level relationships. The more rapidly evolving CO-I gene was informative for recent or local areas of the evolutionary hypothesis, such as within-family relationships. Analyses combining all data from the three character sets yielded one most-parsimonious tree. Most of the higher taxa in recent leech systematics were well corroborated in the resulting topology. However, these results suggested paraphyly of the order Rhynchobdellida, which contradicts the presence of a proboscis as a synapomorphy. The medicinal leech family Hirudinidae was polyphyletic because Haemadipsidae and Haemopidae each have a hirudinid ancestor. In addition, all but one of the genera within the family Erpobdellidae must be either abandoned or renamed. Unusual findings included compelling evidence of historical plasticity in blood-feeding behavior, having been lost at least four times in the course of euhirudinean evolution. Biogeographic patterns supported a New World origin for Arhynchobdellida. (C) 1999 Academic Press.},
	Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	Author = {Apakupakul, K and Siddall, ME and Burreson, EM},
	Date-Added = {2009-11-10 09:39:49 +0000},
	Date-Modified = {2009-11-10 09:39:49 +0000},
	Isi = {000081885600009},
	Isi-Recid = {111325973},
	Isi-Ref-Recids = {84795873 10802511 111325974 66253883 70227041 36588563 111325975 111325976 85384103 39692546 100792391 92283268 94553862 71371073 80934069 74452126 70227034 30943804 60421759 111325977 24670189 4919403 10802592 9022320 40725197 67832263 84076432 111325978 80953391 94050722 84076428 92012264 16481597 19885545 96499754 111325979 75470325 93045259 98617079 104806478 106460718 75215107 111325980 111325981 57713297 7076961 88902632 64612002 84646419},
	Journal = {Molecular Phylogenetics and Evolution},
	Month = aug,
	Number = {3},
	Pages = {350-359},
	Publisher = {ACADEMIC PRESS INC},
	Times-Cited = {48},
	Title = {Higher level relationships of leeches (Annelida : Clitellata : Euhirudinea) based on morphology and gene sequences},
	Volume = {12},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000081885600009}}

@article{Aleshin.Milyutina.ea.1998.a,
	Abstract = {Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa.},
	Address = {175 FIFTH AVE, NEW YORK, NY 10010 USA},
	Author = {Aleshin, VV and Milyutina, IA and Kedrova, OS and Vladychenskaya, NS and Petrov, NB},
	Date-Added = {2009-11-10 09:39:08 +0000},
	Date-Modified = {2009-11-10 09:39:08 +0000},
	Isi = {000076739900011},
	Isi-Recid = {107510474},
	Isi-Ref-Recids = {100558925 105731939 15222962 84958831 102663488 43255992 68944967 56562694 43930323 84933676 64799777 94826354 90553169 57684838 82002924 28684246 71151850 41807846 85293030 93361780 90477791 96240931 107510476 39964069 67832263 95324775 85149692 107510477 86466415 78804499 86320628 80703233 88296200 74733201 90920129 90471065 71971046 97209324 75215107 78763808 94440147 95230555 72113921 89133145 90060040 93445892 86257565 85801419 96191811 83009475 91858287 93361778 73262131},
	Journal = {Journal of Molecular Evolution},
	Keywords = {nematoda; kinorhyncha; priapulida; molecular phylogeny; 18S rRNA gene sequences},
	Month = nov,
	Number = {5},
	Pages = {597-605},
	Publisher = {SPRINGER VERLAG},
	Times-Cited = {21},
	Title = {Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA},
	Volume = {47},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000076739900011}}

@article{Abouheif.Zardoya.ea.1998.a,
	Abstract = {We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, mag; be associated with long branches and phylogenetic position, Importantly, excluding sites with different de,degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale, Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.},
	Address = {175 FIFTH AVE, NEW YORK, NY 10010 USA},
	Author = {Abouheif, E and Zardoya, R and Meyer, A},
	Date-Added = {2009-11-10 09:38:24 +0000},
	Date-Modified = {2009-11-10 09:38:24 +0000},
	Isi = {000076216700004},
	Isi-Recid = {107128626},
	Isi-Ref-Recids = {100558925 84584161 74019025 64158888 94305638 75561117 44383653 56562694 72872254 64799777 100482929 61245268 100660987 88813867 57557770 80934069 87135898 103757391 88736162 103596058 78763845 82113557 90591936 101187183 93859168 101101504 82192017 95230534 99170250 89455961 107128627 101380539 74316122 71047446 90496259 100771117 83638287 86599936 87648946 94567618 84193413 103471530 83550134 86257565 64612002 97846734 103757390 91496539 95661809 97090834 95993163},
	Journal = {Journal of Molecular Evolution},
	Keywords = {18S rRNA; molecular phylogeny; metazoan phylogeny; Cambrian explosion; among-site rate variation},
	Month = oct,
	Number = {4},
	Pages = {394-405},
	Publisher = {SPRINGER VERLAG},
	Times-Cited = {102},
	Title = {Limitations of metazoan 18S rRNA sequence data: Implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion},
	Volume = {47},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000076216700004}}

@article{Wolters.Bengtsson.ea.2006.a,
	Abstract = {Spatially explicit forecasting of changes in species richness is key to designing informative scenarios on the development of diversity on our planet. It might be possible to predict changes in the richness of inadequately investigated groups from that of groups for which enough information is available. Here we evaluate the reliability of this approach by reviewing 237 richness correlations extracted from the recent literature. Of the 43 taxa covered, beetles, vascular plants, butterflies, birds, ants, and mammals (in that order) were the most common ones examined. Forests and grasslands strongly dominated the ecosystem types studied. The variance explanation (R⁲) could be calculated for 152 cases, but only 53 of these were significant. An average correlation effect size of 0.374 (95% CI = $\pm$0.0678) indicates positive but weak correlations between taxa within the very heterogeneous data set. None of the examined explanatory variables (spatial scale, taxonomic distance, trophic position, biome) could account for this heterogeneity. However, studies focusing on 10-km⁲ grid cells had the highest variance explanation. Moreover, within-phylum between-class comparisons had marginally significantly lower correlations than between-phylum comparisons. And finally, the explanatory power of studies conducted in the tropics was significantly higher than that of studies conducted in temperate regions. It is concluded that the potential of a correlative approach to species richness is strongly diminished by the overall low level of variance explanation. So far, no taxon has proved to be a universal or even particularly good predictor for the richness of other taxa. Some suggestions for future research are inclusion of several taxa in models aiming at regional richness predictions, improvement of knowledge on species correlations in human dominated systems, and a better understanding of mechanisms underlying richness correlations.},
	Author = {Wolters, Volkmar and Bengtsson, Janne and Zaitsev, Andrei S.},
	Copyright = {2006 Ecological Society of America},
	Date-Added = {2009-11-04 15:21:13 +0000},
	Date-Modified = {2009-11-04 15:22:15 +0000},
	Issn = {00129658},
	Journal = {Ecology},
	Jstor_Articletype = {primary_article},
	Jstor_Formatteddate = {Aug., 2006},
	Number = {8},
	Pages = {1886-1895},
	Publisher = {Ecological Society of America},
	Title = {Relationship among the Species Richness of Different Taxa},
	Url = {http://www.jstor.org/stable/20069171},
	Volume = {87},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.jstor.org/stable/20069171}}

@article{Nee.Mooers.ea.1992.a,
	Abstract = {The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418},
	Author = {Nee, Sean and Mooers, Arne {\O} and Harvey, Paul H.},
	Date-Added = {2009-11-03 13:45:58 +0000},
	Date-Modified = {2009-11-03 13:47:07 +0000},
	Isi = {A1992JL61400099},
	Isi-Recid = {80791779},
	Isi-Ref-Recids = {45344899 73638706 34771293 62206443 67019755 68770968 54497548 66311377 23212987 44618530 32408723 35222138 75043716 46169363 80791780 5395222 318386 7347097 66311374 60384717 60387890 66311380 43566124 24348788 64051049 67818634 47513589 67145187 75537462 62206449 75537460 3704525 1982903 57274 71680231 4440247 22842001 40512834 24280877 59484350 80791781 22842046 66311375 75722632 9621886 10159310 16045732 949309},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = sep,
	Number = {17},
	Pages = {8322-8326},
	Publisher = {NATL ACAD PRESS},
	Rating = {0},
	Times-Cited = {175},
	Title = {TEMPO AND MODE OF EVOLUTION REVEALED FROM MOLECULAR PHYLOGENIES},
	Volume = {89},
	Year = {1992},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1992JL61400099}}

@article{Nee.2001.a,
	Abstract = {It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question-Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data-the branch lengths in the tree-and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth-death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.},
	Address = {810 E 10TH STREET, LAWRENCE, KS 66044 USA},
	Author = {Nee, S},
	Date-Added = {2009-11-03 13:45:04 +0000},
	Date-Modified = {2009-11-03 13:45:04 +0000},
	Isi = {000168837800002},
	Isi-Recid = {119968552},
	Isi-Ref-Recids = {106499516 95446982 103315099 95244167 22364103 14334510 76319613 119968553 88296976 80118056 39174599 97351096 106822127 318514 93216587 110444512 90565226 99631610 387634 92471115 94636977 87408719 80791779 101969045 106208526 92133314 100114541 94204180 98237532 87283818 77365476 29994611 119968554 96464840 101100726 949309 91809311},
	Journal = {Evolution},
	Keywords = {adaptive radiations; macroevolution; phylogenies; speciation rates},
	Month = apr,
	Number = {4},
	Pages = {661-668},
	Publisher = {SOC STUDY EVOLUTION},
	Times-Cited = {82},
	Title = {Inferring speciation rates from phylogenies},
	Volume = {55},
	Year = {2001},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000168837800002}}

@article{Nee.Holmes.ea.1994.a,
	Abstract = {Molecular phylogenies can be used to reject null models of the way we think evolution occurred, including patterns of lineage extinction. They can also be used to provide maximum likelihood estimates of parameters associated with lineage birth and death rates. We illustrate: (i) how molecular phylogenies provide information about the extent to which particular clades are likely to be under threat from extinction; (ii) how cursory analyses of molecular phylogenies can lead to incorrect conclusions about the evolutionary processes that have been at work; and (iii) how different evolutionary processes leave distinctive marks on the structure of reconstructed phylogenies.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Nee, Sean and Holmes, Edward C. and May, Robert M and Harvey, Paul H.},
	Date-Added = {2009-11-03 13:41:34 +0000},
	Date-Modified = {2009-11-03 13:43:06 +0000},
	Isi = {A1994NM57000012},
	Isi-Recid = {87271066},
	Isi-Ref-Recids = {65381575 32408723 87271067 87271068 87271069 87271070 80118056 39174599 52079755 87271071 14833701 23565964 87271072 80791779 24348788 75537460 85835724 40512834},
	Journal = {Philosophical Transactions of the Royal Society of London Series B-Biological Sciences},
	Month = apr,
	Number = {1307},
	Pages = {77-82},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {117},
	Title = {EXTINCTION RATES CAN BE ESTIMATED FROM MOLECULAR PHYLOGENIES},
	Volume = {344},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994NM57000012}}

@article{Nee.May.ea.1994.a,
	Abstract = {Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON, ENGLAND SW1Y 5AG},
	Author = {Nee, Sean and May, Robert M and Harvey, Paul H.},
	Date-Added = {2009-11-03 10:11:15 +0000},
	Date-Modified = {2009-11-03 10:13:32 +0000},
	Isi = {A1994NQ61800006},
	Isi-Recid = {87408719},
	Isi-Ref-Recids = {87408720 24733871 87271068 87408721 87408722 80118056 77365478 87408723 559267 318386 46149621 87408724 80791779 87271066 24348788 82641908 77365476 50579041 29994611 53234333},
	Journal = {Philosophical Transactions of the Royal Society of London Series B-Biological Sciences},
	Month = may,
	Number = {1309},
	Pages = {305-311},
	Publisher = {ROYAL SOC LONDON},
	Times-Cited = {162},
	Title = {THE RECONSTRUCTED EVOLUTIONARY PROCESS},
	Volume = {344},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994NQ61800006}}

@article{Nagelkerke.1991.a,
	Abstract = {A generalization of the coefficient of determination R2 to general regression models is discussed.  A modification of an earlier definition to allow for discrete models is proposed.},
	Address = {UNIV COLLEGE LONDON GOWER ST-BIOMETRIKA OFFICE, LONDON, ENGLAND WC1E 6BT},
	Author = {Nagelkerke, N. J. D.},
	Date-Added = {2009-10-21 11:44:03 +0100},
	Date-Modified = {2009-10-21 11:46:10 +0100},
	Isi = {A1991GJ30600024},
	Isi-Recid = {77408112},
	Isi-Ref-Recids = {71947888 27614314 21705103 51165978 73381018 24752437},
	Journal = {Biometrika},
	Keywords = {DISCRETE PROBABILITY; LOG LIKELIHOOD; MULTIPLE CORRELATION COEFFICIENT; REGRESSION MODEL; RESIDUAL VARIATION},
	Month = sep,
	Number = {3},
	Pages = {691-692},
	Publisher = {BIOMETRIKA TRUST},
	Times-Cited = {771},
	Title = {A NOTE ON A GENERAL DEFINITION OF THE COEFFICIENT OF DETERMINATION},
	Type = {Note},
	Volume = {78},
	Year = {1991},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1991GJ30600024}}

@article{Mooers.Heard.1997.a,
	Abstract = {Inferences about macroevolutionary process have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has fed to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lengths. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research.

Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuous variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes.

The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.},
	Address = {5720 S WOODLAWN AVE, CHICAGO, IL 60637},
	Author = {Mooers, Arne O and Heard, Stephen B},
	Date-Added = {2009-10-16 14:39:05 +0100},
	Date-Modified = {2009-10-16 14:44:17 +0100},
	Isi = {A1997WM69600002},
	Isi-Recid = {99631610},
	Isi-Ref-Recids = {26416580 72521830 26585316 90616320 96136935 88319314 73638706 14019453 26416582 83268019 94104472 76731905 90983302 97864302 50437306 78849522 70130018 94400441 112715 68770968 80118128 86590325 99631611 71047484 29451809 54497548 67748941 56562694 84933676 318402 54216193 92285811 80216430 77445118 90165207 32408723 75914963 82749589 24046238 88296976 89651281 87271067 94339211 88296979 99631612 88296975 84765867 82131803 98866124 96136971 95243183 79252600 84098058 13641258 80118056 94357582 86389627 92471118 87519821 97260519 50754597 82308359 50517071 86678876 66311374 71151844 93216587 71047475 90565226 88319323 4338208 72714421 94842170 17154446 75503712 79215576 92625540 96886940 99631613 93866274 99631614 94636977 80791779 87271066 87408719 92471115 54432866 72813012 84646465 84483495 82641921 75503707 96191800 99631615 84483497 34348043 99631616 92133314 92133321 60387890 99069389 24348788 90871598 86191804 91494714 82641931 95243181 74389582 35136250 34950872 21472530 35877533 71252142 87283818 94204180 50619856 80078181 38267277 35170674 87863586 74123390 75537460 63833440 45704107 25783078 71680231 85835724 73091861 25941548 4440247 42877176 85910132 50579041 71597048 65067712 90087049 23130070 69994755 79449821 92887774 9353417 10159310 1982272 1980895 86599948 949309 94339203 83672295 91809311 11852521},
	Journal = {Quarterly Review of Biology},
	Month = mar,
	Number = {1},
	Pages = {31-54},
	Publisher = {UNIV CHICAGO PRESS},
	Read = {Yes},
	Times-Cited = {123},
	Title = {Evolutionary process from phylogenetic tree shape},
	Volume = {72},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997WM69600002}}

@article{MARZLUFF.DIAL.1991.a,
	Abstract = {One of the most pervasive, nonrandom evolutionary patterns is extreme domination of a taxon by one subtaxon or only a few subtaxa.  Domination refers to taxonomic diversity and the fraction of the taxon that is classified in the most diverse subtaxon.  We attempt to explain how subtaxa come to dominate their phyletic counterparts by examining correlations between taxonomic diversity and life history traits such as age of first reproduction, longevity, fecundity and partitioning of reproduction, and resource availability in a variety of vertebrate, invertebrate, and plant groups.  Regardless of taxonomic group or rank, the number of taxa within an assemblage, or the school of taxonomy employed, diverse taxa were characterized by short generation time (early age of first reproduction and short life-span) and the ability to contact many resources (high mobility and high resource availability).  We suggest that the intrinsic character of short generation time increases diversity because it promotes speciation and reduces extinction.  Extrinsic factors such as resource availability and environmental complexity and variability may have a secondary influence on diversity by constraining or enhancing speciation for taxa with short generation times.},
	Address = {2010 MASSACHUSETTS AVE, NW, STE 400, WASHINGTON, DC 20036},
	Author = {Marzluff, John M. and Dial, Kenneth P.},
	Date-Added = {2009-10-16 14:36:03 +0100},
	Date-Modified = {2009-10-16 14:37:52 +0100},
	Isi = {A1991FE24800003},
	Isi-Recid = {75468688},
	Isi-Ref-Recids = {34771501 38267278 35810501 26416580 21827591 10254892 75468689 46496408 53297234 28109986 32551105 42089680 1437053 57426533 56608045 57989657 48579746 67019755 68770968 47426144 57504166 26807002 63764347 46485986 17154351 60633890 24875616 64041213 32408723 34634538 28199679 46071919 33636009 53919674 61451498 25186229 75468690 20251548 17152047 21029009 11946823 21209385 14833701 75468691 8143328 31691092 50706097 48670707 39526875 33839490 37182732 50798003 60387890 24348788 43794706 1982903 57274 47655127 22842001 40512834 26721855 42877176 75468692 17224536 51738568 18756314 42089684 24280889 20149815 22842046 39568797 49483653 31335351 28273774 10159310 1982272 29020909 34718744 26721863},
	Journal = {Ecology},
	Keywords = {COLONIZATION ABILITY; DIVERSITY; EXTINCTION; FECUNDITY; GENERATION TIME; LIFE HISTORY; LONGEVITY; SPECIATION},
	Month = apr,
	Number = {2},
	Pages = {428-439},
	Publisher = {ECOLOGICAL SOC AMER},
	Times-Cited = {53},
	Title = {LIFE-HISTORY CORRELATES OF TAXONOMIC DIVERSITY},
	Volume = {72},
	Year = {1991},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1991FE24800003}}

@article{Rabosky.2009.a,
	Abstract = {Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Rabosky, Daniel L.},
	Date-Added = {2009-10-16 14:23:35 +0100},
	Date-Modified = {2009-10-16 14:23:35 +0100},
	Doi = {DOI 10.1111/j.1461-0248.2009.01333.x},
	Isi = {000267660600001},
	Isi-Recid = {181953346},
	Isi-Ref-Recids = {161829430 151524907 181953347 98982906 163305519 172659399 154099624 90616320 176083106 125203746 110749415 145895929 118012549 123155055 97090820 143568714 133377368 145864215 111751738 106788311 147885113 135322727 106191437 6533059 118292149 132777450 158698419 133803689 94357582 159515977 5395238 175141814 152388078 181953348 156357188 159355380 83651840 117770535 159220147 122062632 175838909 156643460 181953349 155194014 96020649 66690949 155120061 99631610 87408719 119968552 153760425 142667086 146195799 151685349 162232797 21319748 59274568 159424374 175560007 172938889 178768513 172295169 21656688 157632187 159851617 152891850 132488482 181953350 134049948 175574183 162030573 151789913 35170674 104155576 53634409 137308737 127844762 19848696 127725576 154881665 150198030 153086046 142230433 179376126},
	Journal = {Ecology Letters},
	Keywords = {Biodiversity; biogeography; diversification; evolutionary rates; extinction; latitudinal diversity gradient; macroevolution; speciation; species richness},
	Month = aug,
	Number = {8},
	Pages = {735-743},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {0},
	Title = {Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000267660600001}}

@article{Ford.Matsen.ea.2009.a,
	Abstract = {In this paper, we present a new way to describe the timing of branching events in phylogenetic trees. Our description is in terms of the relative timing of diversification events between sister clades; as such it is complementary to existing methods using lineages-through-time plots which consider diversification in aggregate. The method can be applied to look for evidence of diversification happening in lineage-specific "bursts", or the opposite, where diversification between 2 clades happens in an unusually regular fashion. In order to be able to distinguish interesting events from stochasticity, we discuss 2 classes of neutral models on trees with relative timing information and develop a statistical framework for testing these models. These model classes include both the coalescent with ancestral population size variation and global rate speciation-extinction models. We end the paper with 2 example applications: first, we show that the evolution of the hepatitis C virus deviates from the coalescent with arbitrary population size. Second, we analyze a large tree of ants, demonstrating that a period of elevated diversification rates does not appear to have occurred in a bursting manner.
},
	Author = {Ford, Daniel and Matsen, Frederick A. and Stadler, Tanja},
	Date-Added = {2009-10-06 13:48:44 +0100},
	Date-Modified = {2009-10-06 13:49:20 +0100},
	Doi = {10.1093/sysbio/syp018},
	Eprint = {http://sysbio.oxfordjournals.org/cgi/reprint/58/2/167.pdf},
	Journal = {Syst Biol},
	Number = {2},
	Pages = {167-183},
	Title = {{A Method for Investigating Relative Timing Information on Phylogenetic Trees}},
	Url = {http://sysbio.oxfordjournals.org/cgi/content/abstract/58/2/167},
	Volume = {58},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://sysbio.oxfordjournals.org/cgi/content/abstract/58/2/167},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/sysbio/syp018}}

@article{Kisel.Barraclough.2010.a,
	Author = {Kisel, Yael and Barraclough, Timothy G.},
	Date-Added = {2009-10-05 11:43:38 +0100},
	Date-Modified = {2010-01-28 17:47:46 +0000},
	Journal = {American Naturalist},
	Number = {3},
	Title = {Speciation Has a Spatial Scale that Depends on Levels of Gene Flow},
	Volume = {175},
	Year = {2010},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1086/650369}}

@article{Murtaugh.2009.a,
	Abstract = {I evaluated the predictive ability of statistical models obtained by applying seven methods of variable selection to 12 ecological and environmental data sets. Cross-validation, involving repeated splits of each data set into training and validation subsets, was used to obtain honest estimates of predictive ability that could be fairly compared among methods. There was surprisingly little difference in predictive ability among five methods based on multiple linear regression. Stepwise methods performed similarly to exhaustive algorithms for subset selection, and the choice of criterion for comparing models (Akaike's information criterion, Schwarz's Bayesian information criterion or F statistics) had little effect on predictive ability. For most of the data sets, two methods based on regression trees yielded models with substantially lower predictive ability. I argue that there is no 'best' method of variable selection and that any of the regression-based approaches discussed here is capable of yielding useful predictive models.},
	Author = {Murtaugh, Paul A},
	Date-Added = {2009-09-19 07:43:29 +0100},
	Date-Modified = {2009-09-19 07:43:29 +0100},
	Doi = {10.1111/j.1461-0248.2009.01361.x},
	Journal = {Ecol Lett},
	Journal-Full = {Ecology letters},
	Month = {Oct},
	Number = {10},
	Pages = {1061-8},
	Pmid = {19702634},
	Title = {Performance of several variable-selection methods applied to real ecological data},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Dunn.Hejnol.ea.2008.a,
	Abstract = {Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data(1,2). These new hypotheses include a clade of moulting animals (Ecdysozoa)(3) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa)(4). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods(5)), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.},
	Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Dunn, Casey W. and Hejnol, Andreas and Matus, David Q. and Pang, Kevin and Browne, William E. and Smith, Stephen A. and Seaver, Elaine and Rouse, Greg W. and Obst, Matthias and Edgecombe, Gregory D. and Sorensen, Martin V. and Haddock, Steven H. D. and Schmidt-Rhaesa, Andreas and Okusu, Akiko and Kristensen, Reinhardt Mobjerg and Wheeler, Ward C. and Martindale, Mark Q. and Giribet, Gonzalo},
	Date-Added = {2009-09-04 15:54:53 +0100},
	Date-Modified = {2009-09-04 15:54:53 +0100},
	Doi = {DOI 10.1038/nature06614},
	Isi = {000254792500044},
	Isi-Recid = {161691562},
	Isi-Ref-Recids = {100558925 155511976 129231029 152836339 114560091 148853221 133948726 124154114 127865271 121423485 150488875 126571583 116768847 142374138 90553169 121556276 121423486 134800285 134036170 142855232 90752113 121805988 135241720 136137848 144053594 153228633 159857648 143935710 148038527 157581760 123548072 161691563 152878775 156160253 129583692 131882855 143718529 89412910 112251470 161691564 132838742},
	Journal = {Nature},
	Month = apr,
	Number = {7188},
	Pages = {745-U5},
	Publisher = {NATURE PUBLISHING GROUP},
	Times-Cited = {124},
	Title = {Broad phylogenomic sampling improves resolution of the animal tree of life},
	Volume = {452},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000254792500044}}

@article{MAY.1988.a,
	Address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005},
	Author = {May, Robert M},
	Date-Added = {2009-09-03 17:18:02 +0100},
	Date-Modified = {2009-09-03 17:18:30 +0100},
	Isi = {A1988Q047900026},
	Isi-Recid = {66814306},
	Isi-Ref-Recids = {66814347 27153724 48700671 51179465 64018333 53297234 63140160 60821689 35392890 56119526 60164587 56119527 64774446 55796377 66814348 52747513 56113127 56035266 52002472 58241070 61220059 45410860 62200519 33416959 5395222 5395238 54553830 66814349 49792202 22980437 31802685 39531614 28454599 66814350 48220456 44632522 3794332 66814351 55319350 32603769 41449972 65077488 53590699 50798003 50422311 42013425 8121949 41247871 66814352 66814353 54186748 56035310 66068630 63150709 61823641 59790958 56216664 42045370 47545486 60384724 66814354 22842046 64144936},
	Journal = {Science},
	Month = sep,
	Number = {4872},
	Pages = {1441-1449},
	Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
	Times-Cited = {392},
	Title = {How many species are there on Earth?},
	Volume = {241},
	Year = {1988},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1988Q047900026}}

@article{Jones.Bielby.ea.2009.a,
	Author = {Jones, Kate E. and Bielby, Jon and Cardillo, Marcel and Fritz, Susanne A. and O'Dell, Justin and Orme, C. David L. and Safi, Kamran and Sechrest, Wes and Boakes, Elizabeth H. and Carbone, Chris and Connolly, Christina and Cutts, Michael J. and Foster, Janine K. and Grenyer, Richard and Habib, Michael and Plaster, Christopher A. and Price, Samantha A. and Rigby, Elizabeth A. and Rist, Janna and Teacher, Amber and Bininda-Emonds, Olaf R. P. and Gittleman, John L. and Mace, Georgina M. and Purvis, Andy and Michener, W. K.},
	Date-Added = {2009-09-01 10:20:30 +0100},
	Date-Modified = {2009-09-01 10:20:38 +0100},
	Doi = {10.1890/08-1494.1},
	Eprint = {http://www.esajournals.org/doi/pdf/10.1890/08-1494.1},
	Journal = {Ecology},
	Number = {9},
	Pages = {2648-2648},
	Title = {PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals},
	Url = {http://www.esajournals.org/doi/abs/10.1890/08-1494.1},
	Volume = {90},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.esajournals.org/doi/abs/10.1890/08-1494.1},
	Bdsk-Url-2 = {http://dx.doi.org/10.1890/08-1494.1}}

@article{Campbell.Nolla.ea.1994.a,
	Abstract = {Assessments of plankton community structure in the oligotrophic oceans based solely on microscopy may overstate the importance of heterotrophic bacterial biomass. Using flow cytometry to distinguish heterotrophic bacteria from the photosynthetic procaryotes Prochlorococcus spp., we found that Prochlorococcus contributed 31\% of total bacterial counts in the upper 100 m at station ALOHA (22-degrees 45'N, 158-degrees-W). In terms of carbon, procaryotic biomass was the largest component (greater-than-or-equal-to 80\%) of the microbial community, but almost half of this was photosynthetic biomass contributed by Prochlorococcus. Overall, the total 200-m integrated photosynthetic biomass exceeded heterotrophic bacterial biomass (55 vs. 45\%). We suggest that the relative proportion of photosynthetic to heterotrophic bacterial biomass varies among oligotrophic regions of the ocean and that dominance by heterotrophic bacteria is not typical.},
	Address = {810 EAST 10TH ST, LAWRENCE, KS 66044-8897},
	Author = {Campbell, Lisa and Nolla, HA and Vaulot, D},
	Date-Added = {2009-08-18 14:50:25 +0100},
	Date-Modified = {2009-08-18 14:52:08 +0100},
	Isi = {A1994PC98200017},
	Isi-Recid = {88298528},
	Isi-Ref-Recids = {85192674 66371406 72593258 82287027 65047386 70591260 74520411 62644920 88298529 51704563 62630429 85950162 79535919 50893020 82616159 84760591 73087043 88298530 84685091 82418683 88298531},
	Journal = {Limnology and Oceanography},
	Month = jun,
	Number = {4},
	Pages = {954-961},
	Publisher = {AMER SOC LIMNOLOGY OCEANOGRAPH},
	Times-Cited = {258},
	Title = {The importance of \textit{Prochlorococcus} to community structure in the Central North Pacific-Ocean},
	Type = {Note},
	Volume = {39},
	Year = {1994},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1994PC98200017}}

@article{Egge.Aksnes.1992.a,
	Abstract = {The development of phytoplankton communities was studied in floating enclosures. The enclosures were supplied with either surface water or water from 40 m depth. Nutrients with or without silicate were added in some of the experiments, while others recieved no artificial fertilization. It is shown that diatom dominance occurred irrespective of season if silicate concentration exceeded a threshold of approximately 2-mu-M. Flagellate dominance changed to diatom dominance within a few days after nutrient addition resulting in silicate concentrations above this threshold. Dominance of Phaeocystis sp. appeared on several occasions after the bloom of another species, but never at high silicate concentrations, The success of the diatom group seemed to be due to a high inherent growth rate at non-limiting silicate concentrations. Calculations indicated that the inherent growth rate for the diatom group had to be 5 to 50 \% higher than for the flagellate group in order to explain the outcome of our experiments.},
	Address = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY},
	Author = {Egge, JK and Aksnes, DL},
	Date-Added = {2009-08-18 14:48:35 +0100},
	Date-Modified = {2009-08-18 14:48:59 +0100},
	Isi = {A1992JF72600017},
	Isi-Recid = {80417396},
	Isi-Ref-Recids = {75187012 55955694 68637852 60346688 51226006 43695862 34932661 16277167 74135010 80417397 48947205 80417398 40997460 11584309 80417399 66967330 63965624 67324533 37015157 40652314 49356278 34932675 69428241 74914761 74914766 66552993 74918680 35484862 47545470 1777425 27181752 80417400 60437826 64998296 60186072},
	Journal = {Marine Ecology-Progress Series},
	Month = jul,
	Number = {2-3},
	Pages = {281-289},
	Publisher = {INTER-RESEARCH},
	Times-Cited = {242},
	Title = {SILICATE AS REGULATING NUTRIENT IN PHYTOPLANKTON COMPETITION},
	Volume = {83},
	Year = {1992},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1992JF72600017}}

@article{Fuhrman.Noble.1995.a,
	Annote = {Mesocosms filled with 80 liters of coastal seawater from Santa Monica, California, were used twice (June 
and November) to budget bacterial production and loss, as well as to assess 
the relative significance of viral 
lysis and Protist grazing in bacterial mortality. Bacterial abundance was -6 x 1 
O9 cells liter-l in June and 
2 x 10'' in November, with viral abundances -2 x lOlo particles liter-l in June and 1.5 x IO'O in November. 
Incorporation of [3H]thymidine and leucine yielded essentially identical production estimates and allowed 
calculation of total bacterial mortality in these closed systems. Bacterial growth rates were l-2 d--l in June 
and l-3 d-l in November. Three independent lines of evidence indicated that bacterial mortality attributed 
to grazing by protists was about equal to that attributed to viruses: size fractionation of disappearance of 
labeled DNA, with a 50% reduction after protists were removed; comparison of Protist grazing rates estimated 
with fluorescently labeled bacteria and virus production-based bacterial lysis rates, with 40-50% of the total 
ascribed to viruses; and model-based interpretation ofthe 3.3-4.6% ofbacteria visibly infected with assembled 
intracellular viruses, suggesting that 24-66% of loss is due to infection. Redundant production and loss 
measurements as well as the independent loss process estimates agreed within -30%, yielding a reasonably 
balanced budget. We believe the loss of bacteria to viruses reflects a significant dissipation of energy in this 
ecosystem and that viruses and protists contribute similarly to bacterial mortality. 
},
	Author = {Jed A. Fuhrman and Rachel T. Noble},
	Date-Added = {2009-08-18 10:26:38 +0100},
	Date-Modified = {2009-08-18 10:28:06 +0100},
	Journal = {Limnology and Oceanography},
	Number = {7},
	Pages = {1236 - 1242},
	Title = {Viruses and protists cause similar bacterial mortality in coastal seawater},
	Volume = {40},
	Year = {1995},
	Bdsk-File-1 = { }}

@article{Pomeroy.Wiebe.1988.a,
	Abstract = {Abstract~~The energetic demand of microorganisms in natural waters and the flux of energy between microorganisms and metazoans has been evaluated by empirical measurements in nature, in microcosms and mesocosms, and by simulation models. Microorganisms in temperate and tropical waters often use half or more of the energy fixed by photosynthesis. Most simulations and some experimental results suggest significant energy transfer to metazoans, but empirical evidence is mixed. Considerations of the range of growth yields of microorganisms and the number of trophic transfers among them indicate major energy losses within microbial food webs. Our ability to verify and quantify these processes is limited by the variability of assimilation efficiency and uncertainty about the structure of microbial food webs. However, even a two-step microbial chain is a major energy sink.  As an energetic link to metazoans, the detritus food web is inefficient, and its significance may have been overstated. There is not enough bacterial biomass associated with detritus to support metazoan detritivores. Much detritus is digestible by metazoans directly. Thus, metazoans and bacteria may to a considerable degree compete for a common resource. Microorganisms, together with metazoans, are important to the stability of planktonic communities through their roles as rapid mineralizers of organic matter, releasing inorganic nutrients. The competition for organic matter and the resultant rapid mineralization help maintain stable populations of phytoplankton in the absence of advective nutrient supply.    At temperatures near O $\,^{\circ}$C, bacterial metabolism is suppressed more than is the rate of photosynthesis. As a result, the products of the spring phytoplankton bloom in high-temperate latitudes are not utilized rapidly by bacteria. At temperatures below 0$\,^{\circ}$C microbial food webs are neither energy sinks or links: they are suppressed. Because the underlying mechanism of low-temperature inhibition is not known, we cannot yet generalize about this as a control of food web processes.    Microorganisms may operate on several trophic levels simultaneously. Therefore, the realism of the trophic level concept and the reality of the use of ecological efficiency calculations in ecosystem models is questionable.   },
	Author = {Pomeroy, Lawrence and Wiebe, William},
	Date = {1988/03/01/},
	Date-Added = {2009-08-18 10:22:57 +0100},
	Date-Modified = {2009-08-18 10:22:57 +0100},
	Day = {01},
	Journal = {Hydrobiologia},
	M3 = {10.1007/BF00007363},
	Month = {03},
	Number = {1},
	Pages = {7--18},
	Title = {Energetics of microbial food webs},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1007/BF00007363},
	Volume = {159},
	Year = {1988},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00007363}}

@article{Fritz.Bininda-Emonds.ea.2009.a,
	Abstract = {Whereas previous studies have investigated correlates of extinction risk either at global or regional scales, our study explicitly models regional effects of anthropogenic threats and biological traits across the globe. Using phylogenetic comparative methods with a newly-updated supertree of 5020 extant mammals, we investigate the impact of species traits on extinction risk within each WWF ecoregion. Our analyses reveal strong geographical variation in the influence of traits on risk: notably, larger species are at higher risk only in tropical regions. We then relate these patterns to current and recent-historical human impacts across ecoregions using spatial modelling. The body-mass results apparently reflect historical declines of large species outside the tropics due to large-scale land conversion. Narrow-ranged and rare species tend to be at high risk in areas of high current human impacts. The interactions we describe between biological traits and anthropogenic threats increase understanding of the processes determining extinction risk.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Fritz, Susanne A. and Bininda-Emonds, Olaf R. P. and Purvis, Andy},
	Date-Added = {2009-08-05 11:11:30 +0100},
	Date-Modified = {2009-08-05 11:11:30 +0100},
	Doi = {DOI 10.1111/j.1461-0248.2009.01307.x},
	Isi = {000266111200007},
	Isi-Recid = {180385747},
	Isi-Ref-Recids = {180385748 155497115 180385749 116434342 143726451 95491232 172659401 156238260 134153336 174391246 155066183 159884035 180385750 145845813 162235422 124583793 150714740 178235519 160545023 111425235 157951052 172659403 128357124 159135186 123378613 135604077 175404022 127500623 156556113 136510614 160524715 126077027 179401757 159559573 125667014 158707766 122306281 180385751 117223810 112336304 157261187 116955607 175141761 160545047 108014312 143237409 129083412 84478843 105790213},
	Journal = {Ecology Letters},
	Keywords = {Anthropogenic impact; body mass; conservation; geographical range size; life history; phylogenetic generalized linear model; population density; spatial autoregressive model; supertree},
	Month = jun,
	Number = {6},
	Pages = {538-549},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Times-Cited = {0},
	Title = {Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics},
	Type = {Letter},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000266111200007}}

@article{Bolker.Brooks.ea.2009.b,
	Abstract = {How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.},
	Address = {84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND},
	Author = {Bolker, Benjamin M. and Brooks, Mollie E. and Clark, Connie J. and Geange, Shane W. and Poulsen, John R. and Stevens, M. Henry H. and White, Jada-Simone S.},
	Date-Added = {2009-07-28 09:55:41 +0100},
	Date-Modified = {2009-07-28 09:55:41 +0100},
	Doi = {DOI 10.1016/j.tree.2008.10.008},
	Isi = {000264615200003},
	Isi-Recid = {178646708},
	Isi-Ref-Recids = {126896496 146825652 173810719 178646709 158450690 156578530 108835474 82650131 168120069 107954853 154805994 126148750 159830873 118012549 96145029 127935546 135028510 149997627 134537277 120106530 125571103 153964486 143880665 100057115 57464396 115225298 97874438 136153141 178646710 129429769 154048913 133392261 122115604 126527675 122606772 149275462 156266646 111709836 149897144 162813335 163274196 117111100 154228869 124387955 133170841 128628963 149192911 116570471 124297842 114541670 120267436 178646711 127550034 178646712 78224679 162053937 62972546 152907359 127205263 143066092 90765973 145120868 157045216 158008023 151548941 158294058 90704225},
	Journal = {Trends In Ecology \& Evolution},
	Month = mar,
	Number = {3},
	Pages = {127-135},
	Publisher = {ELSEVIER SCIENCE LONDON},
	Times-Cited = {2},
	Title = {Generalized linear mixed models: a practical guide for ecology and evolution},
	Volume = {24},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000264615200003}}

@article{Fielding.Bell.1997.a,
	Abstract = {Predicting the distribution of endangered species from habitat data is frequently perceived to be a useful technique. Models that predict the presence or absence of a species are normally judged by the number of prediction errors. These may be of two types: false positives and false negatives. Many of the prediction errors can be traced to ecological processes such as unsaturated habitat and species interactions. Consequently, if prediction errors are not placed in an ecological context the results of the model may be misleading. The simplest, and most widely used, measure of prediction accuracy is the number of correctly classified cases. There are other measures of prediction success that may be more appropriate. Strategies for assessing the causes and costs of these errors are discussed. A range of techniques for measuring error in presence/absence models, including some that are seldom used by ecologists (e.g. ROC plots and cost matrices), are described. A new approach to estimating prediction error, which is based on the spatial characteristics of the errors, is proposed. Thirteen recommendations are made to enable the objective selection of an error assessment technique for ecological presence/absence models.},
	Address = {40 WEST 20TH STREET, NEW YORK, NY 10011-4211},
	Author = {Fielding, AH and Bell, JF},
	Date-Added = {2009-07-23 15:17:16 +0100},
	Date-Modified = {2009-07-23 15:17:16 +0100},
	Isi = {A1997XV97800008},
	Isi-Recid = {102054341},
	Isi-Ref-Recids = {102054342 83952890 87183165 96462606 87264972 89044621 48956293 102054343 102054344 102054345 61752017 84417481 65756344 89430190 93254023 102054346 97301096 84417487 94033769 91378004 35243306 94420518 89469663 95326276 86039133 95920384 3396479 65314412 31340641 84575528 94124627 90872404 102054347 62364362 81006412 39526875 88507565 79355404 77545299 86168139 83877520 92251483 71442219 86193994 41337065 65195244 88717429 83618699 90204045 84996771 94033774 87939572 102054348 100643511 71044096 48238156 61519392 83145410},
	Journal = {Environmental Conservation},
	Keywords = {habitat relationships; data partitioning; habitat-association model; classifier; threshold; validation},
	Month = mar,
	Number = {1},
	Pages = {38-49},
	Publisher = {CAMBRIDGE UNIV PRESS},
	Times-Cited = {795},
	Title = {A review of methods for the assessment of prediction errors in conservation presence/absence models},
	Volume = {24},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1997XV97800008}}

@unpublished{Burns.2009.a,
	Author = {Burns, Patrick},
	Date-Added = {2009-07-17 14:13:56 +0100},
	Date-Modified = {2009-07-17 14:14:49 +0100},
	Month = {January},
	Title = {{The R Inferno}},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Raxworthy.Martinez-Meyer.ea.2003.a,
	Abstract = {Despite the importance of tropical biodiversity(1), informative species distributional data are seldom available for biogeographical study or setting conservation priorities(2,3). Modelling ecological niche distributions of species offers a potential soluion(4-7); however, the utility of old locality data from museums, and of more recent remotely sensed satellite data, remains poorly explored, especially for rapidly changing tropical landscapes. Using 29 modern data sets of environmental land coverage and 621 chameleon occurrence localities from Madagascar ( historical and recent), here we demonstrate a significant ability of our niche models in predicting species distribution. At 11 recently inventoried sites, highest predictive success (85.1\%) was obtained for models based only on modern occurrence data (74.7\% and 82.8\% predictive success, respectively, for pre-1978 and all data combined). Notably, these models also identified three intersecting areas of over-prediction that recently yielded seven chameleon species new to science. We conclude that ecological niche modelling using recent locality records and readily available environmental coverage data provides informative biogeographical data for poorly known tropical landscapes, and offers innovative potential for the discovery of unknown distributional areas and unknown species.},
	Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Raxworthy, CJ and Martinez-Meyer, E and Horning, N and Nussbaum, RA and Schneider, GE and Ortega-Huerta, MA and Peterson, AT},
	Date-Added = {2009-07-01 11:20:29 +0100},
	Date-Modified = {2009-07-01 11:20:29 +0100},
	Doi = {DOI 10.1038/nature02205},
	Isi = {000187342000058},
	Isi-Recid = {132399903},
	Isi-Ref-Recids = {132399904 132399905 124115044 129284829 122078406 60638808 60638809 120561673 129879475 114183698 72009613 132399906 117107138 105541179 113913990 84116085 112320041 127139826 111346681 110590142 124151722 92086876 132399907 132399908 127184853 117227014 116025009 123431407 79792952 109095910},
	Journal = {Nature},
	Month = dec,
	Number = {6968},
	Pages = {837-841},
	Publisher = {NATURE PUBLISHING GROUP},
	Times-Cited = {83},
	Title = {Predicting distributions of known and unknown reptile species in Madagascar},
	Volume = {426},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000187342000058}}

@article{Pearson.Raxworthy.ea.2007.a,
	Abstract = {Aim Techniques that predict species potential distributions by combining observed occurrence records with environmental variables show much potential for application across a range of biogeographical analyses. Some of the most promising applications relate to species for which occurrence records are scarce, due to cryptic habits, locally restricted distributions or low sampling effort. However, the minimum sample sizes required to yield useful predictions remain difficult to determine. Here we developed and tested a novel jackknife validation approach to assess the ability to predict species occurrence when fewer than 25 occurrence records are available.

Location Madagascar.

Methods Models were developed and evaluated for 13 species of secretive leaf-tailed geckos (Uroplatus spp.) that are endemic to Madagascar, for which available sample sizes range from 4 to 23 occurrence localities (at 1 km(2) grid resolution). Predictions were based on 20 environmental data layers and were generated using two modelling approaches: a method based on the principle of maximum entropy (Maxent) and a genetic algorithm (GARP).

Results We found high success rates and statistical significance in jackknife tests with sample sizes as low as five when the Maxent model was applied. Results for GARP at very low sample sizes (less than c. 10) were less good. When sample sizes were experimentally reduced for those species with the most records, variability among predictions using different combinations of localities demonstrated that models were greatly influenced by exactly which observations were included.

Main conclusions We emphasize that models developed using this approach with small sample sizes should be interpreted as identifying regions that have similar environmental conditions to where the species is known to occur, and not as predicting actual limits to the range of a species. The jackknife validation approach proposed here enables assessment of the predictive ability of models built using very small sample sizes, although use of this test with larger sample sizes may lead to overoptimistic estimates of predictive power. Our analyses demonstrate that geographical predictions developed from small numbers of occurrence records may be of great value, for example in targeting field surveys to accelerate the discovery of unknown populations and species.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Pearson, Richard G. and Raxworthy, Christopher J. and Nakamura, Miguel and Peterson, A. Townsend},
	Date-Added = {2009-07-01 11:18:08 +0100},
	Date-Modified = {2009-07-01 11:18:08 +0100},
	Doi = {DOI 10.1111/j.1365-2699.2006.01594.x},
	Isi = {000242790600009},
	Isi-Recid = {153708767},
	Isi-Ref-Recids = {129284829 132762639 124115044 122078406 149655281 145906958 116955616 146248566 68573993 153708768 153708769 146552375 127164718 85748177 42406458 149708427 134010788 151847354 102054341 129635195 136194966 136433730 145780688 135840802 124951256 101098138 148243617 125571143 4351102 107566014 117738652 144470456 132199482 146949887 136510621 113913990 61957095 132677834 134645822 151919713 131013604 125858982 116616248 130924793 104676354 111346681 132636212 147728857 132399908 132399907 127184853 116025009 132399903 142482569 123431407 131747847 143562243 132064232 148031793 142611151 136296413 145454604 134425348 122613891 109095910 123384131 90208801 134939284 132624207 130137902 147973525 151919715 144745203 95738903 127164702},
	Journal = {Journal of Biogeography},
	Keywords = {environmental niche modelling; geckos; jackknife; Madagascar; model validation; small sample size; species distribution modelling},
	Month = jan,
	Number = {1},
	Pages = {102-117},
	Publisher = {BLACKWELL PUBLISHING},
	Times-Cited = {53},
	Title = {Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar},
	Volume = {34},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000242790600009}}

@article{Phillips.Dudik.2008.a,
	Abstract = {Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time-consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use "default settings", tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence-only data. We evaluate our method on independently collected high-quality presence-absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce "hinge features" that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore "background sampling" strategies that cope with sample selection bias and decrease model-building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence-only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) "target-group" background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Phillips, Steven J. and Dudik, Miroslav},
	Date-Added = {2009-07-01 11:17:26 +0100},
	Date-Modified = {2009-07-01 11:17:26 +0100},
	Doi = {DOI 10.1111/j.2007.0906-7590.05203.x},
	Isi = {000254499200001},
	Isi-Recid = {161503292},
	Isi-Ref-Recids = {129304932 145906958 154871006 157636498 147728861 136817025 149708427 155698706 102054341 123078777 75543838 148425690 136433730 161503293 136088052 124951256 94943410 4299476 142452031 144727187 151919713 111346681 132256412 157586129 155698712 161503294 147728857 120223877 151919714 131747847 132624207 147973525 100633068 36833048 161503295 90333301 127164702 115817934},
	Journal = {Ecography},
	Month = apr,
	Number = {2},
	Pages = {161-175},
	Publisher = {BLACKWELL PUBLISHING},
	Times-Cited = {20},
	Title = {Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation},
	Volume = {31},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000254499200001}}

@inproceedings{Phillips.Dudik.ea.2004.a,
	Author = {Phillips, Stephen J. and Dud{\'\i}k, Miroslav and Schapire, Robert E},
	Booktitle = {Proceedings of the 21st International Conference on Machine Learning},
	Date-Added = {2009-06-30 11:11:49 +0100},
	Date-Modified = {2009-06-30 11:13:33 +0100},
	Pages = {655 - 662},
	Title = {A Maximum Entropy Approach to Species Distribution Modeling},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Phillips.Anderson.ea.2006.a,
	Abstract = {The availability of detailed environmental data, together with inexpensive and powerful computers, has fueled a rapid increase in predictive modeling of species environmental requirements and geographic distributions. For some species, detailed presence/absence occurrence data are available, allowing the use of a variety of standard statistical techniques. However, absence data are not available for most species. In this paper, we introduce the use of the maximum entropy method (Maxent) for modeling species geographic distributions with presence-only data. Maxent is a general-purpose machine learning method with a simple and precise mathematical formulation, and it has a number of aspects that make it well-suited for species distribution modeling. In order to investigate the efficacy of the method, here we perform a continental-scale case study using two Neotropical mammals: a lowland species of sloth, Bradypus variegatus, and a small montane murid rodent, Microryzomys minutus. We compared Maxent predictions with those of a commonly used presence-only modeling method, the Genetic Algorithm for Rule-Set Prediction (GARP). We made predictions on 10 random subsets of the occurrence records for both species, and then used the remaining localities for testing. Both algorithms provided reasonable estimates of the species' range, far superior to the shaded outline maps available in field guides. All models were significantly better than random in both binomial tests of omission and receiver operating characteristic (ROC) analyses. The area under the ROC curve (AUC) was almost always higher for Maxent, indicating better discrimination of suitable versus unsuitable areas for the species. The Maxent modeling approach can be used in its present form for many applications with presence-only datasets, and merits further research and development. (c) 2005 Elsevier B.V. All rights reserved.},
	Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
	Author = {Phillips, SJ and Anderson, RP and Schapire, RE},
	Date-Added = {2009-06-30 11:10:33 +0100},
	Date-Modified = {2009-06-30 11:10:33 +0100},
	Doi = {DOI 10.1016/j.ecolmodel.2005.03.026},
	Isi = {000233859600001},
	Isi-Recid = {147728857},
	Isi-Ref-Recids = {119753788 129284829 132762639 125979726 147728858 124115044 129304932 69298277 80085422 127164622 115835879 94476142 116854950 108986359 59844161 147728859 85748177 108640688 121300225 109754694 66885452 147728860 147728861 119753797 136817025 106078949 134010788 135794505 127509994 114888343 102054341 147728862 136433730 118133611 127164613 45519022 49981545 108235704 125571143 47449189 4351102 4299476 163490006 95510787 129304938 129284835 122778112 91924314 109283576 144727187 120317938 144790682 71221414 134645822 147728864 111346681 130924793 130622112 147728865 130801492 129084261 147728866 120223877 130778197 116233991 111949318 131747847 66068615 87026432 123722288 51907916 134425348 110766003 146710416 109095910 127494540 123384131 79792952 132763457 1812647 132624207 84159285 126205371 146134341 90853269 78347330 116537508 147728867 127164702 83145410},
	Journal = {Ecological Modelling},
	Keywords = {maximum entropy; distribution; modeling; niche; range},
	Month = jan,
	Number = {3-4},
	Pages = {231-259},
	Publisher = {ELSEVIER SCIENCE BV},
	Times-Cited = {193},
	Title = {Maximum entropy modeling of species geographic distributions},
	Volume = {190},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000233859600001}}

@article{Freckleton.2009.a,
	Abstract = {Phylogenetic comparative methods are extremely commonly used in evolutionary biology. In this paper, I highlight some of the problems that are frequently encountered in comparative analyses and review how they can be fixed. In broad terms, the problems boil down to a lack of appreciation of the underlying assumptions of comparative methods, as well as problems with implementing methods in a manner akin to more familiar statistical approaches. I highlight that the advent of more flexible computing environments should improve matters and allow researchers greater scope to explore methods and data.},
	Author = {Freckleton, Robert P.},
	Date-Added = {2009-06-24 12:30:54 +0100},
	Date-Modified = {2009-06-24 12:31:16 +0100},
	Doi = {10.1111/j.1420-9101.2009.01757.x},
	Journal = {Journal of Evolutionary Biology},
	Journal-Full = {Journal of evolutionary biology},
	Month = {Jun},
	Pmid = {19508410},
	Title = {The seven deadly sins of comparative analysis},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Antonelli.Nylander.ea.2009.a,
	Abstract = {Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the ‚{\"A}{\'u}Western Andean Portal.‚{\"A}{\`u} The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system (‚{\"A}{\'u}Lake Pebas‚{\"A}{\`u}) in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.
},
	Author = {Antonelli, Alexandre and Nylander, Johan A. A. and Persson, Claes and Sanmart{\'\i}n, Isabel},
	Date-Added = {2009-06-18 10:03:50 +0100},
	Date-Modified = {2009-06-18 10:09:20 +0100},
	Doi = {10.1073/pnas.0811421106},
	Eprint = {http://www.pnas.org/content/106/24/9749.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {24},
	Pages = {9749 - 9754},
	Title = {{Tracing the impact of the Andean uplift on Neotropical plant evolution}},
	Url = {http://www.pnas.org/content/106/24/9749.abstract},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/106/24/9749.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0811421106}}

@article{Cavender-Bares.Kozak.ea.2009.a,
	Abstract = {The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.},
	Address = {Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.},
	Author = {Cavender-Bares, J and Kozak, KH and Fine, PV and Kembel, SW},
	Crdt = {2009/05/29 09:00},
	Da = {20090528},
	Date = {2009 May 18},
	Date-Added = {2009-06-15 11:50:19 +0100},
	Date-Modified = {2009-11-11 16:27:16 +0000},
	Dep = {20090518},
	Doi = {10.1111/j.1461-0248.2009.01314.x},
	Edat = {2009/05/29 09:00},
	Issn = {1461-0248 (Electronic)},
	Jid = {101121949},
	Journal = {Ecology Letters},
	Jt = {Ecology letters},
	Language = {ENG},
	Mhda = {2009/05/29 09:00},
	Month = {May},
	Own = {NLM},
	Pages = {693-715},
	Pii = {ELE1314},
	Pmid = {19473217},
	Pst = {aheadofprint},
	Pt = {JOURNAL ARTICLE},
	Status = {Publisher},
	Title = {The merging of community ecology and phylogenetic biology.},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{McInnes.Purvis.ea.2009.a,
	Author = {McInnes, Lynsey and Purvis, Andy and Orme, C. David L.},
	Date-Added = {2009-06-11 09:54:36 +0100},
	Date-Modified = {2009-08-17 17:03:38 +0100},
	Doi = {10.1098/rspb.2009.0656},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Month = {September},
	Number = {1670},
	Pages = {3063-3070},
	Title = {Where do species' geographic ranges stop and why? Landscape impermeability and the Afrotropical avifauna},
	Volume = {276},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Tuljapurkar.Gaillard.ea.2009.a,
	Abstract = {Environmental stochasticity is known to play an important role in life-history evolution, but most general theory assumes a constant environment. In this paper, we examine life-history evolution in a variable environment, by decomposing average individual fitness (measured by the long-run stochastic growth rate) into contributions from average vital rates and their temporal variation. We examine how generation time, demographic dispersion (measured by the dispersion of reproductive events across the lifespan), demographic resilience (measured by damping time), within-year variances in vital rates, within- year correlations between vital rates and between-year correlations in vital rates combine to determine average individual fitness of stylized life histories. In a fluctuating environment, we show that there is often a range of cohort generation times at which the fitness is at a maximum. Thus, we expect 'optimal' phenotypes in fluctuating environments to differ from optimal phenotypes in constant environments. We show that stochastic growth rates are strongly affected by demographic dispersion, even when deterministic growth rates are not, and that demographic dispersion also determines the response of life-history-specific average fitness to within- and between-year correlations. Serial correlations can have a strong effect on fitness, and, depending on the structure of the life history, may act to increase or decrease fitness. The approach we outline takes a useful first step in developing general life-history theory for non-constant environments.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Tuljapurkar, Shripad and Gaillard, Jean-Michel and Coulson, Tim},
	Date = {JUN 12 2009},
	Date-Added = {2009-06-06 13:35:17 +0100},
	Date-Modified = {2009-06-06 13:35:17 +0100},
	Doi = {DOI 10.1098/rstb.2009.0021},
	Isi = {000265732200003},
	Isi-Recid = {180033483},
	Isi-Ref-Recids = {20740573 149676394 153518611 104346168 119588704 89107817 84021126 23866208 29530076 1437053 153270059 180033476 33174 19464667 144766688 118012562 132777506 47952856 99363583 35930337 152204994 158956241 174659729 175141820 49471507 46269093 157041191 131085467 180033480 51102782 12244409 16334842 42837108 49830991 130612263 153265304 161033553 69687560 94222225 115154612 103590099 161971129 25783091 29235347 33526563 143375471 45498581 116616343 94898877 131704523 105306695 11526663 180033484},
	Journal = {Philosophical Transactions of the Royal Society B-Biological Sciences},
	Keywords = {generation time; demographic dispersion; stochastic growth rate; reproduction; survival; life history},
	Month = {JUN 12},
	Number = {1523},
	Pages = {1499-1509},
	Publisher = {ROYAL SOC},
	Timescited = {1},
	Title = {From stochastic environments to life histories and back},
	Volume = {364},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000265732200003}}

@article{Lichstein.Simons.ea.2002.a,
	Abstract = {Recognition and analysis of spatial autocorrelation has defined a new paradigm in ecology. Attention to spatial pattern can lead to insights that would have been otherwise overlooked, while ignoring space may lead to false conclusions about ecological relationships. We used Gaussian spatial autoregressive models, fit with widely available software, to examine breeding habitat relationships for three common Neotropical migrant songbirds in the southern Appalachian Mountains of North Carolina and Tennessee, USA.

In preliminary models that ignored space, the abundance of all three species was correlated with both local- and landscape-scale habitat variables. These models were then modified to account for broadscale spatial trend (via trend surface analysis) and fine-scale autocorrelation (via an autoregressive spatial covariance matrix). Residuals from ordinary least squares regression models were autocorrelated, indicating that the assumption of independent errors was violated. In contrast, residuals from autoregressive models showed little spatial pattern, suggesting that these models were appropriate.

The magnitude of habitat effects tended to decrease, and the relative importance of different habitat variables shifted when we incorporated broadscale and then fine-scale space into the analysis. The degree to which habitat effects changed when space was added to the models was roughly correlated with the amount of spatial structure in the habitat variables.

Spatial pattern in the residuals from ordinary least squares models may result from failure to include or adequately measure autocorrelated habitat variables. In addition, contagious processes, such as conspecific attraction, may generate spatial patterns in species abundance that cannot be explained by habitat models. For our study species, spatial patterns in the ordinary least squares residuals suggest that a scale of 500-1000 m would be appropriate for investigating possible contagious processes.},
	Address = {1707 H ST NW, STE 400, WASHINGTON, DC 20006-3915 USA},
	Author = {Lichstein, JW and Simons, TR and Shriner, SA and Franzreb, KE},
	Date = {AUG 2002},
	Date-Added = {2009-06-05 09:59:52 +0100},
	Date-Modified = {2009-06-05 09:59:52 +0100},
	Isi = {000176902800008},
	Isi-Recid = {125667014},
	Isi-Ref-Recids = {125667015 115839375 125667016 50283882 89866143 101380541 76534592 96462606 25791554 100149705 79665303 125667017 48367686 108078671 111364917 43397840 42215472 96088460 94033693 98613915 48524855 97517806 100803327 97418641 72602384 47545206 105627853 79634716 101773366 97486160 82828464 74066850 124791294 79634713 98406154 70454288 125667018 124791295 108801745 104112240 69780280 84575528 124791287 124791296 61381502 95589175 92184282 62624136 100471693 77408112 83074428 61117158 111364873 111970118 41623555 70382241 69914580 90710012 79704737 108990462 101944205 94382131 115949054 73618348 35089716 35089713 90496259 93156114 89123650 68187660 114314387 57957370 51000989 87093595 125667019 57961146 58673512 70203592 56457002 118860551},
	Journal = {Ecological Monographs},
	Keywords = {CAR model; habitat model; landscape effects; Moran's 1; Neotropical migrant songbirds; spatial autocorrelation; spatial autoregressive model; trend surface analysis},
	Month = {AUG},
	Number = {3},
	Pages = {445-463},
	Publisher = {ECOLOGICAL SOC AMER},
	Timescited = {194},
	Title = {Spatial autocorrelation and autoregressive models in ecology},
	Volume = {72},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000176902800008}}

@article{Mooers.Atkins.2003.a,
	Abstract = {Using published IUCN red-lists for the threatened bird species of Indonesia (Stattersfield \& Capper, 2000), we document that the species at risk in Indonesia are not a taxonomically random sample, consistent with patterns seen at the global scale (Purvis et al., 2000). This implies that a greater than random proportion of Indonesia's and the world's (through the loss of endemics) phylogenetic diversity (PD) is at risk (Von Euler, 2001). Using cytochrome b (Johns \& Avise, 1998) and a distance-based taxonomy. we attempt to quantify this projected loss of PD in millions of years and conclude with a brief discussion of the conservation implications for Indonesia, and of the use of 'evolutionary heritage' as a measure for conservation at the geopolitical level.},
	Address = {40 WEST 20TH ST, NEW YORK, NY 10011-4221 USA},
	Author = {Mooers, AO and Atkins, RA},
	Date = {MAY 2003},
	Date-Added = {2009-06-02 10:59:37 +0100},
	Date-Modified = {2009-06-02 10:59:59 +0100},
	Doi = {10.1017/S1367943003003226},
	Isi = {000183461600011},
	Isi-Recid = {129879513},
	Isi-Ref-Recids = {89585411 64134973 117223808 127725468 106718871 104636227 103222988 123534053 79838892 90049935 102092581 93813070 114401484 119758595 107691195 125050401 129879514 111425243 110942806 76811905 102480485 114485286 108014312 123706614 75537462 124382224 74302138 105326524 118493355 81908047},
	Journal = {Animal Conservation},
	Month = {MAY},
	Pages = {183-188},
	Publisher = {CAMBRIDGE UNIV PRESS},
	Timescited = {8},
	Title = {Indonesia's threatened birds: over 500 million years of evolutionary heritage at risk},
	Volume = {6},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000183461600011}}

@article{Jetz.Rahbek.ea.2005.a,
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DG, OXON, ENGLAND},
	Author = {Jetz, W and Rahbek, C and Lichstein, JW},
	Date = {JAN 2005},
	Date-Added = {2009-05-31 11:17:32 +0100},
	Date-Modified = {2009-05-31 11:17:46 +0100},
	Isi = {000226395400009},
	Isi-Recid = {142550632},
	Isi-Ref-Recids = {43397840 94935885 128357124 135267078 129304868 126077027 119924840 84575528 114141899 125667014 121548959},
	Journal = {Global Ecology and Biogeography},
	Month = {JAN},
	Note = {Global Ecology and Biogeography},
	Number = {1},
	Pages = {97-98},
	Publisher = {BLACKWELL PUBLISHING LTD},
	Timescited = {18},
	Title = {Local and global approaches to spatial data analysis in ecology},
	Volume = {14},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226395400009}}

@article{Memmott.Martinez.ea.2000.a,
	Abstract = {1. A food web is presented which describes trophic interactions among the herbivores, parasitoids, predators and pathogens associated with broom, Cytisus scoparius (L.) Link. The data come from published work on the community at a single site. The web comprises a total of 154 taxa: one plant, 19 herbivores, 66 parasitoids, 60 predators, five omnivores and three pathogens. There are 370 trophic links between these taxa in the web. The taxa form 82 functionally distinct groups, called trophic species.

2. Predators consumed significantly more species than did parasitoids: a median of two prey species per species of predator (range = 1-9), compared to a median of one host species per species of parasitoid (range = 1-4). Significant differences in the number of species consumed were also found among the five predator groups: birds (median = 4), spiders (median = 5), Coleoptera (median = 1), Diptera (median = 2) and Hemiptera (median = 7).

3. Vulnerability, measured by numbers of consumer species, was significantly affected by the herbivores' feeding styles: externally feeding herbivores were most vulnerable and the concealed herbivores were least vulnerable. Miners were vulnerable to the most parasitoid species and externally feeding herbivores were the most vulnerable to predators.

4. Resource species had a median vulnerability of 13 consumer species, a figure far higher than that in most published food webs. No significant relationship was found between species' vulnerability to predators and vulnerability to parasitoids. However, there was a strong negative relationship between the percentage mortality due to predation and percentage mortality due to parasitism.

5. The broom food web contains nine orders of insects, a figure higher than previously recorded. The web also contains vertebrates, arachnids, bacteria and fungi. Most of the interactions between the orders were weak. Connectance was calculated for the complete web, the parasitoid sub-web and the predator sub-web. The connectance of the predator sub-web, a value of 0.0364, was more than an order of magnitude larger than the connectance of the entire web (0.0156) or the parasitoid sub-web (0.018).

6. The body lengths of 52 species in the food web were estimated from field guides or museum specimens. Larger predators consumed smaller prey in 93\% of predator-prey interactions. Smaller parasitoids consumed larger hosts in 79\% of parasitoid-host interactions. Parasitoids were significantly smaller than predators.

7. The 52 species were arranged in order of increasing body length along the columns and down the rows of a food web matrix. The predator sub-web was predominantly upper triangular with 8\% of non-zero elements falling below the leading diagonal. The parasitoid sub-web was predominantly lower triangular with 21\% non-zero elements falling above the leading diagonal. The entire web contains entries both above and below the main diagonal and thus violates a central assumption of the cascade model.},
	Address = {P O BOX 88, OSNEY MEAD, OXFORD OX2 0NE, OXON, ENGLAND},
	Author = {Memmott, Jane and Martinez, Neo D and Cohen, J E},
	Date = {JAN 2000},
	Date-Added = {2009-05-30 10:56:52 +0100},
	Date-Modified = {2009-05-30 10:57:32 +0100},
	Isi = {000084678500001},
	Isi-Recid = {113304528},
	Isi-Ref-Recids = {38429201 20895570 109396940 51179465 82293935 56119526 82042968 68227050 70144837 35392890 18558061 11527698 12729219 11527697 6527632 36948 94379155 67535402 83480036 86628642 85014709 62200519 64732418 102365027 97070918 90680588 61873736 85944077 92016949 69856997 101395688 82935343 111462179 96482594 79909321 77847753 83204975 89558022 48220456 107341969 87861239 85464164 82818783 109685952 67479136 78224387 75684367 41247871 76641083 76942328 70342325 89191372 96060143 56216664 98083032 94946418 57206455 18558064 64144936 69856993 11527716 73339051},
	Journal = {Journal of Animal Ecology},
	Keywords = {broom; cascade model; connectance; source web; trophic species},
	Month = {JAN},
	Number = {1},
	Pages = {1-15},
	Publisher = {BLACKWELL SCIENCE LTD},
	Timescited = {85},
	Title = {Predators, parasitoids and pathogens: species richness, trophic generality and body sizes in a natural food web},
	Volume = {69},
	Year = {2000},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000084678500001}}

@manual{Oliphant.2006.a,
	Author = {Oliphant, Travis E.},
	Date-Added = {2009-05-19 14:02:33 +0100},
	Date-Modified = {2009-05-19 14:03:23 +0100},
	Month = {December},
	Title = {Guide to NumPy},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Beale.Lennon.ea.2009.a,
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Beale, C. M. and Lennon, J. J. and Gimona, A.},
	Date = {APR 21 2009},
	Date-Added = {2009-05-19 10:07:04 +0100},
	Date-Modified = {2009-05-19 10:09:12 +0100},
	Doi = {DOI 10.1073/pnas.0902229106},
	Isi = {000265506800087},
	Isi-Recid = {180037626},
	Isi-Ref-Recids = {180037627 180037628 175258305 180037629},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {APR 21},
	Note = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {16},
	Pages = {E41-E43},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {0},
	Title = {European bird distributions still show few climate associations},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000265506800087}}

@article{Araujo.Thuiller.ea.2009.a,
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Araujo, Miguel B. and Thuiller, Wilfried and Yoccoz, Nigel G.},
	Date = {APR 21 2009},
	Date-Added = {2009-05-19 10:06:33 +0100},
	Date-Modified = {2009-05-19 10:09:32 +0100},
	Doi = {DOI 10.1073/pnas.0813294106},
	Isi = {000265506800089},
	Isi-Recid = {180037632},
	Isi-Ref-Recids = {151919711 175258305 979271 103647123 66068615 161428195 177014912},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {APR 21},
	Note = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {16},
	Pages = {E45-E46},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {0},
	Title = {Reopening the climate envelope reveals macroscale associations with climate in European birds},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000265506800089}}

@article{Peterson.Barve.ea.2009.a,
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Peterson, A. Townsend and Barve, Narayani and Bini, Luis Mauricio and Diniz-Filho, Jose Alexandre and Jimenez-Valverde, Alberto and Lira-Noriegaa, Andres and Lobo, Jorge and Maher, Sean and de Marco, Paulo, Jr. and Martinez-Meyer, Enrique and Nakazawa, Yoshinori and Soberon, Jorge},
	Date = {APR 21 2009},
	Date-Added = {2009-05-19 10:05:39 +0100},
	Date-Modified = {2009-05-19 10:08:56 +0100},
	Doi = {DOI 10.1073/pnas.0809722106},
	Isi = {000265506800090},
	Isi-Recid = {180037633},
	Isi-Ref-Recids = {145906958 158662049 175258305 133698598 150995077},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {APR 21},
	Number = {16},
	Pages = {E47-E47},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {0},
	Title = {The climate envelope may not be empty},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000265506800090}}

@article{Aspinall.Miller.ea.2009.a,
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Aspinall, Richard J. and Miller, Jennifer A. and Franklin, Janet},
	Date = {APR 21 2009},
	Date-Added = {2009-05-19 10:04:57 +0100},
	Date-Modified = {2009-05-19 10:09:20 +0100},
	Doi = {DOI 10.1073/pnas.0809891106},
	Isi = {000265506800088},
	Isi-Recid = {180037630},
	Isi-Ref-Recids = {175258305 106855067 79998408 81772641 180037631},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = {APR 21},
	Note = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {16},
	Pages = {E44-E44},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {0},
	Title = {Calculations on the back of a climate envelope: Addressing the geography of species distributions},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000265506800088}}

@article{Beale.Lennon.ea.2008.a,
	Abstract = {Predicting how species distributions might shift as global climate changes is fundamental to the successful adaptation of conservation policy. An increasing number of studies have responded to this challenge by using climate envelopes, modeling the association between climate variables and species distributions. However, it is difficult to quantify how well species actually match climate. Here, we use null models to show that species-climate associations found by climate envelope methods are no better than chance for 68 of 100 European bird species. In line with predictions, we demonstrate that the species with distribution limits determined by climate have more northerly ranges. We conclude that scientific studies and climate change adaptation policies based on the indiscriminate use of climate envelope methods irrespective of species sensitivity to climate may be misleading and in need of revision.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Beale, Colin M. and Lennon, Jack J. and Gimona, Alessandro},
	Date = {SEP 30 2008},
	Date-Added = {2009-05-19 10:00:48 +0100},
	Date-Modified = {2009-05-19 10:01:00 +0100},
	Doi = {10.1073/pnas.0803506105},
	Isi = {000261914300017},
	Isi-Recid = {175258305},
	Isi-Ref-Recids = {150035229 145906958 151919711 96666958 127654676 151178403 98458438 113933781 97798297 103944401 162524674 149708427 94873707 103647123 135840802 153989458 121261181 134381766 175258306 172998149 151247660 84575528 160544985 135267073 136482649 109283576 162232715 127580979 131013604 79936798 142611151 106818164 114024429 150995075 126806289 154214312 156266687 175258307 132624207 120004637 144745203 131529340},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {bioclimatic niche; global change; null models; ornithology; species distribution},
	Month = {SEP 30},
	Number = {39},
	Pages = {14908-14912},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {6},
	Title = {Opening the climate envelope reveals no macroscale associations with climate in European birds},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000261914300017}}

@article{Whittingham.Stephens.ea.2006.a,
	Abstract = {1. The biases and shortcomings of stepwise multiple regression are well established within the statistical literature. However, an examination of papers published in 2004 by three leading ecological and behavioural journals suggested that the use of this technique remains widespread: of 65 papers in which a multiple regression approach was used, 57\% of studies used a stepwise procedure.

2. The principal drawbacks of stepwise multiple regression include bias in parameter estimation, inconsistencies among model selection algorithms, an inherent (but often overlooked) problem of multiple hypothesis testing, and an inappropriate focus or reliance on a single best model. We discuss each of these issues with examples.

3. We use a worked example of data on yellowhammer distribution collected over 4 years to highlight the pitfalls of stepwise regression. We show that stepwise regression allows models containing significant predictors to be obtained from each year's data. In spite of the significance of the selected models, they vary substantially between years and suggest patterns that are at odds with those determined by analysing the full, 4-year data set.

4. An information theoretic (IT) analysis of the yellowhammer data set illustrates why the varying outcomes of stepwise analyses arise. In particular, the IT approach identifies large numbers of competing models that could describe the data equally well, showing that no one model should be relied upon for inference.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Whittingham, Mark J. and Stephens, Philip A. and Bradbury, Richard B. and Freckleton, Robert P.},
	Date = {SEP 2006},
	Date-Added = {2009-05-18 16:51:09 +0100},
	Date-Modified = {2009-05-18 16:51:09 +0100},
	Doi = {DOI 10.1111/j.1365-2656.2006.01141.x},
	Isi = {000239516500016},
	Isi-Recid = {151548941},
	Isi-Ref-Recids = {25921756 117289316 117111092 109409185 151548942 35264361 94747076 89552760 103254122 81738154 103319042 133795241 126382494 145822373 73380997 133392261 134010792 110933010 71621125 21197362 145895946 134010784 143066092 111852439 143811445 37640640 132199472},
	Journal = {Journal of Animal Ecology},
	Keywords = {ecological modelling; habitat selection; minimum adequate model; multivariate statistical analysis; statistical bias},
	Month = {SEP},
	Number = {5},
	Pages = {1182-1189},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {90},
	Title = {Why do we still use stepwise modelling in ecology and behaviour?},
	Volume = {75},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000239516500016}}

@article{Romdal.Colwell.ea.2005.a,
	Abstract = {Although the mid-domain effect (MDE) model for species richness in bounded geographical domains has proved controversial, several studies have revealed its explanatory potential for patterns of species richness. This paper investigates unexplored aspects of one-dimensional MDE, based on a data set of latitudinal distributions of New World birds (3706 species) on a V scale. Two previously published data sets for other taxa are also considered. We adjusted band sums (number of species per latitudinal band) for longitudinal area by constructing species-area curves for each band. Area-corrected richness patterns differed substantially from raw band sums, although both confirmed a strong, mid-tropical peak in richness. An MDE model accounted for 47\% of the adjusted pattern, whereas area alone explained 13\% of variation. Area-adjusted band sum data proved preferable to coastal transect data from the same data set. MDE was relatively more important in smaller latitudinal domains and/or for taxa with relatively large ranges. On fundamental grounds, we concluded that MDE randomizations based on empirical ranges are more appropriate than those based on theoretical range size distributions. Models that, like MDE, produce quantitative richness predictions should be evaluated statistically against the null hypothesis of equality, not simply correlation, of empirical vs. predicted richness values.},
	Address = {1707 H ST NW, STE 400, WASHINGTON, DC 20006-3915 USA},
	Author = {Romdal, Tom S. and Colwell, Robert K. and Rahbek, Carsten},
	Date = {JAN 2005},
	Date-Added = {2009-05-15 15:22:37 +0100},
	Date-Modified = {2009-05-15 15:26:55 +0100},
	Isi = {000226791700023},
	Isi-Recid = {142777755},
	Isi-Ref-Recids = {126077025 134645825 121632742 97798295 97019357 99610874 115625965 133698598 88873228 113933781 115625967 142777756 131006685 16654374 75547181 142777757 124318080 86879702 106186297 114504823 99122025 103580212 92086796 122433693 126532250 94120823 126077027 119924840 98852223 121729235 120729162 126987059 95927772 111365867 112942102 123004260 19464611 132603481 39672997 134343308 91146463 26711836 101507145 119470571 117605542 100028297 111418406 74221732 113730925 81780762 92086885 101380523 124317870 91666674 121530123 75537462 70992864 114519079 132203247 101923920 82525512 103685926 132328727 130254190},
	Journal = {Ecology},
	Keywords = {band sum area; birds; geographical domain extent; latitudinal gradient; Madagascar; MDE model; mid-domain effect; New World; randomizations; range size distribution; species-area curves; species richness},
	Month = {JAN},
	Number = {1},
	Pages = {235-244},
	Publisher = {ECOLOGICAL SOC AMER},
	Timescited = {14},
	Title = {The influence of band sum area, domain extent, and range sizes on the latitudinal mid-domain effect},
	Volume = {86},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226791700023}}

@article{Olalla-Tarraga.Rodriguez.ea.2006.a,
	Abstract = {Aim To document geographical interspecific patterns of body size of European and North American squamate reptile assemblages and explore the relationship between body size patterns and environmental gradients.

Location North America and western Europe.

Methods We processed distribution maps for native species of squamate reptiles to document interspecific spatial variation of body size at a grain size of 110 x 110 km. We also examined seven environmental variables linked to four hypotheses possibly influencing body size gradients. We used simple and multiple regression, evaluated using information theory, to identify the set of models best supported by the data.

Results Europe is characterized by clear latitudinal trends in body size, whereas geographical variation in body size in North America is complex. There is a consistent association of mean body size with measures of ambient energy in both regions, although lizards increase in size northwards whereas snakes show the opposite pattern. Our best models accounted for almost 60\% of the variation in body size of lizards and snakes within Europe, but the proportions of variance explained in North America were less than 20\%.

Main conclusions Although body size influences the energy balance of thermoregulating ectotherms, inconsistent biogeographical patterns and contrasting associations with energy in lizards and snakes suggest that no single mechanism can explain variation of reptile body size in the northern temperate zone.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Olalla-Tarraga, Miguel Angel and Rodriguez, Miguel Angel and Hawkins, Bradford A.},
	Date = {MAY 2006},
	Date-Added = {2009-04-28 13:28:04 +0100},
	Date-Modified = {2009-04-28 13:31:06 +0100},
	Doi = {DOI 10.1111/j.1365-2699.2006.01435.x},
	Isi = {000236943100003},
	Isi-Recid = {149839642},
	Isi-Ref-Recids = {131739812 149839643 119414542 131660642 116692102 146264939 127654732 123301762 130013503 90158721 99677696 33526969 33904451 89256113 52907132 9931337 99083011 117605384 142270887 128732855 1905233 35257862 91999521 144228375 79152166 110341793 92635388 69770009 146442 146443 94935885 147231137 75547181 83264296 84358732 98297541 107491341 128357124 83356433 149839644 119282909 5344570 62587343 116706249 133916021 131013613 133992748 135267079 91546563 130625357 91370343 56666829 50242568 127844756 18542171 133392261 132430377 126360964 35034472 12739598 57047892 99242815 20666009 128858516 102723674 103985276 100368459 57561087 130155013 49507195 39312079 149839645 128251058 149839646 145752320 15695578 15237487 34984089 3611650 146264944 134372209 142378755 112368559 111222781 125737118},
	Journal = {Journal of Biogeography},
	Keywords = {Bergmann's rule; body size gradients; Europe; macroecology; North America; squamate reptiles; thermoregulation},
	Month = {MAY},
	Number = {5},
	Pages = {781-793},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {19},
	Title = {Broad-scale patterns of body size in squamate reptiles of Europe and North America},
	Volume = {33},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000236943100003}}

@article{Engler.Guisan.2009.a,
	Author = {Engler, Robin and Guisan, Antoine},
	Date-Added = {2009-04-22 11:14:02 +0100},
	Date-Modified = {2009-04-22 11:15:17 +0100},
	Journal = {Diversity and Distributions},
	Pages = {1-12},
	Title = {MIGCLIM: Predicting plant distribution and dispersal in a changing climate},
	Volume = {1},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Pagel.1999.a,
	Abstract = {Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.},
	Address = {{PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}},
	Author = {Pagel, M},
	Date = {OCT 28 1999},
	Date-Added = {2009-04-22 11:05:36 +0100},
	Date-Modified = {2011-01-11 16:47:36 +0000},
	Isi = {000083464700048},
	Isi-Recid = {112336304},
	Isi-Ref-Recids = {107960089 103692980 112336305 84584161 107352113 103146643 103133493 90123966 99287968 109299382 53560838 85165354 22364103 54497548 75952957 109396824 112336306 108423901 80759959 104606502 85354827 75043716 106880547 95626677 64135288 95817177 78450651 97351096 102096270 102897515 25132987 90392597 8405954 112336307 95230586 101214652 110444512 101620619 86002423 72714421 76218624 43711448 99676097 98042675 111632817 112176433 102791346 88546938 100199596 86050888 69468637 112176434 80134800 105408080 85105165 100359553 86763569 92133321 104606534 112336308 98068978 112336309 105306667 107154369 103730521 92754402 109040366 100225043 112336310 94567618 100751105 88781475 106824982 62523217 97846734 93773020 109767950},
	Journal = {Nature},
	Month = {OCT 28},
	Number = {6756},
	Pages = {877-884},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Timescited = {368},
	Title = {Inferring the historical patterns of biological evolution},
	Volume = {401},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000083464700048}}

@article{Koleff.Gaston.ea.2003.a,
	Abstract = {1. Little consensus has been reached as to general features of spatial variation in beta diversity, a fundamental component of species diversity. This could reflect a genuine lack of simple gradients in beta diversity, or a lack of agreement as to just what constitutes beta diversity. Unfortunately, a large number of approaches have been applied to the investigation of variation in beta diversity, which potentially makes comparisons of the findings difficult.

2. We review 24 measures of beta diversity for presence/absence data (the most frequent form of data to which such measures are applied) that have been employed in the literature, express many of them for the first time in common terms, and compare some of their basic properties.

3. Four groups of measures are distinguished, with a fundamental distinction arising between 'broad sense' measures incorporating differences in composition attributable to species richness gradients, and 'narrow sense' measures that focus on compositional differences independent of such gradients. On a number of occasions on which the former have been employed in the literature the latter may have been more appropriate, and there are many situations in which consideration of both kinds of measures would be valuable.

4. We particularly recommend (i) considering beta diversity measures in terms of matching/mismatching components (usually denoted a , b and c) and thereby identifying the contribution of different sources of variation in species composition, and (ii) the use of ternary plots to express the relationship between the values of these measures and of the components, and as a way of understanding patterns in beta diversity.},
	Address = {{9600 GARSINGTON RD, OXFORD OX4 2DG, OXON, ENGLAND}},
	Author = {Koleff, Patricia and Gaston, Kevin J. and Lennon, Jack J.},
	Date = {MAY 2003},
	Date-Added = {2009-04-21 11:52:57 +0100},
	Date-Modified = {2011-01-16 18:27:10 +0000},
	Isi = {000182322500001},
	Isi-Recid = {129210415},
	Isi-Ref-Recids = {129210416 98068965 91999521 108986359 117017453 87630329 29212819 67757048 88086417 862333 114924076 97019360 118817973 119282909 87769416 78849614 101944197 103180413 2635925 43529246 120729162 111019594 96776544 122706012 114245042 11002466 72322471 102850046 128817140 109553825 56709365 98903143 108977462 33005978 51450094 108657409 54798310 48685 3099140 117541835 127026968 90540977 28273774 22881351 7418322 37888177 96136931 101923920 117919337 112490241 98068971 53980563 44074458},
	Journal = {Journal of Animal Ecology},
	Keywords = {beta diversity; biodiversity; presence-absence; similarity indices; spatial turnover},
	Month = {MAY},
	Number = {3},
	Pages = {367-382},
	Publisher = {BLACKWELL PUBLISHING LTD},
	Timescited = {166},
	Title = {Measuring beta diversity for presence-absence data},
	Volume = {72},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000182322500001}}

@article{Kearney.Porter.2009.a,
	Abstract = {Species distribution models (SDMs) use spatial environmental data to make inferences on species' range limits and habitat suitability. Conceptually, these models aim to determine and map components of a species' ecological niche through space and time, and they have become important tools in pure and applied ecology and evolutionary biology. Most approaches are correlative in that they statistically link spatial data to species distribution records. An alternative strategy is to explicitly incorporate the mechanistic links between the functional traits of organisms and their environments into SDMs. Here, we review how the principles of biophysical ecology can be used to link spatial data to the physiological responses and constraints of organisms. This provides a mechanistic view of the fundamental niche which can then be mapped to the landscape to infer range constraints. We show how physiologically based SDMs can be developed for different organisms in different environmental contexts. Mechanistic SDMs have different strengths and weaknesses to correlative approaches, and there are many exciting and unexplored prospects for integrating the two approaches. As physiological knowledge becomes better integrated into SDMs, we will make more robust predictions of range shifts in novel or non-equilibrium contexts such as invasions, translocations, climate change and evolutionary shifts.},
	Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	Author = {Kearney, Michael and Porter, Warren},
	Date = {APR 2009},
	Date-Added = {2009-04-20 15:32:11 +0100},
	Date-Modified = {2009-04-20 15:32:11 +0100},
	Doi = {DOI 10.1111/j.1461-0248.2008.01277.x},
	Isi = {000264067600007},
	Isi-Recid = {177963755},
	Isi-Ref-Recids = {98434187 84533918 3523009 158662050 154250301 127164622 123290413 162200510 160004313 118180737 132488521 162524863 152179348 150702345 149567580 103944401 158705059 73666867 149708427 153798252 43189633 137153425 121617491 151073207 145780688 118133611 103727769 143757907 129686602 158734231 171770065 87248379 129044241 69773136 37394591 124654617 4351102 81907948 172431834 152260846 152486983 177963756 137481846 172998127 40294116 45632264 116616302 161724244 16334842 128250931 144470456 114960615 37394575 149981978 172488379 157354663 99848839 152486985 95833468 131013604 161724250 132636212 160037830 52459791 127179872 153481701 87522517 23434316 17227194 117911909 177963757 28736699 116233991 134646044 43858136 129635551 108735736 159018084 23112589 54497576 161971162 94782486 97173101 132624207 30090238 59232042 177963758 156341344 148326927},
	Journal = {Ecology Letters},
	Keywords = {Biophysical ecology; climate; fundamental niche; geographical information systems; microclimate; physiological ecology; realized niche; species distribution modelling},
	Month = {APR},
	Number = {4},
	Pages = {334-350},
	Publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	Timescited = {0},
	Title = {Mechanistic niche modelling: combining physiological and spatial data to predict species' ranges},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000264067600007},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01277.x}}

@article{Lawler.Shafer.ea.2009.a,
	Abstract = {Climate change is predicted to be one of the greatest drivers of ecological change in the coming century. Increases in temperature over the last century have clearly been linked to shifts in species distributions. Given the magnitude of projected future climatic changes, we can expect even larger range shifts in the coming century. These changes will, in turn, alter ecological communities and the functioning of ecosystems. Despite the seriousness of predicted climate change, the uncertainty in climate-change projections makes it difficult for conservation managers and planners to proactively respond to climate stresses. To address one aspect of this uncertainty, we identified predictions of faunal change for which a high level of consensus was exhibited by different climate models. Specifically, we assessed the potential effects of 30 coupled atmosphere-ocean general circulation model (AOGCM) future-climate simulations on the geographic ranges of 2954 species of birds, mammals, and amphibians in the Western Hemisphere. Eighty percent of the climate projections based on a relatively low greenhouse-gas emissions scenario result in the local loss of at least 10\% of the vertebrate fauna over much of North and South America. The largest changes in fauna are predicted for the tundra, Central America, and the Andes Mountains where, assuming no dispersal constraints, specific areas are likely to experience over 90\% turnover, so that faunal distributions in the future will bear little resemblance to those of today.},
	Address = {1990 M STREET NW, STE 700, WASHINGTON, DC 20036 USA},
	Author = {Lawler, Joshua J. and Shafer, Sarah L. and White, Denis and Kareiva, Peter and Maurer, Edwin P. and Blaustein, Andrew R. and Bartlein, Patrick J.},
	Date = {MAR 2009},
	Date-Added = {2009-04-20 15:31:06 +0100},
	Date-Modified = {2009-04-20 15:31:06 +0100},
	Isi = {000263776800002},
	Isi-Recid = {177014909},
	Isi-Ref-Recids = {130032091 152115711 145906958 129746827 124704726 127654676 86815089 155102212 121151946 77045880 159259761 148215481 145780688 145231726 143037178 157503094 4351102 120150781 156727663 151247660 146300673 177014910 158533130 134537099 129284329 127654672 144706642 116944955 109605871 126110725 109283576 105541146 127580979 152154559 158775841 144790682 135840804 131013604 124151722 148142512 119470571 142663313 104652165 142104629 129901396 120150783 177014911 83847309 156911754 137301762 132624207 144745203 177014912 149283914 137494572 131360414 143852304},
	Journal = {Ecology},
	Keywords = {amphibians; birds; climate change; climate envelope models; future projections; mammals; range shifts; species distributions},
	Month = {MAR},
	Number = {3},
	Pages = {588-597},
	Publisher = {ECOLOGICAL SOC AMER},
	Timescited = {0},
	Title = {Projected climate-induced faunal change in the Western Hemisphere},
	Volume = {90},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000263776800002}}

@article{Tjorve.Tjorve.2008.a,
	Abstract = {The power model, S = cA(z) ( where S is number of species, A is area, and c and z are fitted constants), is the model most commonly fitted to species-area data assessing species diversity. We use the self-similarity properties of this model to reveal patterns implicated by the z parameter. We present the basic arithmetic leading both to the fraction of new species added when two areas are combined and to species overlap between two areas of the same size, given a continuous sampling scheme. The fraction of new species resulting from expansion of an area can be expressed as a alpha(z) - 1, where alpha is the expansion factor. Consequently, z-values can be converted to a scale-invariant species overlap between two equally sized areas, since the proportion of species in common between the two areas is 2 - 2(z). Calculating overlap when adding areas of the same size reveals the intrinsic effect of distance assumed by the bisectional scheme. We use overlap - area relationships from empirical data sets to illustrate how answers to the single large or several small reserves (SLOSS) question vary between data sets and with scale. We conclude that species overlap and the effect of distance between sample areas or isolates should be addressed when discussing species - area relationships, and lack of fit to the power model can be caused by its assumption of a scale-invariant overlap relationship.},
	Address = {1990 M STREET NW, STE 700, WASHINGTON, DC 20036 USA},
	Author = {Tj{\o}rve, Even and Tj{\o}rve, Kathleen M. Calf},
	Date = {DEC 2008},
	Date-Added = {2009-04-20 14:53:42 +0100},
	Date-Modified = {2009-04-20 14:55:32 +0100},
	Isi = {000261524000026},
	Isi-Recid = {174919711},
	Isi-Ref-Recids = {51166781 109923722 71409011 174919712 61425752 108986359 37595607 28370960 131181868 103180413 109519233 119282907 124419334 40252364 42230289 129210415 135910253 171821617 125804735 126608087 134240791 113305462 133260510 134240795 126774946 133992943 116849189 92086885 37222111 97496805 29697030 132488514 42841113 129835357 147207362 129808186},
	Journal = {Ecology},
	Keywords = {power law; self-similarity; single large or several small reserves; SLOSS; species-area relationship; species overlap; z-value},
	Month = {DEC},
	Number = {12},
	Pages = {3528-3533},
	Publisher = {ECOLOGICAL SOC AMER},
	Timescited = {0},
	Title = {The Species-Area relationship, self-similarity, and the true meaning of the z-value},
	Volume = {89},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000261524000026}}

@article{Burns.McHardy.ea.2009.a,
	Author = {Kevin C. Burns and R. Paul McHardy and Shirley Pledger},
	Date-Added = {2009-04-20 14:52:20 +0100},
	Date-Modified = {2009-04-20 14:52:54 +0100},
	Journal = {Ecography},
	Title = {The small-island effect: fact or artefact?},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Leek.Storey.2008.a,
	Abstract = {We develop a general framework for performing large-scale significance testing in the presence of arbitrarily strong dependence. We derive a low-dimensional set of random vectors, called a dependence kernel, that fully captures the dependence structure in an observed high-dimensional dataset. This result shows a surprising reversal of the "curse of dimensionality" in the high-dimensional hypothesis testing setting. We show theoretically that conditioning on a dependence kernel is sufficient to render statistical tests independent regardless of the level of dependence in the observed data. This framework for multiple testing dependence has implications in a variety of common multiple testing problems, such as in gene expression studies, brain imaging, and spatial epidemiology.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Leek, Jeffrey T. and Storey, John D.},
	Date = {DEC 2 2008},
	Date-Added = {2009-04-20 14:50:07 +0100},
	Date-Modified = {2009-04-20 14:50:07 +0100},
	Doi = {DOI 10.1073/pnas.0808709105},
	Isi = {000261489100022},
	Isi-Recid = {175028289},
	Isi-Ref-Recids = {7078644 122752833 90155838 150022304 112926028 130593191 134121278 130238762 175028290 158636564 46411338 154289665 158086869 104912088 122812035 134168640 144949150 151470011 110773747 158086871 95243179 174495957 90186174 69613185 150090009 132525499 126051257 130864652 119668320 96259290 131788612 112504865},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {empirical null; false discovery rate; latent structure; simultaneous inference; surrogate variable analysis},
	Month = {DEC 2},
	Number = {48},
	Pages = {18718-18723},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {0},
	Title = {A general framework for multiple testing dependence},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000261489100022},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0808709105}}

@article{Drakare.Lennon.ea.2006.a,
	Abstract = {Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Drakare, Stina and Lennon, Jack J. and Hillebrand, Helmut},
	Date = {FEB 2006},
	Date-Added = {2009-04-20 14:48:23 +0100},
	Date-Modified = {2009-04-20 14:48:54 +0100},
	Doi = {DOI 10.1111/j.1461-0248.2005.00848.x},
	Isi = {000234799700014},
	Isi-Recid = {148352402},
	Isi-Ref-Recids = {145780548 122598499 862277 124990879 133570649 143779596 123961518 37595607 121382941 78849522 148352403 126071446 102396793 105006642 112528818 97319132 124658694 862353 136847547 135840809 137283220 86389612 98912130 119282907 144119950 109519233 124419334 97697053 133803689 118180789 126318645 113685467 137283221 145456443 121261181 129210415 131638254 109030702 134939302 100968856 122706012 125804735 123004260 14833701 126608087 123729315 115351537 50798003 8122103 124297842 142663313 132488482 61209000 135910195 118180794 92086885 119924641 136847490 131638228 122598511 117444828 143779576 132624207 107136012 129835357 145135778 125853637},
	Journal = {Ecology Letters},
	Keywords = {body size; latitudinal gradients; meta-analysis; power-law; spatial scale; species-area-curve},
	Month = {FEB},
	Number = {2},
	Pages = {215-227},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {62},
	Title = {The imprint of the geographical, evolutionary and ecological context on species-area relationships},
	Volume = {9},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000234799700014},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2005.00848.x}}

@article{Thorpe.2009.a,
	Abstract = {Anthropogenic processes are responsible for between 55\% and 70\% of the estimated 600 Tg of methane that is released annually into the atmosphere, with enteric fermentation a major contributor to emissions in a number of countries. This paper therefore reviews current levels of CH4 discharges by both animal type and country, and shows how the growth or decline in national herds over the last 20 years has significantly altered the global composition of enteric emissions. As developing countries are now responsible for almost three-quarters of such emissions, this has important implications in terms of mitigation strategies-particularly as such countries are presently outside the remit of the Kyoto Protocol.},
	Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
	Author = {Thorpe, Andy},
	Date = {APR 2009},
	Date-Added = {2009-04-20 14:47:25 +0100},
	Date-Modified = {2009-04-20 14:47:25 +0100},
	Doi = {DOI 10.1007/s10584-008-9506-x},
	Isi = {000264477100008},
	Isi-Recid = {178565359},
	Isi-Ref-Recids = {178565360 178565361 178565362 147469983 178565363 178565364 178565365 178565366 178565367 145442060 178565368 178565369 178565370 133086922 155550465 178565371 178565372 178565373 121969214 120220739 157177569 158396399 107526628 178565374 178565375 178565376 178565377 178565378 178565379 178565380 178565381 171414615 178565382 178565383 159871493 178565384 178565385 135912457 83227301 56144618 145637234 178565386 11697171 137211854 106435894 122270616 61762530 178565387 80751540 177613674 76676542 159871528 178565388 178565389 99550235 124794298 112722019 178565390 92408562 96977434 178565391 38469259 34870902 159871634 105096266 71980540 159871489 71811147 178565392 113086980 151847605 159871505 85651504 197092 111469747 107087488 116118269 87625564 33914348 42282542 144948879 115881689 178565393 111339297 178565394 143048184 111343814 94206966 142397910 178565395 172269374 125801765 178565396 178565397 43438761 118823996 136627024},
	Journal = {Climatic Change},
	Month = {APR},
	Number = {3-4},
	Pages = {407-431},
	Publisher = {SPRINGER},
	Timescited = {0},
	Title = {Enteric fermentation and ruminant eructation: the role (and control?) of methane in the climate change debate},
	Volume = {93},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000264477100008},
	Bdsk-Url-2 = {http://dx.doi.org/10.1007/s10584-008-9506-x}}

@article{Melo.Rangel.ea.2009.a,
	Author = {Adriano S. Melo and Thiago Fernando L. V. B. Rangel and Jos{\'e} Alexandre F. Diniz-Filho},
	Date-Added = {2009-04-20 14:43:41 +0100},
	Date-Modified = {2009-04-20 14:44:32 +0100},
	Journal = {Ecography},
	Title = {Environmental drivers of beta-diversity patterns in New-World birds and mammals},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{McCain.2009.a,
	Abstract = {In 1967, Daniel Janzen proposed the influential, but largely untested hypothesis, that tropical mountain passes are physiologically higher than temperate mountains. I test his key prediction, the one upon which all the others rely: namely, that elevational range sizes of organisms get larger on mountains at increasing latitudes. My analyses use 170 montane gradients spanning 36.5S to 48.2N latitude compiled from over 80 years of research and 16500 species of rodents, bats, birds, lizards, snakes, salamanders, and frogs. In support of Janzen's prediction, I find that elevational range size increases with increasing latitude for all vertebrate groups except rodents. I document additional lines of evidence for temperature variability as a plausible mechanism for trends in vertebrate range size, including strong effects of thermoregulation and daily temperature variability, and a weak effect of precipitation.},
	Author = {Christy M. McCain},
	Date-Added = {2009-04-20 12:22:25 +0100},
	Date-Modified = {2009-04-20 12:23:37 +0100},
	Journal = {Ecology Letters},
	Title = {Vertebrate range sizes indicate that mountains may be 'higher' in the tropics},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Santos.Coloma.ea.2009.a,
	Abstract = {The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Choco resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.},
	Address = {Section of Integrative Biology and Texas Natural Science Center, The University of Texas, Austin, TX, USA. jcsantos@mail.utexas.edu},
	Author = {Santos, Juan C and Coloma, Luis A and Summers, Kyle and Caldwell, Janalee P and Ree, Richard and Cannatella, David C},
	Crdt = {2009/03/13 09:00},
	Da = {20090402},
	Date = {2009 Mar 10},
	Date-Added = {2009-04-20 10:37:48 +0100},
	Date-Modified = {2009-06-02 12:06:14 +0100},
	Doi = {10.1371/journal.pbio.1000056},
	Edat = {2009/03/13 09:00},
	Issn = {1545-7885 (Electronic)},
	Jid = {101183755},
	Journal = {PLoS Biology},
	Jt = {PLoS biology},
	Language = {eng},
	Mhda = {2009/03/13 09:00},
	Month = {Mar},
	Number = {3},
	Oid = {NLM: PMC2653552},
	Own = {NLM},
	Pages = {e56},
	Phst = {2008/04/07 {$[$}received{$]$}; 2009/01/26 {$[$}accepted{$]$}},
	Pii = {08-PLBI-RA-1340},
	Pl = {United States},
	Pmc = {PMC2653552},
	Pmid = {19278298},
	Pst = {ppublish},
	Pt = {Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.},
	Sb = {IM},
	Status = {In-Process},
	Title = {Amazonian amphibian diversity is primarily derived from late Miocene Andean lineages.},
	Volume = {7},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pbio.1000056}}

@article{Woodruff.Turner.2009.a,
	Abstract = {
Aim We describe the distributions of mammal species between the Indochinese 
and Sundaic subregions and examine the traditional view that the two faunas 
show a transition near the Isthmus of Kra on the Thai--Malay peninsula. 
Location Species distributions are described along a 2000-km transect from 
20$\,^{\circ}$ N (northernmost Thailand) to 1$\,^{\circ}$ N (Singapore). 
Methods For the 325 species of native non-marine mammals occurring along 
the transect we used published records to provide a database of their 
distributional records by degree of latitude. 
Results Along the transect we found 128 Indochinese species with southern 
range limits, 121 Sundaic species with northern range limits, four un-assignable 
endemics and 72 widespread species. In total, 152 southern and 147 northern 
range limits were identified, and their distribution provides no evidence for a 
narrow faunal transition near the Isthmus of Kra (10$\,^{\circ}$30¢ N) or elsewhere. Range 
limits of both bats and non-volant mammals cluster in northernmost peninsular 
Malaysia (5$\,^{\circ}$ N) and 800 km further north, where the peninsula joins the 
continent proper (14$\,^{\circ}$ N). The clusters of northern and southern range limits are 
not concordant but overlap by 100--200 km. Similarly, the range limits of bats 
and non-volant mammals cluster at slightly different latitudes. There are 30% 
fewer species and range limits in the central and northern peninsula (between 6 
and 13$\,^{\circ}$ N), and 35 more widely distributed species have range gaps in this 
region. In addition, we found 70 fewer species at the southern tip of the peninsula 
(1$\,^{\circ}$ N) than at 3--4$\,^{\circ}$ N. 
Main conclusions The deficiencies of both species and species range limits in 
the central and northern peninsula are attributed to an area effect caused by 
repeated sea-level changes. Using a new global glacioeustatic curve developed by 
Miller and associates we show that there were > 58 rapid sea-level rises of > 40 m 
in the last 5 Myr that would have resulted in significant faunal compression and 
local population extirpation in the narrow central and northern parts of the 
peninsula. This new global sea-level curve appears to account for the observed 
patterns of the latitudinal diversity of mammal species, the concentration of 
species range limits north and south of this area, the nature and position 
of the transition between biogeographical subregions, and possibly the divergence 
of the faunas themselves during the Neogene. The decline of species diversity at 
the southern end of the transect is attributed to a peninsula effect similar to that 
described elsewhere. 
},
	Author = {Woodruff, David S. and Turner, Leslie M.},
	Date-Added = {2009-04-20 10:18:08 +0100},
	Date-Modified = {2009-04-20 10:24:39 +0100},
	Journal = {Journal of Biogeography},
	Number = {5},
	Pages = {803-821},
	Title = {The Indochinese-Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions},
	Volume = {36},
	Year = {2009},
	Bdsk-File-1 = { }}

@article{Caughley.Grice.ea.1988.a,
	Abstract = {(1) We suggest a theoretical framework for considering limits to relatively stable distributions and illustrate some of the points raised with information on the distribution of two species of kangaroos. (2) If an attribute such as density or condition is low at the periphery but rises progressively towards the core of the distribution, its trend is described as a `ramp'. If the level of the attribute differs little between the periphery and the core of the distribution its trend forms a `step' at the range boundary. (3) Should density form a ramp inwards from the boundary whereas the mean well-being of the animals (e.g. body condition, growth, weight, recruitment) forms a step, the factor limiting distribution is likely to be a resource that is utilized consumptively or pre-emptively. (4) Should both density and well-being form a ramp, the implicated factor is a component of climate, an unmodifiable resource, or a facultative predator, parasite or pathogen. (5) Should both density and well-being step at the range boundary, the factor controlling the position of the boundary is likely to be the substrate (e.g. a rock type). (6) Two kangaroo populations were sampled at the core and periphery of their respective ranges. The southern (=`western') grey kangaroo Macropus fuliginosus (Desmarest) exhibited a ramp of both density and well-being which, in combination with ecological information on this species, suggested that the edge of the range was positioned by a component of climate perhaps interacting with an unmodifiable resource. (7) The eastern grey kangaroo Macropus giganteus Shaw exhibited a ramp of density but a step of well-being, implicating a renewable resource as the factor determining the inland boundary of distribution. (8) Density and distribution are likely to be different aspects of the same thing except where the limiting factor or combination of factors is or includes a renewable resource consumed by the animals.},
	Author = {Caughley, G. and Grice, D. and Barker, R. and Brown, B.},
	Copyright = {Copyright {\copyright} 1988 British Ecological Society},
	Date-Added = {2009-04-07 13:57:58 +0100},
	Date-Modified = {2009-04-07 13:58:44 +0100},
	Issn = {00218790},
	Journal = {The Journal of Animal Ecology},
	Jstor_Articletype = {primary_article},
	Jstor_Formatteddate = {Oct., 1988},
	Number = {3},
	Pages = {771--785},
	Publisher = {British Ecological Society},
	Title = {The Edge of the Range},
	Url = {http://www.jstor.org/stable/5092},
	Volume = {57},
	Year = {1988},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.jstor.org/stable/5092}}

@incollection{Purvis.Orme.ea.2009.a,
	Author = {Purvis, Andy and Orme, C. David L. and Toomey, Nicola H. and Pearson, Paul N.},
	Booktitle = {Speciation and Patterns of Diversity},
	Chapter = {15},
	Crossref = {Butlin.Bridle.ea.2009.a},
	Date-Added = {2009-04-01 17:47:10 +0100},
	Date-Modified = {2009-04-01 17:48:32 +0100},
	Pages = {278-300},
	Title = {Temporal patterns in diversification rates},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@book{Butlin.Bridle.ea.2009.a,
	Author = {Butlin, Roger K. and Bridle, Jon R. and Schluter, Dolph},
	Date-Added = {2009-04-01 17:40:54 +0100},
	Date-Modified = {2009-04-01 17:44:01 +0100},
	Editor = {Butlin, Roger K. and Bridle, Jon R. and Schluter, Dolph},
	Publisher = {Cambridge University Press},
	Title = {Speciation and Patterns of Diversity},
	Year = {2009}}

@article{Cassemiro.Barreto.ea.2007.a,
	Author = {Cassemiro , Fernanda Aparecida da Silva and Barreto, Bruno de Souza and Rangel, Thiago Fernando L. V. B. and Diniz-Filho, Jos{\'e} Alexandre Felizola},
	Date-Added = {2009-03-19 21:46:38 +0000},
	Date-Modified = {2009-03-19 21:50:45 +0000},
	Journal = {Global Ecology and Biogeography},
	Number = {6},
	Pages = {820-822},
	Title = {Non-stationarity, diversity gradients and the metabolic theory of ecology},
	Volume = {16},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Moore.Donoghue.2009.a,
	Abstract = {Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction). We describe a Bayesian approach for evaluating the correlation between such events and differential rates of diversification that relies on cross-validation predictive densities. This approach exploits estimates of the marginal posterior probability for the rate of diversification (in the unaffected part of the tree) and the marginal probability for the timing of the event to generate a predictive distribution of species diversity that would be expected had the event not occurred. The realized species diversity can then be compared to this predictive diversity distribution to assess whether rates of diversification associated with the event are significantly higher or lower than expected. Although simple, this Bayesian approach provides a robust inference framework that accommodates various sources of uncertainty, including error associated with estimates of divergence times, diversification-rate parameters, and event history. Furthermore, the proposed approach is relatively flexible, allowing exploration of various types of events (including changes in discrete morphological traits, episodes of biogeographic movement, etc.) under both hypothesis-testing and data-exploration inference scenarios. Importantly, the cross-validation predictive densities approach facilitates evaluation of both replicated and unique historical events. We demonstrate this approach with empirical examples concerning the impact of morphological and biogeographic events on rates of diversification in Adoxaceae and , respectively.
},
	Author = {Moore, Brian R. and Donoghue, Michael J.},
	Date-Added = {2009-03-18 13:33:09 +0000},
	Date-Modified = {2009-03-18 13:33:15 +0000},
	Doi = {10.1073/pnas.0807230106},
	Eprint = {http://www.pnas.org/content/106/11/4307.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {11},
	Pages = {4307-4312},
	Title = {{A Bayesian approach for evaluating the impact of historical events on rates of diversification}},
	Url = {http://www.pnas.org/content/106/11/4307.abstract},
	Volume = {106},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/106/11/4307.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0807230106}}

@article{Bolker.Brooks.ea.2009.a,
	Abstract = {How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.},
	Address = {Department of Botany and Zoology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA.},
	Author = {Bolker, BM and Brooks, ME and Clark, CJ and Geange, SW and Poulsen, JR and Stevens, MH and White, JS},
	Crdt = {2009/02/03 09:00},
	Da = {20090202},
	Date = {2009 Jan 28},
	Date-Added = {2009-02-23 17:47:28 +0000},
	Date-Modified = {2009-10-16 14:31:31 +0100},
	Dep = {20090128},
	Doi = {10.1016/j.tree.2008.10.008},
	Edat = {2009/02/03 09:00},
	Issn = {0169-5347 (Print)},
	Jid = {8805125},
	Journal = {Trends In Ecology \& Evolution},
	Jt = {Trends in ecology \& evolution (Personal edition)},
	Language = {ENG},
	Mhda = {2009/02/03 09:00},
	Month = {Jan},
	Own = {NLM},
	Phst = {2008/06/27 {$[$}received{$]$}; 2008/09/30 {$[$}revised{$]$}; 2008/10/08 {$[$}accepted{$]$}},
	Pii = {S0169-5347(09)00019-6},
	Pmid = {19185386},
	Pst = {aheadofprint},
	Pt = {JOURNAL ARTICLE},
	Status = {Publisher},
	Title = {Generalized linear mixed models: a practical guide for ecology and evolution.},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tree.2008.10.008}}

@article{Jablonski.2008.a,
	Abstract = { Species selection in the broad sense---also termed species sorting---shapes evolutionary patterns through differences in speciation and extinction rates (and their net outcome, often termed the emergent fitness of clades) that arise by interaction of intrinsic biological traits with the environment. Effect-macroevolution occurs when those biotic traits, such as body size or fecundity, reside at the organismic level. Strict-sense species selection occurs when those traits are emergent at the species level, such as geographic range or population size. The fields of paleontology, comparative phylogenetic analysis, macroecology, and conservation biology are rich in examples of species sorting, but relatively few instances have been well documented, so the extent and efficacy of the specific processes remain poorly known. A general formalization of these processes remains challenging, but approaches drawing on hierarchical covariance models appear promising. Analyses integrating paleontological and neontological data for a single set of clades would be especially powerful. },
	Author = {Jablonski, David},
	Date-Added = {2009-02-23 17:45:37 +0000},
	Date-Modified = {2009-02-23 17:46:07 +0000},
	Doi = {10.1146/annurev.ecolsys.39.110707.173510},
	Eprint = {http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.39.110707.173510},
	Journal = {Annual Review of Ecology, Evolution, and Systematics},
	Number = {1},
	Pages = {501-524},
	Title = {Species Selection: Theory and Data},
	Url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.39.110707.173510},
	Volume = {39},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.39.110707.173510},
	Bdsk-Url-2 = {http://dx.doi.org/10.1146/annurev.ecolsys.39.110707.173510}}

@article{Olson.Davies.ea.2009.a,
	Abstract = {In 1847, Karl Bergmann proposed that temperature gradients are the key to understanding geographic variation in the body sizes of warm-blooded animals. Yet both the geographic patterns of body-size variation and their underlying mechanisms remain controversial. Here, we conduct the first assemblage-level global examination of 'Bergmann's rule' within an entire animal class. We generate global maps of avian body size and demonstrate a general pattern of larger body sizes at high latitudes, conforming to Bergmann's rule. We also show, however, that median body size within assemblages is systematically large on islands and small in species-rich areas. Similarly, while spatial models show that temperature is the single strongest environmental correlate of body size, there are secondary correlations with resource availability and a strong pattern of decreasing body size with increasing species richness. Finally, our results suggest that geographic patterns of body size are caused both by adaptation within lineages, as invoked by Bergmann, and by taxonomic turnover among lineages. Taken together, these results indicate that while Bergmann's prediction based on physiological scaling is remarkably accurate, it is far from the full picture. Global patterns of body size in avian assemblages are driven by interactions between the physiological demands of the environment, resource availability, species richness and taxonomic turnover among lineages.},
	Author = {Olson, Val{\'e}rie A. and Davies, Richard G. and Orme, C. David L. and Thomas, Gavin H. and Meiri, Shai and Blackburn, Tim M. and Gaston, Kevin J. and Owens, Ian P. F. and Bennett, Peter M.},
	Date = {2009 %@ 1461-0248 %+ Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK; Institute of Zoology, Zoological Society of London, Regents Park, London NW1 4RY, UK; School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK; Biodiversity and Macroecology Group, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK; Division of Biology, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK; NERC Centre for Population Biology, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK; School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, Kent CT2 7NR, UK},
	Date-Added = {2009-02-23 11:54:36 +0000},
	Date-Modified = {2009-02-23 11:57:48 +0000},
	Journal = {Ecology Letters},
	Number = {3},
	Pages = {249-259},
	Refer1 = {10.1111/j.1461-0248.2009.01281.x},
	Title = {Global biogeography and ecology of body size in birds},
	Url = {http://dx.doi.org/10.1111/j.1461-0248.2009.01281.x},
	Volume = {12},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1461-0248.2009.01281.x}}

@article{Adams.Church.2008.a,
	Abstract = {The tendency for organisms to be larger in cooler climates (Bergmann's rule) is widely observed in endotherms, and has been reputed to apply to some ectotherms including amphibians. However, recent reports provide conflicting support for the pattern, questioning whether Bergmann's clines are generally present in amphibians. In this study, we measured 96,996 adult Plethodon from 3974 populations to test for the presence of Bergmann's clines in these salamanders. Only three Plethodon species exhibited a significant negative correlation between body size and temperature consistent with Bergmann's rule, whereas 37 of 40 species did not display a pattern consistent with this prediction. Further, a phylogenetic comparative analysis found no relationship between body size and temperature among species. A meta-analysis combining our data with the available data for other amphibian species revealed no support for Bergmann's rule at the genus (Plethodon), order (Caudata), or class (Amphibia) levels. Our findings strongly suggest that negative thermal body size clines are not common in amphibians, and we conclude that Bergmann's rule is not generally applicable to these taxa. Thus, evolutionary explanations of Bergmann's clines in other tetrapods need not account for unique life-history attributes of amphibians.},
	Address = {Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA. dcadams@iastate.edu},
	Author = {Adams, Dean C and Church, James O},
	Crdt = {2007/11/15 09:00},
	Da = {20080227},
	Date = {2008 Feb},
	Date-Added = {2009-02-19 07:32:51 +0000},
	Date-Modified = {2009-02-19 07:52:20 +0000},
	Dcom = {20080425},
	Dep = {20071112},
	Doi = {10.1111/j.1558-5646.2007.00297.x},
	Edat = {2007/11/15 09:00},
	Issn = {0014-3820 (Print)},
	Jid = {0373224},
	Journal = {Evolution},
	Jt = {Evolution; international journal of organic evolution},
	Language = {eng},
	Lr = {20081121},
	Mh = {Adaptation, Biological; Amphibians; Animals; *Body Size; Body Temperature; Classification; Climate; Evolution; Evolution, Molecular; Geography; *Models, Genetic; Species Specificity; Temperature; United States; Urodela/*anatomy \& histology/*genetics},
	Mhda = {2008/04/26 09:00},
	Month = {Feb},
	Number = {2},
	Own = {NLM},
	Pages = {413--420},
	Phst = {2007/11/12 {$[$}aheadofprint{$]$}},
	Pii = {EVO297},
	Pl = {United States},
	Pmid = {17999723},
	Pst = {ppublish},
	Pt = {Journal Article; Research Support, U.S. Gov't, Non-P.H.S.},
	Sb = {IM},
	Status = {MEDLINE},
	Title = {{Amphibians do not follow Bergmann's rule.}},
	Volume = {62},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2007.00297.x}}

@article{Lubchenko.1978.a,
	Author = {Lubchenko, Jane},
	Date-Added = {2009-01-23 16:00:19 +0000},
	Date-Modified = {2009-01-23 16:01:13 +0000},
	Journal = {American Naturalist},
	Number = {983},
	Pages = {23-39},
	Title = {Plant Species Diversity in a Marine Intertidal Community: Importance of Herbivore FoodPreference and Algal Competitive Abilities},
	Volume = {112},
	Year = {1978},
	Bdsk-File-1 = { }}

@article{Daniel.Boyden.1975.a,
	Author = {Daniel, M J and Boyden, C R},
	Date-Added = {2009-01-23 15:57:39 +0000},
	Date-Modified = {2009-01-23 15:59:23 +0000},
	Journal = {Field Studies},
	Pages = {161-176},
	Title = {Diurnal variations in physico-chemical conditions within intertidal rockpools},
	Volume = {4},
	Year = {1975},
	Bdsk-File-1 = { }}

@article{Buckland.Burnham.ea.1997.a,
	Abstract = {We argue that model selection uncertainty should be fully incorporated into statistical inference whenever estimation is sensitive to model choice and that choice is made with reference to the data. We consider different philosophies for achieving this goal and suggest strategies for data analysis. We illustrate our methods through three examples. The first is a Poisson regression of bird counts in which a choice is to be made between inclusion of one or both of two covariates. The second is a line transect data set for which different models yield substantially different estimates of abundance. The third is a simulated example in which truth is known.},
	Author = {Buckland, S. T. and Burnham, K. P. and Augustin, N. H.},
	Copyright = {Copyright {\copyright} 1997 International Biometric Society},
	Date-Added = {2009-01-16 16:04:27 +0000},
	Date-Modified = {2009-01-16 16:04:32 +0000},
	Issn = {0006341X},
	Journal = {Biometrics},
	Jstor_Articletype = {primary_article},
	Jstor_Formatteddate = {Jun., 1997},
	Number = {2},
	Pages = {603--618},
	Publisher = {International Biometric Society},
	Title = {Model Selection: An Integral Part of Inference},
	Url = {http://www.jstor.org/stable/2533961},
	Volume = {53},
	Year = {1997},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.jstor.org/stable/2533961}}

@article{Mundry.Nunn.2009.a,
	Abstract = { Abstract: Statistical inference based on stepwise model selection is applied regularly in ecological, evolutionary, and behavioral research. In addition to fundamental shortcomings with regard to finding the best model, stepwise procedures are known to suffer from a multiple-testing problem, yet the method is still widely used. As an illustration of this problem, we present results of a simulation study of artificial data sets of uncorrelated variables, with two to 10 predictor variables and one dependent variable. We then compared results from stepwise regression with a regression model in which all predictor variables were entered simultaneously. These analyses clearly demonstrate that significance tests based on stepwise procedures lead to greatly inflated Type I error rates (i.e., the probability of erroneously rejecting a true null hypothesis). By using a simple simulation design, our study amplifies previous warnings about using stepwise procedures, and we follow others in recommending that biologists refrain from applying these methods. },
	Author = {Mundry, Roger and Nunn, Charles L.},
	Date-Added = {2008-12-18 14:35:16 +0000},
	Date-Modified = {2008-12-18 14:35:20 +0000},
	Doi = {10.1086/593303},
	Eprint = {http://www.journals.uchicago.edu/doi/pdf/10.1086/593303},
	Journal = {The American Naturalist},
	Note = {PMID: 19049440},
	Number = {1},
	Pages = {119-123},
	Title = {Stepwise Model Fitting and Statistical Inference: Turning Noise into Signal Pollution.},
	Url = {http://www.journals.uchicago.edu/doi/abs/10.1086/593303},
	Volume = {173},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.journals.uchicago.edu/doi/abs/10.1086/593303},
	Bdsk-Url-2 = {http://dx.doi.org/10.1086/593303}}

@book{Pilgrim.2004.a,
	Author = {Pilgrim, Mark},
	Date-Added = {2008-12-15 12:03:25 +0000},
	Date-Modified = {2008-12-15 12:04:11 +0000},
	Publisher = {Apress},
	Title = {Dive into Python},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@manual{McCoy.2004.a,
	Author = {McCoy, Jill},
	Date-Added = {2008-12-15 11:54:00 +0000},
	Date-Modified = {2008-12-15 11:55:07 +0000},
	Organization = {ESRI},
	Title = {{Geoprocessing in ArcGIS}},
	Year = {2004},
	Bdsk-File-1 = { }}

@manual{Tucker.2004.a,
	Author = {Tucker, Corey},
	Date-Added = {2008-12-15 11:52:30 +0000},
	Date-Modified = {2008-12-15 11:53:33 +0000},
	Organization = {ESRI},
	Title = {Writing Geoprocessing Scripts},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Foote.Crampton.ea.2008.a,
	Abstract = {Geographic range and taxonomic duration are known to be positively correlated in a number of biologic groups; this is usually attributed to the influence of range upon duration rather than the other way about. Here we analyze two distinct components of this correlation within species and genera of marine invertebrates and microfossils by partitioning the total duration into two parts: the time it takes a taxon to attain its maximum geographic range, and the time a taxon persists after attaining its peak range. We find that the longer it takes a taxon to attain its maximum geographic range, the wider is that range. We also find that the broader the maximum range, the greater is the duration after this maximum is attained. These two correlations are equally strong on average. There is thus a reciprocal relationship between duration and geographic range, and there is no compelling evidence that range generally determines duration more or less than duration determines range.},
	Address = {810 EAST 10TH ST, LAWRENCE, KS 66044 USA},
	Author = {Foote, Michael and Crampton, James S. and Beu, Alan G. and Cooper, Roger A.},
	Date = {FAL 2008},
	Date-Added = {2008-12-11 12:10:52 +0000},
	Date-Modified = {2008-12-11 12:13:07 +0000},
	Doi = {10.1666/08023.1},
	Journal = {Paleobiology},
	Pages = {421-433},
	Publisher = {PALEONTOLOGICAL SOC INC},
	Timescited = {0},
	Title = {On the bidirectional relationship between geographic range and taxonomic duration},
	Volume = {34},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1666/08023.1}}

@book{Dominus.2005.a,
	Author = {Dominus, Mark Jason},
	Date-Added = {2008-12-10 16:45:51 +0000},
	Date-Modified = {2008-12-10 16:46:54 +0000},
	Publisher = {Morgan Kaufmann},
	Title = {Higher-Order Perl},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Jetz.Kreft.ea.2009.a,
	Abstract = {In both ecology and conservation, often a strong positive association is assumed between the diversity of plants as primary producers and that of animals, specifically primary consumers. Such a relationship has been observed at small spatial scales, and a begetting of diversity by diversity is expected under various scenarios of co-evolution and co-adaptation. But positive producer--consumer richness relationships may also arise from similar associations with past opportunities for diversification or contemporary environmental conditions, or from emerging properties of plant diversity such as vegetation complexity or productivity. Here we assess whether the producer--consumer richness relationship generalizes from plot to regional scale and provide a first global test of its strength for vascular plants and endothermic vertebrates. We find strong positive richness associations, but only limited congruence of the most diverse regions. The richness of both primary and higher-level consumers increases with plant richness at similar strength and rate. Environmental conditions emerge as much stronger predictors of consumer richness, and after accounting for environmental differences little variation is explained by plant diversity. We conclude that biotic interactions and strong local associations between plants and consumers only relatively weakly scale up to broad geographical scales and to functionally diverse taxa, for which environmental constraints on richness dominate.},
	Author = {Jetz, Walter and Kreft, Holger and Ceballos, Gerardo and Mutke, Jens},
	Date-Added = {2008-12-10 10:02:43 +0000},
	Date-Modified = {2010-01-28 17:49:27 +0000},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	M3 = {10.1098/rspb.2008.1005},
	Number = {1655},
	Pages = {269--278},
	Rating = {0},
	Title = {Global associations between terrestrial producer and vertebrate consumer diversity},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1098/rspb.2008.1005},
	Volume = {276},
	Year = {2009},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-File-3 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2008.1005}}

@article{Damschen.Brudvig.ea.2008.a,
	Abstract = {A conceptual model of movement ecology has recently been advanced to explain all movement by considering the interaction of four elements: internal state, motion capacity, navigation capacities, and external factors. We modified this framework to generate predictions for species richness dynamics of fragmented plant communities and tested them in experimental landscapes across a 7-year time series. We found that two external factors, dispersal vectors and habitat features, affected species colonization and recolonization in habitat fragments and their effects varied and depended on motion capacity. Bird-dispersed species richness showed connectivity effects that reached an asymptote over time, but no edge effects, whereas wind-dispersed species richness showed steadily accumulating edge and connectivity effects, with no indication of an asymptote. Unassisted species also showed increasing differences caused by connectivity over time, whereas edges had no effect. Our limited use of proxies for movement ecology (e.g., dispersal mode as a proxy for motion capacity) resulted in moderate predictive power for communities and, in some cases, highlighted the importance of a more complete understanding of movement ecology for predicting how landscape conservation actions affect plant community dynamics.
},
	Author = {Damschen, Ellen I. and Brudvig, Lars A. and Haddad, Nick M. and Levey, Douglas J. and Orrock, John L. and Tewksbury, Joshua J.},
	Date-Added = {2008-12-10 09:54:08 +0000},
	Date-Modified = {2008-12-10 09:54:13 +0000},
	Doi = {10.1073/pnas.0802037105},
	Eprint = {http://www.pnas.org/content/105/49/19078.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {49},
	Pages = {19078-19083},
	Title = {{The movement ecology and dynamics of plant communities in fragmented landscapes}},
	Url = {http://www.pnas.org/content/105/49/19078.abstract},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/105/49/19078.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0802037105}}

@inproceedings{Purvis.Orme.2005.a,
	Address = {Berlin},
	Author = {Purvis, Andy and Orme, C. David L.},
	Booktitle = {Deciphering Growth},
	Date-Added = {2008-12-09 09:43:59 +0000},
	Date-Modified = {2008-12-09 09:47:43 +0000},
	Editor = {Carel, Jean-Claude and Kelly, Paul A and Christen, Yves},
	Pages = {1-18},
	Publisher = {Springer-Verlag},
	Series = {Research and Perspectives on Endocrine Interactions},
	Title = {Evolutionary Trends in Body Size},
	Year = {2005},
	Bdsk-File-1 = { }}

@manual{Cooper.2004.a,
	Author = {Cooper, Mendel},
	Date-Added = {2008-11-21 14:38:06 +0000},
	Date-Modified = {2008-11-21 14:38:54 +0000},
	Edition = {2.8},
	Title = {Advanced Bash-Scripting Guide},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Isaac.Cowlishaw.2004.a,
	Abstract = {It is well established that different species vary in their vulnerability to extinction risk and that species biology can underpin much of this variation. By contrast, very little is known about how the same species responds to different threat processes. The purpose of this paper is therefore twofold: to examine the extent to which a species' vulnerability to different types of threat might covary and to explore the biological traits that are associated with threat-specific responses. We use an objective and quantitative measure of local extinction risk to show that vulnerability to local population decline in primates varies substantially among species and between threat types. Our results show that a species' response to one threat type does not predict its response to others. Multivariate analyses also suggest that different mechanisms of decline are associated with each type of threat, since different biological traits are correlated with each threat-specific response. Primate species at risk from forestry tend to exhibit low ecological flexibility, while those species vulnerable to agriculture tend to live in the canopy and eat low-fruit diets, in further contrast, primates at risk from hunting tend to exhibit large body size. Our analyses therefore indicate that a species' vulnerability to local extinction can be highly variable and is likely to depend on both threat type and biology.},
	Address = {6 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Isaac, NJB and Cowlishaw, G},
	Date = {JUN 7 2004},
	Date-Added = {2008-11-17 09:31:36 +0000},
	Date-Modified = {2008-11-17 09:32:31 +0000},
	Doi = {DOI 10.1098/rspb.2004.2724},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {extinction risk; hunting; habitat disturbance; primates},
	Pages = {1135-1141},
	Publisher = {ROYAL SOC LONDON},
	Timescited = {17},
	Title = {How species respond to multiple extinction threats},
	Volume = {271},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2004.2724}}

@incollection{He.Condit.2007.a,
	Author = {He, Fangliang and Condit, Rick},
	Booktitle = {Scaling Biodiversity},
	Crossref = {Storch.Marquet.ea.2007.a},
	Date-Added = {2008-11-16 17:37:45 +0000},
	Date-Modified = {2008-11-16 17:39:16 +0000},
	Pages = {32 - 50},
	Title = {The distribution of species: occupancy, scale, and rarity}}

@book{Storch.Marquet.ea.2007.a,
	Address = {Cambridge},
	Author = {Storch, David and Marquet, Pablo A. and Brown, James H},
	Date-Added = {2008-11-16 17:25:26 +0000},
	Date-Modified = {2008-11-16 17:37:37 +0000},
	Editor = {Storch, David and Marquet, Pablo A. and Brown, James H},
	Publisher = {Cambridge University Press},
	Title = {Scaling Biodiversity},
	Year = {2007}}

@article{Prendergast.Quinn.ea.1993.a,
	Abstract = {SPECIES conservation in situ requires networks of protected areas selected for high conservation interest1-3. Throughout most of the world, however, there are neither the resources nor the time to carry out detailed inventories for most taxa2,4 before designating protected areas. Site selection (on grounds other than availability) would be easier and more effective if two things were true: (1) habitats that are species-rich for one taxon are also species-rich for others5; and (2) rare1 species occur in, and therefore benefit from the conservation of, species-rich habitats. Diversity (usually, species richness) and the presence of rare species are the most frequently cited criteria for site selection by conservationists6-8. Here, we use data on British plants and animals held by the Biological Records Centre (BRC)9 and the British Trust for Ornithology (BTO), mapped on a grid of 10 km x 10 km ('10 km squares') to examine the extent to which species-rich areas for different taxa coincide, and whether species-rich areas contain substantial numbers of rare species. The fine scale and high intensity of recording in Britain produces distributional datasets at least as good as and, in most cases, better than those available elsewhere. For Britain at least, we do not find strong support for either proposition. Species-rich areas ('hotspots'10) frequently do not coincide for different taxa, and many rare species do not occur in the most species-rich squares.},
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON, ENGLAND N1 9XW},
	Author = {Prendergast, J R and Quinn, R M and Lawton, John H and Eversham, B C and Gibbons, D W},
	Date = {SEP 23 1993},
	Date-Added = {2008-11-16 12:44:06 +0000},
	Date-Modified = {2008-11-16 12:44:11 +0000},
	Journal = {Nature},
	Pages = {335-337},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Timescited = {504},
	Title = {Rare species, the coincidence of diversity hotspots and conservation strategies},
	Volume = {365},
	Year = {1993},
	Bdsk-File-1 = { }}

@article{Buckley.Jetz.2008.a,
	Abstract = {Patterns of species turnover are central to the geography of biodiversity and resulting challenges for conservation, but at broad scales remain relatively little understood. Here, we take a first spatially-explicitly and global perspective to link the spatial turnover of species and environments. We compare how major groups of vertebrate ectotherms (amphibians) and endotherms (birds) respond to spatial environmental gradients. We find that high levels of species turnover occur regardless of environmental turnover rates, but environmental turnover provides a lower bound for species turnover. This lower bound increases more steeply with environmental turnover in tropical realms. While bird and amphibian turnover rates are correlated, the rate of amphibian turnover is four times steeper than bird rates. This is the same factor by which average geographic ranges of birds are larger than those of amphibians. Narrow-ranged birds exhibit rapid rates of species turnover similar to those for amphibians, while wide-ranged birds largely drive the aggregate patterns of avian turnover. We confirm a strong influence of the environment on species turnover that is mediated by range sizes and regional history. In contrast to geographic patterns of species richness, we find that the turnover in one group (amphibians) is a much better predictor for the turnover in another (birds) than is environment. This result confirms the role of amphibian sensitivity to environmental conditions for patterns of turnover and supports their value as a surrogate group. This spatially-explicit analysis of environmental turnover provides understanding for conservation planning in changing environments.
},
	Author = {Buckley, Lauren B. and Jetz, Walter},
	Date-Added = {2008-11-12 09:47:09 +0000},
	Date-Modified = {2008-11-12 09:47:57 +0000},
	Doi = {10.1073/pnas.0803524105},
	Eprint = {http://www.pnas.org/content/early/2008/11/10/0803524105.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {46},
	Pages = {17836 --17841},
	Title = {{Linking global turnover of species and environments}},
	Url = {http://www.pnas.org/content/early/2008/11/10/0803524105.abstract},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/early/2008/11/10/0803524105.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0803524105}}

@article{Sahr.White.ea.2003.a,
	Author = {Sahr, Kevin and White, Denis and Kimerling, A. Jon},
	Date-Added = {2008-10-30 14:04:35 +0000},
	Date-Modified = {2008-10-30 14:05:57 +0000},
	Journal = {Cartography and Geographic Information Science},
	Number = {2},
	Pages = {121-134},
	Title = {Geodesic Discrete Global Grid Systems},
	Volume = {30},
	Year = {2003},
	Bdsk-File-1 = { }}

@article{Meiri.2008.a,
	Abstract = {Aim  Body size is instrumental in influencing animal physiology, morphology, ecology and evolution, as well as extinction risk. I examine several hypotheses regarding the influence of body size on lizard evolution and extinction risk, assessing whether body size influences, or is influenced by, species richness, herbivory, island dwelling and extinction risk.Location   World-wide.Methods   I used literature data and measurements of museum and live specimens to estimate lizard body size distributions.Results   I obtained body size data for 99% of the world's lizard species. The body size2013frequency distribution is highly modal and right skewed and similar distributions characterize most lizard families and lizard assemblages across biogeographical realms. There is a strong negative correlation between mean body size within families and species richness. Herbivorous lizards are larger than omnivorous and carnivorous ones, and aquatic lizards are larger than non-aquatic species. Diurnal activity is associated with small body size. Insular lizards tend towards both extremes of the size spectrum. Extinction risk increases with body size of species for which risk has been assessed.Main conclusions   Small size seems to promote fast diversification of disparate body plans. The absence of mammalian predators allows insular lizards to attain larger body sizes by means of release from predation and allows them to evolve into the top predator niche. Island living also promotes a high frequency of herbivory, which is also associated with large size. Aquatic and nocturnal lizards probably evolve large size because of thermal constraints. The association between large size and high extinction risk, however, probably reflects a bias in the species in which risk has been studied. a},
	Author = {Meiri, Shai},
	Date-Added = {2008-10-30 11:41:41 +0000},
	Date-Modified = {2008-10-30 11:42:43 +0000},
	Doi = {10.1111/j.1466-8238.2008.00414.x},
	Journal = {Global Ecology and Biogeography},
	Number = {6},
	Pages = {724-734},
	Title = {Evolution and ecology of lizard body sizes},
	Url = {http://dx.doi.org/10.1111/j.1466-8238.2008.00414.x},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2008.00414.x}}

@article{Cadotte.Cardinale.ea.2008.a,
	Abstract = {Loss of biological diversity because of extinction is one of the most pronounced changes to the global environment. For several decades, researchers have tried to understand how changes in biodiversity might impact biomass production by examining how biomass correlates with a number of biodiversity metrics (especially the number of species and functional groups). This body of research has focused on species with the implicit assumption that they are independent entities. However, functional and ecological similarities are shaped by patterns of common ancestry, such that distantly related species might contribute more to production than close relatives, perhaps by increasing niche breadth. Here, we analyze 2 decades of experiments performed in grassland ecosystems throughout the world and examine whether the evolutionary relationships among the species comprising a community predict how biodiversity impacts plant biomass production. We show that the amount of phylogenetic diversity within communities explained significantly more variation in plant community biomass than other measures of diversity, such as the number of species or functional groups. Our results reveal how evolutionary history can provide critical information for understanding, predicting, and potentially ameliorating the effects of biodiversity loss and should serve as an impetus for new biodiversity experiments.
},
	Author = {Cadotte, Marc W. and Cardinale, Bradley J. and Oakley, Todd H.},
	Date-Added = {2008-10-30 11:07:01 +0000},
	Date-Modified = {2008-10-30 11:07:39 +0000},
	Doi = {10.1073/pnas.0805962105},
	Eprint = {http://www.pnas.org/content/early/2008/10/28/0805962105.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {44},
	Pages = {17012 - 17017},
	Title = {{Evolutionary history and the effect of biodiversity on plant productivity}},
	Url = {http://www.pnas.org/content/early/2008/10/28/0805962105.abstract},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/early/2008/10/28/0805962105.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0805962105}}

@article{Bremer.Bremer.ea.2003.a,
	Abstract = {A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pandanales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids 1), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae, (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae, and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae, and Amaryllidaceae in Alliaceae s.l., Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l., Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l. (C) 2003 The Linnean Society of London.},
	Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
	Author = {Bremer, B and Bremer, K and Chase, MW and Reveal, JL and Soltis, DE and Soltis, PS and Stevens, PF and Anderberg, AA and Fay, MF and Goldblatt, P and Judd, WS and Kallersjo, M and Karehed, J and Kron, KA and Lundberg, J and Nickrent, DL and Olmstead, RG and Oxelman, B and Pires, JC and Rodman, JE and Rudall, PJ and Savolainen, V and Sytsma, KJ and van der Bank, M and Wurdack, K and Xiang, JQY and Zmarzty, S},
	Date = {APR 2003},
	Date-Added = {2008-10-22 17:56:14 +0100},
	Date-Modified = {2008-10-22 17:57:28 +0100},
	Journal = {Botanical Journal of the Linnean Society},
	Keywords = {angiosperms; gene sequences; phylogenetics},
	Pages = {399-436},
	Publisher = {ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD},
	Timescited = {670},
	Title = {An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: {APG II}},
	Volume = {141},
	Year = {2003}}

@article{Fox.Monette.1992.a,
	Abstract = {Working in the context of the linear model y = X-beta + epsilon, we generalize the concept of variance inflation as a measure of collinearity to a subset of parameters in beta (denoted by beta-1 with the associated columns of X given by X1). The essential idea underlying this generalization is to examine the impact on the precision of estimation-in particular, the size of an ellipsoidal joint confidence region for beta-1-of less-than-optimal selection of other columns of the design matrix (X2), treating still other columns (X0) as unalterable, even hypothetically. In typical applications, X1 contains a set of dummy regressors coding categories of a qualitative variable or a set of polynomial regressors in a quantitative variable; X2 contains all other regressors in the model, save the constant, which is in X0. If sigma-2V denotes the realized variance of beta-1 and sigma-2U is the variance associated with an optimal selection of X2, then the corresponding scaled dispersion ellipsoids to be compared are E(V), = {x : x'V-1x less-than-or-equal-to 1} and E(U) = {x : x'U-1x less-than-or-equal-to 1}, where E(U) is contained in E(V). The two ellipsoids can be compared by considering the radii of E(V) relative to E(U), obtained through the spectral decomposition of V relative to U. We proceed to explore the geometry of generalized variance inflation, to show the relationship of these measures to correlation-matrix determinants and canonical correlations, to consider X matrices structured by relations of marginality among regressor subspaces, to develop the relationship of generalized variance inflation to hypothesis tests in the multivariate normal linear model, and to present several examples.},
	Address = {1429 DUKE ST, ALEXANDRIA, VA 22314},
	Author = {Fox, John and Monette, George},
	Date = {MAR 1992},
	Date-Added = {2008-10-22 17:52:40 +0100},
	Date-Modified = {2008-10-22 17:55:22 +0100},
	Journal = {Journal of the American Statistical Association},
	Keywords = {CANONICAL CORRELATION; JOINT CONFIDENCE REGIONS; SPECTRAL DECOMPOSITION; VARIANCE INFLATION},
	Pages = {178-183},
	Publisher = {AMER STATISTICAL ASSOC},
	Timescited = {18},
	Title = {GENERALIZED COLLINEARITY DIAGNOSTICS},
	Volume = {87},
	Year = {1992},
	Bdsk-File-1 = { }}

@article{Rahbek.Gotelli.ea.2007.a,
	Abstract = {The causes of global variation in species richness have been debated for nearly two centuries with no clear resolution in sight. Competing hypotheses have typically been evaluated with correlative models that do not explicitly incorporate the mechanisms responsible for biotic diversity gradients. Here, we employ a fundamentally different approach that uses spatially explicit Monte Carlo models of the placement of cohesive geographical ranges in an environmentally heterogeneous landscape. These models predict species richness of endemic South American birds ( 2248 species) measured at a continental scale. We demonstrate that the principal single-factor and composite ( species-energy, water-energy and temperature-kinetics) models proposed thus far fail to predict ( r(2) <= 0.05) the richness of species with small to moderately large geographical ranges ( first three range-size quartiles). These species constitute the bulk of the avifauna and are primary targets for conservation. Climate-driven models performed reasonably well only for species with the largest geographical ranges ( fourth quartile) when range cohesion was enforced. Our analyses suggest that present models inadequately explain the extraordinary diversity of avian species in the montane tropics, the most species-rich region on Earth. Our findings imply that correlative climatic models substantially underestimate the importance of historical factors and small-scale niche-driven assembly processes in shaping contemporary species-richness patterns.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Rahbek, Carsten and Gotelli, Nicholas J. and Colwell, Robert K. and Entsminger, Gary L. and Rangel, Thiago Fernando L. V. B. and Graves, Gary R.},
	Date = {JAN 22 2007},
	Date-Added = {2008-10-22 17:48:44 +0100},
	Date-Modified = {2008-10-22 17:49:04 +0100},
	Doi = {DOI 10.1098/rspb.2006.3700},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {diversity gradients; South American avifauna; climate-based models; species richness patterns; mid-domain effect; spatially explicit stochastic models},
	Pages = {165-174},
	Publisher = {ROYAL SOCIETY},
	Timescited = {20},
	Title = {Predicting continental-scale patterns of bird species richness with spatially explicit models},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2006.3700}}

@article{Martin.Goldenfeld.2006.a,
	Abstract = {We present an explanation for the widely reported power-law species-area relationship (SAR), which relates the area occupied by a biome to the number of species that it supports. We argue that power-law SARs are a robust consequence of a skewed species abundance distribution resembling a lognormal with higher rarity, together with the observation that individuals of a given species tend to cluster. We show that the precise form of the SAR transcends the specific details of organism interactions, enabling us to characterize its broad trends across taxa.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Martin, Hector Garcia and Goldenfeld, Nigel},
	Date = {JUL 5 2006},
	Date-Added = {2008-10-22 17:46:14 +0100},
	Date-Modified = {2008-10-22 17:46:37 +0100},
	Doi = {DOI 10.1073/pnas.0510605103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {clustering; lognormal},
	Pages = {10310-10315},
	Publisher = {NATL ACAD SCIENCES},
	Rating = {0},
	Timescited = {9},
	Title = {On the origin and robustness of power-law species-area relationships in ecology},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0510605103}}

@article{Fahrig.2003.a,
	Abstract = {The literature on effects of habitat fragmentation on biodiversity is huge. It is also very diverse, with different authors measuring fragmentation in different ways and, as a consequence, drawing different conclusions regarding both the magnitude and direction of its effects. Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat. Results of empirical studies of habitat fragmentation are often difficult to interpret because (a) many researchers measure fragmentation at the patch scale, not the landscape scale and (b) most researchers measure fragmentation in ways that do not distinguish between habitat loss and habitat fragmentation per se, i.e., the breaking apart of habitat after controlling for habitat loss. Empirical studies to date suggest that habitat loss has large, consistently negative effects on biodiversity. Habitat fragmentation per se has much weaker effects on biodiversity that are at least as likely to be positive as negative. Therefore, to correctly interpret the influence of habitat fragmentation on biodiversity, the effects of these two components of fragmentation must be measured independently. More studies of the independent effects of habitat loss and fragmentation per se are needed to determine the factors that lead to positive versus negative effects of fragmentation per se. I suggest that the term "fragmentation" should be reserved for the breaking apart of habitat, independent of habitat loss.},
	Address = {4139 EL CAMINO WAY, PO BOX 10139, PALO ALTO, CA 94303-0139 USA},
	Author = {Fahrig, L},
	Date = {2003},
	Date-Added = {2008-10-22 17:44:08 +0100},
	Date-Modified = {2008-10-22 17:44:42 +0100},
	Doi = {DOI 10.1146/annurev.ecolsys.34.011802.132419},
	Journal = {Annual Review of Ecology Evolution and Systematics},
	Keywords = {habitat loss; landscape scale; habitat configuration; patch size; patch isolation; extinction threshold; landscape complementation},
	Pages = {487-515},
	Publisher = {ANNUAL REVIEWS},
	Timescited = {360},
	Title = {Effects of habitat fragmentation on biodiversity},
	Volume = {34},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.ecolsys.34.011802.132419}}

@article{Southwood.May.ea.2006.a,
	Abstract = {We observe a relationship among three independently derived power laws in ecology: (i) total number of species versus area, (ii) species frequency versus species length, and (iii) maximal body size versus area. Aside from showing how these historically disparate phenomena are connected, we show how recent empirical results relating the maximal body size of top terrestrial vertebrates to the square root of land area conform to a prior theoretical expectation given by two of the above power laws. Of particular interest is the observation that the exponent relating species length to species frequency suggests a dimension for niche space for terrestrial vertebrate assemblages of D approximate to 3/2. This value, along with power law for maximal body size, versus area, gives rise to the canonical species area exponent z approximate to 1/4.},
	Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
	Author = {Southwood, T Richard E and May, Robert M and Sugihara, George},
	Date = {MAY 2 2006},
	Date-Added = {2008-10-22 17:38:15 +0100},
	Date-Modified = {2008-10-22 17:39:52 +0100},
	Doi = {DOI 10.1073/pnas.0600988103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {scaling; power law; dimensionality; species-area; canonical hypothesis},
	Pages = {6931-6933},
	Publisher = {NATL ACAD SCIENCES},
	Timescited = {5},
	Title = {Observations on related ecological exponents},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0600988103}}

@article{Dormann.McPherson.ea.2007.a,
	Abstract = {Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species' distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Dormann, Carsten F. and McPherson, Jana M. and Araujo, Miguel B. and Bivand, Roger and Bolliger, Janine and Carl, Gudrun and Davies, Richard G. and Hirzel, Alexandre and Jetz, Walter and Kissling, W. Daniel and Kuehn, Ingolf and Ohlemueller, Ralf and Peres-Neto, Pedro R. and Reineking, Bjoern and Schroeder, Boris and Schurr, Frank M. and Wilson, Robert},
	Date = {OCT 2007},
	Date-Added = {2008-10-20 10:54:30 +0100},
	Date-Modified = {2008-10-20 11:34:11 +0100},
	Doi = {DOI 10.1111/j.2007.0906-7590.05171.x},
	Journal = {Ecography},
	Pages = {609-628},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {19},
	Title = {Methods to account for spatial autocorrelation in the analysis of species distributional data: a review},
	Volume = {30},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.2007.0906-7590.05171.x}}

@article{Losos.2008.a,
	Abstract = {Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Losos, Jonathan B.},
	Date = {OCT 2008},
	Date-Added = {2008-10-13 12:28:03 +0100},
	Date-Modified = {2008-10-13 12:28:21 +0100},
	Doi = {DOI 10.1111/j.1461-0248.2008.01229.x},
	Journal = {Ecology Letters},
	Keywords = {phylogenetic effect; phylogenetic niche conservatism; phylogenetic signal},
	Pages = {995-1003},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {2},
	Title = {Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species},
	Volume = {11},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01229.x}}

@incollection{Foden.Mace.ea.2008.a,
	Address = {Gland, Switzerland.},
	Author = {Foden, Wendy and Mace, Georgina M. and Vie, Jean-Christophe and Angulo, Ariadne and Butchart, Stuart and DeVantier, Lyndon and Dublin, Holly T. and Gutsche Alexander and Stuart, Simon N. and Turak, Emre},
	Booktitle = {The 2008 Review of The IUCN Red List of Threatened Species},
	Date-Added = {2008-10-13 12:05:17 +0100},
	Date-Modified = {2008-10-13 12:09:22 +0100},
	Editor = {Vie, Jean-Christophe and Hilton-Taylor, Craig and Stuart, Simon N.},
	Publisher = {IUCN},
	Title = {Species susceptibility to climate change impacts},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{RobertKColwell10102008,
	Abstract = {Many studies suggest that global warming is driving species ranges poleward and toward higher elevations at temperate latitudes, but evidence for range shifts is scarce for the tropics, where the shallow latitudinal temperature gradient makes upslope shifts more likely than poleward shifts. Based on new data for plants and insects on an elevational transect in Costa Rica, we assess the potential for lowland biotic attrition, range-shift gaps, and mountaintop extinctions under projected warming. We conclude that tropical lowland biotas may face a level of net lowland biotic attrition without parallel at higher latitudes (where range shifts may be compensated for by species from lower latitudes) and that a high proportion of tropical species soon faces gaps between current and projected elevational ranges.
},
	Author = {Colwell, Robert K. and Brehm, Gunnar and Cardelus, Catherine L. and Gilman, Alex C. and Longino, John T.},
	Date-Added = {2008-10-13 12:03:17 +0100},
	Date-Modified = {2008-10-13 12:03:17 +0100},
	Doi = {10.1126/science.1162547},
	Eprint = {http://www.sciencemag.org/cgi/reprint/322/5899/258.pdf},
	Journal = {Science},
	Number = {5899},
	Pages = {258-261},
	Title = {{Global Warming, Elevational Range Shifts, and Lowland Biotic Attrition in the Wet Tropics}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/322/5899/258},
	Volume = {322},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1162547},
	Bdsk-Url-2 = {http://www.sciencemag.org/cgi/content/abstract/322/5899/258}}

@article{Schipper.Chanson.ea.2008.a,
	Abstract = {Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.
},
	Author = {Schipper, Jan and Chanson, Janice S. and Chiozza, Federica and Cox, Neil A. and Hoffmann, Michael and Katariya, Vineet and Lamoreux, John and Rodrigues, Ana S. L. and Stuart, Simon N. and Temple, Helen J. and Baillie, Jonathan and Boitani, Luigi and Lacher, Thomas E., Jr. and Mittermeier, Russell A. and Smith, Andrew T. and Absolon, Daniel and Aguiar, John M. and Amori, Giovanni and Bakkour, Noura and Baldi, Ricardo and Berridge, Richard J. and Bielby, Jon and Black, Patricia Ann and Blanc, J. Julian and Brooks, Thomas M. and Burton, James A. and Butynski, Thomas M. and Catullo, Gianluca and Chapman, Roselle and Cokeliss, Zoe and Collen, Ben and Conroy, Jim and Cooke, Justin G. and da Fonseca, Gustavo A. B. and Derocher, Andrew E. and Dublin, Holly T. and Duckworth, J. W. and Emmons, Louise and Emslie, Richard H. and Festa-Bianchet, Marco and Foster, Matt and Foster, Sabrina and Garshelis, David L. and Gates, Cormack and Gimenez-Dixon, Mariano and Gonzalez, Susana and Gonzalez-Maya, Jose Fernando and Good, Tatjana C. and Hammerson, Geoffrey and Hammond, Philip S. and Happold, David and Happold, Meredith and Hare, John and Harris, Richard B. and Hawkins, Clare E. and Haywood, Mandy and Heaney, Lawrence R. and Hedges, Simon and Helgen, Kristofer M. and Hilton-Taylor, Craig and Hussain, Syed Ainul and Ishii, Nobuo and Jefferson, Thomas A. and Jenkins, Richard K. B. and Johnston, Charlotte H. and Keith, Mark and Kingdon, Jonathan and Knox, David H. and Kovacs, Kit M. and Langhammer, Penny and Leus, Kristin and Lewison, Rebecca and Lichtenstein, Gabriela and Lowry, Lloyd F. and Macavoy, Zoe and Mace, Georgina M. and Mallon, David P. and Masi, Monica and McKnight, Meghan W. and Medellin, Rodrigo A. and Medici, Patricia and Mills, Gus and Moehlman, Patricia D. and Molur, Sanjay and Mora, Arturo and Nowell, Kristin and Oates, John F. and Olech, Wanda and Oliver, William R. L. and Oprea, Monik and Patterson, Bruce D. and Perrin, William F. and Polidoro, Beth A. and Pollock, Caroline and Powel, Abigail and Protas, Yelizaveta and Racey, Paul and Ragle, Jim and Ramani, Pavithra and Rathbun, Galen and Reeves, Randall R. and Reilly, Stephen B. and Reynolds, John E., III and Rondinini, Carlo and Rosell-Ambal, Ruth Grace and Rulli, Monica and Rylands, Anthony B. and Savini, Simona and Schank, Cody J. and Sechrest, Wes and Self-Sullivan, Caryn and Shoemaker, Alan and Sillero-Zubiri, Claudio and De Silva, Naamal and Smith, David E. and Srinivasulu, Chelmala and Stephenson, Peter J. and van Strien, Nico and Talukdar, Bibhab Kumar and Taylor, Barbara L. and Timmins, Rob and Tirira, Diego G. and Tognelli, Marcelo F. and Tsytsulina, Katerina and Veiga, Liza M. and Vie, Jean-Christophe and Williamson, Elizabeth A. and Wyatt, Sarah A. and Xie, Yan and Young, Bruce E.},
	Date-Added = {2008-10-13 12:01:51 +0100},
	Date-Modified = {2008-10-13 12:02:08 +0100},
	Doi = {10.1126/science.1165115},
	Eprint = {http://www.sciencemag.org/cgi/reprint/322/5899/225.pdf},
	Journal = {Science},
	Number = {5899},
	Pages = {225-230},
	Title = {{The Status of the World's Land and Marine Mammals: Diversity, Threat, and Knowledge}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/322/5899/225},
	Volume = {322},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/322/5899/225},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1165115}}

@article{Jetz.Freckleton.ea.2008.a,
	Author = {Jetz, Walter and Freckleton, Robert P. and McKechnie, Andrew E.},
	Date-Added = {2008-10-13 11:58:57 +0100},
	Date-Modified = {2008-10-13 11:59:53 +0100},
	Journal = {PLoS One},
	Number = {9},
	Pages = {1 - 9},
	Title = {Environment, Migratory Tendency, Phylogeny and Basal Metabolic Rate in Birds},
	Volume = {3},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Jetz.Kreft.ea.2008.a,
	Author = {Jetz, Walter and Kreft, Holger and Ceballos, Gerardo and Mutke, Jens},
	Date-Added = {2008-10-13 11:57:11 +0100},
	Date-Modified = {2008-10-13 11:58:18 +0100},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Title = {Global associations between terrestrial producer and vertebrate consumer diversity},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Emerson.Gillespie.2008.a,
	Author = {Emerson, Brent C and Gillespie, Rosemary G.},
	Date-Added = {2008-10-13 11:40:59 +0100},
	Date-Modified = {2008-10-13 11:41:33 +0100},
	Journal = {Trends In Ecology \& Evolution},
	Title = {Phylogenetic analysis of community assembly and structure over space and time},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Schwartz.2008.a,
	Author = {Schwartz, Martin A.},
	Date-Added = {2008-10-06 12:14:09 +0100},
	Date-Modified = {2008-10-06 12:14:14 +0100},
	Doi = {10.1242/jcs.033340},
	Eprint = {http://jcs.biologists.org/cgi/reprint/121/11/1771.pdf},
	Journal = {J Cell Sci},
	Number = {11},
	Pages = {1771-},
	Title = {{The importance of stupidity in scientific research}},
	Url = {http://jcs.biologists.org},
	Volume = {121},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://jcs.biologists.org},
	Bdsk-Url-2 = {http://dx.doi.org/10.1242/jcs.033340}}

@article{Thomas.Telfer.ea.2004.a,
	Abstract = {There is growing concern about increased population, regional, and global extinctions of species. A key question is whether extinction rates for one group of organisms are representative of other taxa. We present a comparison at the national scale of population and regional extinctions of birds, butterflies, and vascular plants from Britain in recent decades. Butterflies experienced the greatest net losses, disappearing on average from 13{\%} of their previously occupied 10-kilometer squares. If insects elsewhere in the world are similarly sensitive, the known global extinction rates of vertebrate and plant species have an unrecorded parallel among the invertebrates, strengthening the hypothesis that the natural world is experiencing the sixth major extinction event in its history. },
	Annote = {10.1126/science.1095046},
	Author = {Thomas, J. A. and Telfer, M. G. and Roy, D. B. and Preston, C. D. and Greenwood, J. J. D. and Asher, J. and Fox, R. and Clarke, R. T. and Lawton, J. H.},
	Date-Added = {2008-10-02 21:35:50 +0100},
	Date-Modified = {2008-10-02 21:35:50 +0100},
	Journal = {Science},
	Journal1 = {Science},
	Number = {5665},
	Pages = {1879--1881},
	Title = {Comparative Losses of British Butterflies, Birds, and Plants and the Global Extinction Crisis},
	Ty = {JOUR},
	Url = {http://www.sciencemag.org/cgi/content/abstract/303/5665/1879},
	Volume = {303},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/303/5665/1879}}

@article{Blackburn.Gaston.2006.a,
	Abstract = {Macroecology sits at the junction of, and can contribute to, the fields of ecology, biogeography, palaeontology and macroevolution, using a broad range of approaches to tackle a diverse set of questions. Here, we argue that there is more to macroecology than mapping, and that while they are potentially useful, maps are insufficient to assess macroecological pattern and process. The true nature of pattern can only be assessed, and competing hypotheses about process can only be disentangled, by adopting a statistical approach, and it is this that has been key to the development of macroecology as a respected and rigorous scientific discipline.},
	Author = {Blackburn, T. M. and Gaston, K. J.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Global Ecology and Biogeography},
	Number = {6},
	Pages = {537-540},
	Title = {There's more to macroecology than meets the eye},
	Volume = {15},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Burgess.Balmford.ea.2007.a,
	Abstract = {This paper explores whether spatial variation in the biodiversity values of vertebrates and plants (species richness, range-size rarity and number or proportion of IUCN Red Listed threatened species) of three African tropical mountain ranges (Eastern Arc, Albertine Rift and Cameroon-Nigeria mountains within the Biafran Forests and Highlands) co-vary with proxy measures of threat (human population density and human infrastructure). We find that species richness, range-size rarity, and threatened species scores are all significantly higher in these three tropical African mountain ranges than across the rest of sub-Saharan Africa. When compared with the rest of sub-Saharan Africa, human population density is only significantly higher in the Albertine Rift mountains, whereas human infrastructure is only significantly higher in the Albertine Rift and the Cameroon-Nigeria mountains. Statistically there are strong positive correlations between human density and species richness, endemism and density or proportion of threatened species across the three tropical African mountain ranges, and all of sub-Saharan Africa. Kendall partial rank-order correlation shows that across the African tropical mountains human population density, but not human infrastructure, best correlates with biodiversity values. This is not the case across all of sub-Saharan Africa where human density and human infrastructure both correlate almost equally well with biodiversity values. The primary conservation challenge in the African tropical mountains is a fairly dense and poor rural population that is reliant on farming for their livelihood. Conservation strategies have to address agricultural production and expansion, in some cases across the boundaries and into existing reserves. Strategies also have to maintain, or finalise, an adequate protected area network. Such strategies cannot be implemented in conflict with the local population, but have to find ways to provide benefits to the people living adjacent to the remaining forested areas, in return for their assistance in conserving the forest habitats, their biodiversity, and their ecosystem functions. (c) 2006 Elsevier Ltd. All rights reserved.},
	Author = {Burgess, N. D. and Balmford, A. and Cordeiro, N. J. and Fjeldsa, J. and Kuper, W. and Rahbek, C. and Sanderson, E. W. and Scharlemann, J. P. W. and Sommer, J. H. and Williams, P. H.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Biological Conservation},
	Note = {Times Cited: 6},
	Pages = {164-177},
	Title = {Correlations among species distributions, human density and human infrastructure across the high biodiversity tropical mountains of Africa},
	Volume = {134},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Conlisk.Bloxham.ea.2007.a,
	Abstract = {We analyze a new class of models of spatial distribution, developing mathematical properties and performing empirical tests. The models are based on a simple colonization rule operating on a rectangular grid. Two special cases within the class are traditional random placement and negative binomial models. Over three large data sets, these two cases are strongly outperformed by more flexible models within the class, in particular, models that allow more general patterns of aggregation. The models are simple and broadly applicable, with only one adjustable parameter, representing aggregation. Shortcomings of the colonization rule are studied, and extensions and applications of the models are discussed.},
	Author = {Conlisk, E. and Bloxham, M. and Conlisk, J. and Enquist, B. and Harte, J.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecological Monographs},
	Number = {2},
	Pages = {269-284},
	Title = {A new class of models of spatial distribution},
	Volume = {77},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Green.Harte.ea.2003.a,
	Abstract = {Although scaling relationships that characterize fractal species distributions offer an exciting potential for unification in biogeography, empirical support for fractal theory remains the subject of debate. We synthesize and test multiple predictions of two interrelated fractal models and a null model of random placement using Californian serpentine grassland data describing the spatial location of over 37 000 individually identified plants. The endemics- area relationship and species-abundance distribution recently derived from a community-level fractal property performed poorly because of an inaccurate assumption of homogeneity among species. In contrast, a species-level fractal model that incorporates species-level differences predicted abundances well, but systematically overestimated endemism and predicted a species - area relationship that violated the observed power law. These findings indicate that in order to make predictions based on the existence of a power-law species - area relationship, ecologists need a unifying theory of how the community-level fractal property arises in the presence of species-level distributional differences.},
	Author = {Green, J. L. and Harte, J. and Ostling, A.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecology Letters},
	Number = {10},
	Pages = {919-928},
	Title = {Species richness, endemism and abundance patterns: tests of two fractal models in a serpentine grassland},
	Volume = {6},
	Year = {2003},
	Bdsk-File-1 = { }}

@article{Halley.Hartley.ea.2004.a,
	Abstract = {Fractals have found widespread application in a range of scientific fields, including ecology. This rapid growth has produced substantial new insights, but has also spawned confusion and a host of methodological problems. In this paper, we review the value of fractal methods, in particular for applications to spatial ecology, and outline potential pitfalls. Methods for measuring fractals in nature and generating fractal patterns for use in modelling are surveyed. We stress the limitations and the strengths of fractal models. Strictly speaking, no ecological pattern can be truly fractal, but fractal methods may nonetheless provide the most efficient tool available for describing and predicting ecological patterns at multiple scales.},
	Author = {Halley, J. M. and Hartley, S. and Kallimanis, A. S. and Kunin, W. E. and Lennon, J. J. and Sgardelis, S. P.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecology Letters},
	Number = {3},
	Pages = {254-271},
	Title = {Uses and abuses of fractal methodology in ecology},
	Volume = {7},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Harte.Conlisk.ea.2005.a,
	Abstract = {A theory of spatial structure in ecological communities is presented and tested. At the core of the theory is a simple allocation rule for the assembly of species in space. The theory leads, with no adjustable parameters, to nonrandorn statistical predictions for the spatial distribution of species at multiple spatial scales. The distributions are such that the abundance of a species at the largest measured scale uniquely determines the spatial-abundance distribution of the individuals of that species at smaller spatial scales. The shape of the species-area relationship, the endemics-area relationship, a scale-dependent community-level spatial-abundance distribution, the species-abundance distribution at small spatial scales, an index of intraspecific aggregation, the range-area relationship, and the dependence of species turnover on interpatch distance and on patch size are also uniquely predicted as a function solely of the list of abundances of the species at the largest spatial scale. We show that the spatial structure of three spatially explicit vegetation census data sets (i.e., a 64-m(2) serpentine grassland plot, a 50-ha moist. tropical forest plot, and a 9.68-ha dry tropical forest plot) are generally consistent with the predictions of the theory, despite the very simple statistical assumption upon which the theory is based, and the absence of adjustable parameters. However, deviations between predicted and observed distributions do arise for the species with the highest abundances; the pattern of those deviations indicates that the theory, which currently contains no explicit description of interaction mechanisms among individuals within species, could be improved with the incorporation of intraspecific density dependence.},
	Author = {Harte, J. and Conlisk, E. and Ostling, A. and Green, J. L. and Smith, A. B.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecological Monographs},
	Number = {2},
	Pages = {179-197},
	Title = {A theory of spatial structure in ecological communities at multiple spatial scales},
	Volume = {75},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Hickling.Roy.ea.2005.a,
	Abstract = {Many species are predicted to shift their ranges to higher latitudes and altitudes in response to climate warming. This study presents evidence for 37 species of nonmigratory British dragonflies and damselflies shifting northwards at their range margins over the past 40 years, seemingly as a result of climate change. This response by an exemplar group of insects associated with fresh water, parallels polewards range changes observed in terrestrial invertebrates and other taxa.},
	Author = {Hickling, R. and Roy, D. B. and Hill, J. K. and Thomas, C. D.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Global Change Biology},
	Number = {3},
	Pages = {502-506},
	Title = {A northward shift of range margins in British Odonata},
	Volume = {11},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Hickling.Roy.ea.2006.a,
	Abstract = {Evidence is accumulating of shifts in species' distributions during recent climate warming. However, most of this information comes predominantly from studies of a relatively small selection of taxa (i.e., plants, birds and butterflies), which may not be representative of biodiversity as a whole. Using data from less well-studied groups, we show that a wide variety of vertebrate and invertebrate species have moved northwards and uphill in Britain over approximately 25 years, mirroring, and in some cases exceeding, the responses of better-known groups.},
	Author = {Hickling, R. and Roy, D. B. and Hill, J. K. and Fox, R. and Thomas, C. D.},
	Date = {MAR},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Di = {10.1111/j.1365-2486.2006.01116.x},
	Isi = {ISI:000236023000004},
	Issn = {1354-1013},
	Journal = {GLOBAL CHANGE BIOLOGY},
	Month = {Mar},
	Number = {3},
	Pages = {450--455},
	Publication-Type = {J},
	Title = {The distributions of a wide range of taxonomic groups are expanding polewards},
	Volume = {12},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Hui.McGeoch.2007.a,
	Abstract = {Species distributions are commonly measured as the number of sites, or geographic grid cells occupied. These data may then be used to model species distributions and to examine patterns in both intraspecific and interspecific distributions. Harte et al. (1999) used a model based on a bisection rule and assuming self-similarity in species distributions to do so. However, this approach has also been criticized for several reasons. Here we show that the self-similarity in species distributions breaks down according to a power relationship with spatial scales, and we therefore adopt a power-scaling assumption for modeling species occupancy distributions. The outcomes of models based on these two assumptions (self-similar and power-scaling) have not previously been compared. Based on Harte's bisection method and an occupancy probability transition model under these two assumptions (self-similar and power-scaling), we compared the scaling pattern of occupancy (also known as the area-of-occupancy) and the spatial distribution of species. The two assumptions of species distribution lead to a relatively similar interspecific occupancy frequency distribution pattern, although the spatial distribution of individual species and the scaling pattern of occupancy differ significantly. The bimodality in occupancy frequency distributions that is common in species communities, is confirmed to a result for certain mathematical and statistical properties of the probability distribution of occupancy. The results thus demonstrate that the use of the bisection method in combination with a power-scaling assumption is more appropriate for modeling species distributions than the use of a self-similarity assumption, particularly at fine scales.},
	Author = {Hui, C. and McGeoch, M. A.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Oikos},
	Number = {12},
	Pages = {2097-2107},
	Title = {Modeling species distributions by breaking the assumption of self-similarity},
	Volume = {116},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Kalmar.Currie.2007.a,
	Abstract = {How many species in a given taxon should be found in a delimited area in a specified place in the world? Some recent literature suggests that the answer to this question depends strongly on the geographical, evolutionary, and ecological context. For example, current theory suggests that species accumulate as a function of area differently on continents and islands. Species richness-climate relationships have been examined separately on continents and on islands. This study tests the hypotheses that (1) the functional relationship between richness and climate is the same on continents and islands; (2) the species-area slope depends on distance-based isolation; (3) species-area relationships differ among land bridge islands, oceanic islands, and continents; (4) richness differs among biogeographic regions independently of climate and isolation. We related bird species numbers in a worldwide sample of 240 continental parcels and 346 islands to several environmental variables. We found that breeding bird richness varies similarly on islands and on continents as a function of mean annual temperature, an area X precipitation interaction, and the distance separating insular samples from the nearest continent (R-2 = 0.86). Most studies to date have postulated that the slope of the species-area relationship depends upon isolation. In contrast, we found no such interaction. A richness-environment relationship derived using 2 Old World sites accurately predicts patterns of richness in the New World and vice versa (R-2 = 0.85). Our results suggest that most of the global variation in richness is not strongly context-specific; rather, it reflects a small number of general environmental constraints operating on both continents and islands.},
	Author = {Kalmar, A. and Currie, D. J.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecology},
	Number = {5},
	Pages = {1309-1321},
	Title = {A unified model of avian species richness on islands and continents},
	Volume = {88},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Kerr.Kharouba.ea.2007.a,
	Abstract = {Anthropogenic global changes threaten species and the ecosystem services upon which society depends. Effective solutions to this multifaceted crisis need scientific responses spanning disciplines and spatial scales. Macroecology develops broad-scale predictions of species' distributions and abundances, complementing the frequently local focus of global change biology. Macroecological discoveries rely particularly on correlative methods but have still proven effective in predicting global change impacts on species. However, global changes create pseudo-experimental opportunities to build stronger, mechanistic theories in macroecology that successfully predict multiple phenomena across spatial scales. Such macroecological perspectives will help address the biotic consequences of global change.
},
	Author = {Kerr, Jeremy T. and Kharouba, Heather M. and Currie, David J.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-04 21:15:56 +0100},
	Doi = {10.1126/science.1133267},
	Eprint = {http://www.sciencemag.org/cgi/reprint/316/5831/1581.pdf},
	Journal = {Science},
	Number = {5831},
	Pages = {1581-1584},
	Rating = {0},
	Title = {{The Macroecological Contribution to Global Change Solutions}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/316/5831/1581},
	Volume = {316},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/316/5831/1581},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1133267}}

@article{Kunin.Hartley.ea.2000.a,
	Author = {Kunin, W. E. and Hartley, S. and Lennon, J. J.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {American Naturalist},
	Number = {5},
	Pages = {560-566},
	Title = {Scaling down: On the challenge of estimating abundance from occurrence patterns},
	Volume = {156},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Lennon.Kunin.ea.2002.a,
	Abstract = {Aim Species generally become rarer and more patchily distributed as the margins of their ranges are approached. We predicted that in such marginal sites, tree species would tend to occur where some key environmental factors are at particularly favourable levels, compensating in part for the low overall suitability of marginal sites. Location The article considers the spatial distributions of trees in Southeast Alaska (the Alaskan 'panhandle'). Methods We quantified range marginality using spatial distributions of eight tree species across more than one thousand surveyed sites in Southeast Alaska. For each species we derived a site core/margin index using a three-dimensional trend surface generated from logistic regression on site coordinates. For each species, the relationships between the environmental factors slope, aspect and site marginality were then compared for occupied and unoccupied sets of sites. Results We found that site slope is important for more Alaskan tree species than aspect. Three out of eight had a significant core/margin by occupied/unoccupied interaction, tending to be present in significantly shallower-sloped (more favourable) sites in the marginal areas than the simple core/margin trend predicted. For site aspect, one species had a significant interaction, selecting potentially more favourable northerly aspects in marginal areas. A finer-scale analysis based on the same data came to the same overall conclusions. Conclusions There is evidence that several tree species in Alaska tend to occur in especially favourable sites in marginal areas. In these marginal areas, these species amplify habitat preferences shown in core areas.},
	Author = {Lennon, J. J. and Kunin, W. E. and Corne, S. and Carver, S. and Van Hees, W. W. S.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Global Ecology and Biogeography},
	Number = {2},
	Pages = {103-114},
	Title = {Are Alaskan trees found in locally more favourable sites in marginal areas?},
	Volume = {11},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Lennon.Kunin.ea.2002.b,
	Abstract = {We derive the species-area relationship (SAR) expected from an assemblage of fractally distributed species. If species have truly fractal spatial distributions with different fractal dimensions, we show that the expected SAR is not the classical power-law function, as suggested recently in the literature. This analytically derived SAR has a distinctive shape that is not commonly observed in nature: upward-accelerating richness with increasing area (when plotted on log-log axes). This suggests that, in reality, most species depart from true fractal spatial structure. We demonstrate the fitting of a fractal SAR using two plant assemblages (Alaskan trees and British grasses). We show that in both cases, when modelled as fractal patterns, the modelled SAR departs from the observed SAR in the same way, in accord with the theory developed here. The challenge is to identify how species depart from fractality, either individually or within assemblages, and more importantly to suggest reasons why species distributions are not self-similar and what, if anything, this can tell us about the spatial processes involved in their generation.},
	Author = {Lennon, J. J. and Kunin, W. E. and Hartley, S.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Oikos},
	Number = {3},
	Pages = {378-386},
	Title = {Fractal species distributions do not produce power-law species-area relationships},
	Volume = {97},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Naidoo.Ricketts.2006.a,
	Abstract = {Resources for biodiversity conservation are severely limited, requiring strategic investment. Understanding both the economic benefits and costs of conserving ecosystems will help to allocate scarce dollars most efficiently. However, although cost-benefit analyses are common in many areas of policy, they are not typically used in conservation planning. We conducted a spatial evaluation of the costs and benefits of conservation for a landscape in the Atlantic forests of Paraguay. We considered five ecosystem services ( i.e., sustainable bushmeat harvest, sustainable timber harvest, bioprospecting for pharmaceutical products, existence value, and carbon storage in aboveground biomass) and compared them to estimates of the opportunity costs of conservation. We found a high degree of spatial variability in both costs and benefits over this relatively small (similar to 3,000 km(2)) landscape. Benefits exceeded costs in some areas, with carbon storage dominating the ecosystem service values and swamping opportunity costs. Other benefits associated with conservation were more modest and exceeded costs only in protected areas and indigenous reserves. We used this cost-benefit information to show that one potential corridor between two large forest patches had net benefits that were three times greater than two otherwise similar alternatives. Spatial cost-benefit analysis can powerfully inform conservation planning, even though the availability of relevant data may be limited, as was the case in our study area. It can help us understand the synergies between biodiversity conservation and economic development when the two are indeed aligned and to clearly understand the trade-offs when they are not.},
	Author = {Naidoo, R. and Ricketts, T. H.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Plos Biology},
	Note = {Times Cited: 13},
	Pages = {2153-2164},
	Title = {Mapping the economic costs and benefits of conservation},
	Volume = {4},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Naidoo.Balmford.ea.2008.a,
	Abstract = {Global efforts to conserve biodiversity have the potential to deliver economic benefits to people (i.e., "ecosystem services"). However, regions for which conservation benefits both biodiversity and ecosystem services cannot be identified unless ecosystem services can be quantified and valued and their areas of production mapped. Here we review the theory, data, and analyses needed to produce such maps and find that data availability allows us to quantify imperfect global proxies for only four ecosystem services. Using this incomplete set as an illustration, we compare ecosystem service maps with the global distributions of conventional targets for biodiversity conservation. Our preliminary results show that regions selected to maximize biodiversity provide no more ecosystem services than regions chosen randomly. Furthermore, spatial concordance among different services, and between ecosystem services and established conservation priorities, varies widely. Despite this lack of general concordance, "win-win" areas-regions important for both ecosystem services and biodiversity-can be usefully identified, both among ecoregions and at finer scales within them. An ambitious interdisciplinary research effort is needed to move beyond these preliminary and illustrative analyses to fully assess synergies and trade-offs in conserving biodiversity and ecosystem services.},
	Author = {Naidoo, R. and Balmford, A. and Costanza, R. and Fisher, B. and Green, R. E. and Lehner, B. and Malcolm, T. R. and Ricketts, T. H.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {28},
	Pages = {9495-9500},
	Title = {Global mapping of ecosystem services and conservation priorities},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Petrik.Bruelheide.2006.a,
	Abstract = {To test whether species groups (i.e. assemblages of species co-occurring in nature) that are statistically derived at one scale (broad, medium, or fine scale) can be transferred to another scale, and to identify the driving forces that determine species groups at the various scales. Northern Bohemia (Czech Republic, central Europe) in the Jestedsky hrbet mountain range and its neighbourhood. Three data sets were sampled: a floristic data set at the broad scale, another floristic data set at the intermediate scale, and a vegetation data set at the habitat scale. First, in each data set, species groups were produced by the COCKTAIL algorithm, which ensures maximized joint occurrence in the data set using a fidelity coefficient. Corresponding species groups were produced in the individual data sets by employing the same species for starting the algorithm. Second, the species groups formed in one data set, i.e. at a particular scale, were applied crosswise to the other data sets, i.e. to the other scales. Correspondence of a species group formed at a particular scale with a species group at another scale was determined. Third, to highlight the driving factors for the distribution of the plant species groups at each scale, canonical correspondence analysis was carried out. Twelve species groups were used to analyse the transferability of the groups across the three scales, but only six of them were found to be common to all scales. Correspondence of species groups derived from the finest scale with those derived at the broadest scale was, on average, higher than in the opposite direction. Forest (tree layer) cover, altitude and bedrock type explained most of the variability in canonical correspondence analysis across all scales. Transferability of species groups distinguished at a fine scale to broader scales is better than it is in the opposite direction. Therefore, a possible application of the results is to use species groups to predict the potential occurrence of missing species in broad-scale floristic surveys from fine-scale vegetation-plot data.},
	Author = {Petrik, P. and Bruelheide, H.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Journal of Biogeography},
	Number = {9},
	Pages = {1628-1642},
	Title = {Species groups can be transferred across different scales},
	Volume = {33},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Pocock.Hartley.ea.2006.a,
	Abstract = {1 The distribution patterns of 391 rare and scarce British plants (species recorded in 100 or fewer 10 x 10 km squares) were characterized by their distributional area (area of occupancy at 1-km scale: AOO(1)) and levels of aggregation (as reflected in fractal dimensions measured across two scales: D1-10 and D10-100). 2 Eighteen plant traits were tested for relationships to AOO, and to fractal dimension while controlling for AOO. These included both directly heritable traits (e.g. life-form) and emergent properties that are, at most, indirectly heritable (e.g. typical local density). The latter set included an index of net distributional change and an index of range dynamism. 3 Only two traits, habitat preference and local abundance, were significantly related to AOO(1), but about half were associated with fractal dimension. 4 Relatively aggregated fine-scale distributions (high D1-10) were related to high local abundance, lack of specialized, long-distance dispersal mechanisms, habitat preference and an increasing range size with relatively few local extinctions (i.e. a positive index of change with low dynamism). 5 Relatively aggregated coarse-scale distributions (high D10-100) were related to the use of insect pollinators, obligate outcrossing, habitat preference and relatively stable ranges (low dynamism). 6 Multivariate analyses of subsets of conceptually related variables showed that few variables interacted to affect distributional variables. 7 A highly significant negative relationship between dynamism and fractal dimension appears to be driven primarily by high rates of local extinction, leading to relatively scattered, diffuse range structures. Furthermore, it suggests that recent population trends may be inferred from snapshots of contemporary distribution patterns. 8 The role and interpretation of phylogenetically informed analyses in studies such as this are debatable. However, we found similar relationships in both phylogenetically informed and conventional analyses for all variables except pollination vector (a strongly conserved trait). 9 The spatial pattern of plant species distributions is associated with a range of ecological traits, particularly those describing past changes in distribution. The analysis of distribution patterns therefore has the potential to inform future conservation effort.},
	Author = {Pocock, M. J. O. and Hartley, S. and Telfer, M. G. and Preston, C. D. and Kunin, W. E.},
	Date = {MAY},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Di = {10.1111/j.1365-2745.2006.01123.x},
	Isi = {ISI:000236717700007},
	Issn = {0022-0477},
	Journal = {JOURNAL OF ECOLOGY},
	Month = {May},
	Number = {3},
	Pages = {581--596},
	Publication-Type = {J},
	Title = {Ecological correlates of range structure in rare and scarce British plants},
	Volume = {94},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Ricketts.Regetz.ea.2008.a,
	Abstract = {Pollination by bees and other animals increases the size, quality, or stability of harvests for 70% of leading global crops. Because native species pollinate many of these crops effectively, conserving habitats for wild pollinators within agricultural landscapes can help maintain pollination services. Using hierarchical Bayesian techniques, we synthesize the results of 23 studies - representing 16 crops on five continents - to estimate the general relationship between pollination services and distance from natural or semi-natural habitats. We find strong exponential declines in both pollinator richness and native visitation rate. Visitation rate declines more steeply, dropping to half of its maximum at 0.6 km from natural habitat, compared to 1.5 km for richness. Evidence of general decline in fruit and seed set - variables that directly affect yields - is less clear. Visitation rate drops more steeply in tropical compared with temperate regions, and slightly more steeply for social compared with solitary bees. Tropical crops pollinated primarily by social bees may therefore be most susceptible to pollination failure from habitat loss. Quantifying these general relationships can help predict consequences of land use change on pollinator communities and crop productivity, and can inform landscape conservation efforts that balance the needs of native species and people.},
	Author = {Ricketts, T. H. and Regetz, J. and Steffan-Dewenter, I. and Cunningham, S. A. and Kremen, C. and Bogdanski, A. and Gemmill-Herren, B. and Greenleaf, S. S. and Klein, A. M. and Mayfield, M. M. and Morandin, L. A. and Ochieng, A. and Viana, B. F.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Ecology Letters},
	Note = {Times Cited: 0},
	Number = {5},
	Pages = {499-515},
	Title = {Landscape effects on crop pollination services: are there general patterns?},
	Volume = {11},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Schroter.Cramer.ea.2005.a,
	Abstract = {Global change will alter the supply of ecosystem services that are vital for human well-being. To investigate ecosystem service supply during the 21st century, we used a range of ecosystem models and scenarios of climate and land-use change to conduct a Europe-wide assessment. Large changes in climate and land use typically resulted in large changes in ecosystem service supply. Some of these trends may be positive (for example, increases in forest area and productivity) or offer opportunities (for example, "surplus land" for agricultural extensification and bioenergy production). However, many changes increase vulnerability as a result of a decreasing supply of ecosystem services (for example, declining soil fertility, declining water availability, increasing risk of forest fires), especially in the Mediterranean and mountain regions.},
	Author = {Schroter, D. and Cramer, W. and Leemans, R. and Prentice, I. C. and Araujo, M. B. and Arnell, N. W. and Bondeau, A. and Bugmann, H. and Carter, T. R. and Gracia, C. A. and de la Vega-Leinert, A. C. and Erhard, M. and Ewert, F. and Glendining, M. and House, J. I. and Kankaanpaa, S. and Klein, R. J. T. and Lavorel, S. and Lindner, M. and Metzger, M. J. and Meyer, J. and Mitchell, T. D. and Reginster, I. and Rounsevell, M. and Sabate, S. and Sitch, S. and Smith, B. and Smith, J. and Smith, P. and Sykes, M. T. and Thonicke, K. and Thuiller, W. and Tuck, G. and Zaehle, S. and Zierl, B.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Science},
	Number = {5752},
	Pages = {1333-1337},
	Title = {Ecosystem service supply and vulnerability to global change in Europe},
	Volume = {310},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Storch.Sizling.ea.2008.a,
	Abstract = {There have been several attempts to build a unified framework for macroecological patterns. However, these have mostly been based either on questionable assumptions or have had to be parameterized to obtain realistic predictions. Here, we propose a new model explicitly considering patterns of aggregated species distributions on multiple spatial scales, the property which lies behind all spatial macroecological patterns, using the idea we term 'generalized fractals'. Species' spatial distributions were modelled by a random hierarchical process in which the original 'habitat' patches were randomly replaced by sets of smaller patches nested within them, and the statistical properties of modelled species assemblages were compared with macroecological patterns in observed bird data. Without parameterization based on observed patterns, this simple model predicts realistic patterns of species abundance, distribution and diversity, including fractal-like spatial distributions, the frequency distribution of species occupancies/abundances and the species-area relationship. Although observed macroecological patterns may differ in some quantitative properties, our concept of random hierarchical aggregation can be considered as an appropriate null model of fundamental macroecological patterns which can potentially be modified to accommodate ecologically important variables.},
	Af = {Storch, David Sizling, Arnost L. Reif, Jiri Polechova, Jitka Sizlingova, Eva Gaston, Kevin J.},
	Author = {Storch, D. and Sizling, A. L. and Reif, J. and Polechova, J. and Sizlingova, E. and Gaston, K. J.},
	Date = {AUG},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Di = {10.1111/j.1461-0248.2008.01206.x},
	Isi = {ISI:000257655400002},
	Issn = {1461-023X},
	Journal = {Ecology Letters},
	Month = {Aug},
	Number = {8},
	Pages = {771--784},
	Publication-Type = {J},
	Title = {The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales},
	Volume = {11},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Tilman.2004.a,
	Abstract = {Stochastic niche theory resolves many of the differences between neutral theory and classical tradeoff-based niche theories of resource competition and community structure. In stochastic niche theory, invading species become established only if propagules can survive stochastic mortality while growing to maturity on the resources left unconsumed by established species. The theory makes three predictions about community structure. First, stochastic niche assembly creates communities in which species dominate approximately equally wide "slices" of the habitat's spatial heterogeneity. These niche widths generate realistic distributions of species relative abundances for which, contrary to neutral theory but consistent with numerous observations, there are strong correlations among species traits, species abundances, and environmental conditions. Second, slight decreases in resource levels are predicted to cause large decreases in the probability that a propagule would survive to be an adult. These decreases cause local diversity to be limited by the inhibitory effects of resource use by established species on the establishment (recruitment) of potential invaders. If resource pulses or disturbance allowed invaders to overcome this recruitment limitation, many more species could indefinitely coexist. Third, the low invasibility of high diversity communities is predicted to result not from diversity per se, but from the uniformly low levels of resources that occur in high-diversity communities created by stochastic competitive assembly. This prediction provides a potential solution to the invasion paradox, which is the tendency for highly diverse regions to be more heavily-invaded.},
	Author = {Tilman, D.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Number = {30},
	Pages = {10854-10861},
	Title = {Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly},
	Volume = {101},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Hartley.Kunin.ea.2004.a,
	Abstract = {The spatial distribution of a species can be characterized at many different spatial scales, from fine-scale measures of local population density to coarse-scale geographical-range structure. Previous studies have shown a degree of correlation in species' distribution patterns across narrow ranges of scales, making it possible to predict fine-scale properties from coarser-scale distributions. To test the limits of such extrapolation, we have compiled distributional information on 16 species of British plants, at scales ranging across six orders of magnitude in linear resolution (1 in to 100 km). As expected, the correlation between patterns at different spatial scales tends to degrade as the scales become more widely separated. There is, however, an abrupt breakdown in cross-scale correlations across intermediate (ca. 0.5 km) scales, suggesting that local and regional patterns are influenced by essentially non-overlapping sets of processes. The scaling discontinuity may also reflect characteristic scales of human land use in Britain, suggesting a novel method for analysing the 'footprint' of humanity on a landscape.},
	Author = {Hartley, S. and Kunin, W. E. and Lennon, J. J. and Pocock, M. J. O.},
	Date-Added = {2008-10-02 15:43:15 +0100},
	Date-Modified = {2008-10-02 15:43:15 +0100},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Number = {1534},
	Pages = {81-88},
	Title = {Coherence and discontinuity in the scaling of species' distribution patterns},
	Volume = {271},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Taylor.Keller.2007.a,
	Abstract = {For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.},
	Address = {810 E 10TH STREET, LAWRENCE, KS 66044 USA},
	Author = {Taylor, Douglas R. and Keller, Stephen R.},
	Date = {FEB 2007},
	Date-Added = {2008-09-26 12:14:31 +0100},
	Date-Modified = {2008-09-26 12:15:43 +0100},
	Doi = {DOI 10.1111/j.1558-5646.2007.00037.x},
	Journal = {Evolution},
	Keywords = {chloroplast DNA; coalescent; invasion; mismatch distribution; phylogeography; range expansion; Silene},
	Pages = {334-345},
	Publisher = {SOC STUDY EVOLUTION},
	Timescited = {8},
	Title = {Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion},
	Volume = {61},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2007.00037.x}}

@article{Wilson.Thomas.ea.2004.a,
	Abstract = {Interpretation of global biodiversity change is hampered by a lack of information on the historical status of most species in most parts of the world. Here we show that declines and increases can be deduced from current species distributions alone, using spatial patterns of occupancy combined with distribution size. Declining species show sparse, fragmented distributions for their distribution size, reflecting the extinction process; expanding species show denser, more aggregated distributions, reflecting colonization. Past distribution size changes for British butterflies were deduced successfully from current distributions, and former distributions had some power to predict future change. What is more, the relationship between distribution pattern and change in British butterflies independently predicted distribution change for butterfly species in Flanders, Belgium, and distribution change in British rare plant species is similarly related to spatial distribution pattern. This link between current distribution patterns and processes of distribution change could be used to assess relative levels of threat facing different species, even for regions and taxa lacking detailed historical and ecological information.},
	Annote = {10.1038/nature03031},
	Author = {Wilson, Robert J. and Thomas, Chris D. and Fox, Richard and Roy, David B. and Kunin, William E.},
	Date-Added = {2008-09-10 11:30:00 +0100},
	Date-Modified = {2008-10-02 23:09:24 +0100},
	Isbn = {0028-0836},
	Journal = {Nature},
	L3 = {http://www.nature.com/nature/journal/v432/n7015/suppinfo/nature03031_S1.html},
	M3 = {10.1038/nature03031},
	Number = {7015},
	Pages = {393--396},
	Rating = {0},
	Title = {Spatial patterns in species distributions reveal biodiversity change},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nature03031},
	Volume = {432},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature03031}}

@article{Davies.Fritz.ea.2008.a,
	Abstract = {Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerable to increased human pressure. We outline how the approach might be extended to consider future trends in anthropogenic drivers, to identify likely future battlegrounds of mammalian conservation, and the likely casualties. This framework could help to highlight consequences of choosing among different future climatic and socioeconomic scenarios. We end by discussing priority-setting, showing how alternative currencies for diversity can suggest very different priorities. We argue that aiming to maximize long-term evolutionary responses is inappropriate, that conservation planning needs to consider costs as well as benefits, and that proactive conservation of largely intact systems should be part of a balanced strategy.
},
	Author = {Davies, T. Jonathan and Fritz, Susanne A. and Grenyer, Richard and Orme, C. David L. and Bielby, Jon and Bininda-Emonds, Olaf R. P. and Cardillo, Marcel and Jones, Kate E. and Gittleman, John L. and Mace, Georgina M. and Purvis, Andy},
	Date-Added = {2008-08-29 10:13:14 +0100},
	Date-Modified = {2008-08-29 10:13:55 +0100},
	Doi = {10.1073/pnas.0801917105},
	Eprint = {http://www.pnas.org/content/105/suppl.1/11556.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {Supplement 1},
	Pages = {11556-11563},
	Title = {{Phylogenetic trees and the future of mammalian biodiversity}},
	Url = {http://www.pnas.org/content/105/suppl.1/11556.abstract},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/content/105/suppl.1/11556.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0801917105}}

@article{Pagel.1992.a,
	Abstract = {Felsenstein (1985) developed a method for analyzing comparative data that calculates a set of mutually independent comparisons among the species. The method was designed to be used with phylogenies for which the true dichotomous branching pattern is known. However, available phylogenies often contain many incompletely resolved nodes, or nodes from which three or more branches emanate. This paper reports a generalization of Felsenstein's method that permits the analysis of incompletely resolved phylogenies. The method is general to any sort of phylogeny and, like Felsenstein's model can accommodate more than one model of evolutionary change. The method is implemented in a computer program which can make use of information on branch lengths, or, if branch length information is not available, an algorithm is used to calculate a set of branch lengths. The wider implications of the method are that it makes explicit the assumptions about unknown branching patterns and branch lengths that all comparative methods that are applied to incompletely resolved phylogenies must make.},
	Address = {24-28 OVAL RD, LONDON, ENGLAND NW1 7DX},
	Author = {Pagel, Mark D},
	Date = {JUN 21 1992},
	Date-Added = {2008-08-22 15:08:37 +0100},
	Date-Modified = {2008-08-22 15:14:44 +0100},
	Journal = {Journal of Theoretical Biology},
	Number = {4},
	Pages = {431-442},
	Publisher = {ACADEMIC PRESS LTD},
	Timescited = {362},
	Title = {A method for the analysis of comparative data},
	Volume = {156},
	Year = {1992}}

@article{Paradis.Claude.ea.2004.a,
	Author = {Paradis, Emmanuel and Claude, Julien and Strimmer, Korbinian},
	Date-Added = {2008-08-22 15:04:07 +0100},
	Date-Modified = {2008-08-22 15:06:07 +0100},
	Journal = {Bioinformatics},
	Number = {2},
	Pages = {289-290},
	Title = {APE: analyses of phylogenetics and evolution in {R} language},
	Volume = {20},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Felsenstein.1985.a,
	Address = {5720 S WOODLAWN AVE, CHICAGO, IL 60637},
	Author = {Felsenstein, Joseph},
	Date = {1985},
	Date-Added = {2008-08-20 17:46:37 +0100},
	Date-Modified = {2008-08-20 17:47:36 +0100},
	Journal = {American Naturalist},
	Pages = {1-15},
	Publisher = {UNIV CHICAGO PRESS},
	Timescited = {2661},
	Title = {Phylogenies and the comparative method},
	Volume = {125},
	Year = {1985},
	Bdsk-File-1 = { }}

@article{Devictor.Julliard.ea.2008.a,
	Abstract = {Range shifts of many species are now documented as a response to global warming. But whether these observed changes are occurring fast enough remains uncertain and hardly quantifiable. Here, we developed a simple framework to measure change in community composition in response to climate warming. This framework is based on a community temperature index (CTI) that directly reflects, for a given species assemblage, the balance between low- and high-temperature dwelling species. Using data from the French breeding bird survey, we first found a strong increase in CTI over the last two decades revealing that birds are rapidly tracking climate warming. This increase corresponds to a 91km northward shift in bird community composition, which is much higher than previous estimates based on changes in species range edges. During the same period, temperature increase corresponds to a 273km northward shift in temperature. Change in community composition was thus insufficient to keep up with temperature increase: birds are lagging approximately 182km behind climate warming. Our method is applicable to any taxa with large-scale survey data, using either abundance or occurrence data. This approach can be further used to test whether different delays are found across groups or in different land-use contexts.},
	Author = {Devictor, Vincent and Julliard, Romain and Couvet, Denis and Jiguet, Fr{\'e}d{\'e}ric},
	Date-Added = {2008-08-20 12:01:15 +0100},
	Date-Modified = {2008-10-21 10:12:17 +0100},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	M3 = {10.1098/rspb.2008.0878},
	Number = {1652},
	Pages = {2743-2748},
	Title = {Birds are tracking climate warming, but not fast enough},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1098/rspb.2008.0878},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2008.0878}}

@article{Weir.Schluter.2008.b,
	Abstract = {Tobias et al. suggest that taxonomic uncertainty, an underestimated correction for the lag-time to speciation, and the sister-species method undermine our estimates of speciation rates at tropical latitudes. However, our estimates incorporated a correction for taxonomic uncertainty and are robust to small increases in the lag-time correction. Contrary to the claim of Tobias et al., we find no indication that the sister-species method underestimates tropical diversification rates. },
	Annote = {10.1126/science.1150828},
	Author = {Weir, J. T. and Schluter, D.},
	Date-Added = {2008-07-22 15:28:53 +0100},
	Date-Modified = {2008-07-22 15:28:53 +0100},
	Journal = {Science},
	Journal1 = {Science},
	Number = {5865},
	Pages = {901d--},
	Title = {Response to Comment on "The Latitudinal Gradient in Recent Speciation and Extinction Rates of Birds and Mammals"},
	Ty = {JOUR},
	Url = {http://www.sciencemag.org/cgi/content/abstract/319/5865/901d},
	Volume = {319},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/319/5865/901d}}

@article{Tobias.Bates.ea.2008.a,
	Abstract = {Weir and Schluter (Reports, 16 March 2007, p. 1574) used variation in the age distribution of sister species to estimate that recent rates of speciation decline toward the tropics. However, this conclusion may be undermined by taxonomic biases, sampling artifacts, and the sister-species method, all of which tend to underestimate diversification rates at low latitudes. },
	Annote = {10.1126/science.1150568},
	Author = {Tobias, Joseph A. and Bates, John M. and Hackett, Shannon J. and Seddon, Nathalie},
	Date-Added = {2008-07-22 15:28:41 +0100},
	Date-Modified = {2008-07-22 15:28:41 +0100},
	Journal = {Science},
	Journal1 = {Science},
	Number = {5865},
	Pages = {901c--},
	Title = {Comment on "The Latitudinal Gradient in Recent Speciation and Extinction Rates of Birds and Mammals"},
	Ty = {JOUR},
	Url = {http://www.sciencemag.org/cgi/content/abstract/319/5865/901c},
	Volume = {319},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/319/5865/901c}}

@article{Burgess.Nicoll.ea.2008.a,
	Abstract = {Spatial processes could play an important role in density-dependent population regulation because the disproportionate use of poor quality habitats as population size increases is widespread in animal populations---the so-called buffer effect. While the buffer effect patterns and their demographic consequences have been described in a number of wild populations, much less is known about how dispersal affects distribution patterns and ultimately density dependence. Here, we investigated the role of dispersal in spatial density dependence using an extraordinarily detailed dataset from a reintroduced Mauritius kestrel (Falco punctatus) population with a territorial (despotic) breeding system. We show that recruitment rates varied significantly between territories, and that territory occupancy was related to its recruitment rate, both of which are consistent with the buffer effect theory. However, we also show that restricted dispersal affects the patterns of territory occupancy with the territories close to release sites being occupied sooner and for longer as the population has grown than the territories further away. As a result of these dispersal patterns, the strength of spatial density dependence is significantly reduced. We conclude that restricted dispersal can modify spatial density dependence in the wild, which has implications for the way population dynamics are likely to be impacted by environmental change.},
	Author = {Burgess, Malcolm D. and Nicoll, Malcolm A. C. and Jones, Carl G. and Norris, Ken},
	Date-Added = {2008-07-22 15:26:08 +0100},
	Date-Modified = {2008-07-22 15:26:08 +0100},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	M3 = {10.1098/rspb.2007.1751},
	Number = {1639},
	Pages = {1209--1216},
	Title = {Restricted dispersal reduces the strength of spatial density dependence in a tropical bird population},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1098/rspb.2007.1751},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.1751}}

@article{Lee.Jetz.2008.a,
	Abstract = {Global biodiversity is under significant threat from the combined effects of human-induced climate and land-use change. Covering 12{\%} of the Earth's terrestrial surface, protected areas are crucial for conserving biodiversity and supporting ecological processes beneficial to human well-being, but their selection and design are usually uninformed about future global change. Here, we quantify the exposure of the global reserve network to projected climate and land-use change according to the Millennium Ecosystem Assessment and set these threats in relation to the conservation value and capacity of biogeographic and geopolitical regions. We find that geographical patterns of past human impact on the land cover only poorly predict those of forecasted change, thus revealing the inadequacy of existing global conservation prioritization templates. Projected conservation risk, measured as regional levels of land-cover change in relation to area protected, is the greatest at high latitudes (due to climate change) and tropics/subtropics (due to land-use change). Only some high-latitude nations prone to high conservation risk are also of high conservation value, but their high relative wealth may facilitate additional conservation efforts. In contrast, most low-latitude nations tend to be of high conservation value, but they often have limited capacity for conservation which may exacerbate the global biodiversity extinction crisis. While our approach will clearly benefit from improved land-cover projections and a thorough understanding of how species range will shift under climate change, our results provide a first global quantitative demonstration of the urgent need to consider future environmental change in reserve-based conservation planning. They further highlight the pressing need for new reserves in target regions and support a much extended `north--south'transfer of conservation resources that maximizes biodiversity conservation while mitigating global climate change.},
	Author = {Lee, Tien Ming and Jetz, Walter},
	Date-Added = {2008-07-22 14:24:52 +0100},
	Date-Modified = {2008-07-22 14:24:52 +0100},
	Journal = {Proceedings of the Royal Society B: Biological Sciences},
	M3 = {10.1098/rspb.2007.1732},
	Number = {1640},
	Pages = {1261--1270},
	Title = {Future battlegrounds for conservation under global change},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1098/rspb.2007.1732},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.1732}}

@article{Morgan-Richards.Trewick.ea.2008.a,
	Author = {Morgan-Richards, Mary and Trewick, Steve A and Bartosch-H{\"a}rlid, Anna and Kardailsky, Olga and Phillips, Matthew J and McLenachan, Patricia A and Penny, David},
	Date-Added = {2008-07-22 14:08:12 +0100},
	Date-Modified = {2008-07-22 14:11:08 +0100},
	Doi = {10.1186/1471-2148-8-20},
	Journal = {BMC Evolutionary Biology},
	Pages = {20},
	Title = {Bird evolution: testing the Metaves clade with six new mitochondrial genomes},
	Volume = {8},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1471-2148-8-20}}

@article{Hackett.Kimball.ea.2008.a,
	Abstract = {Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined [~]32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.
},
	Author = {Hackett, Shannon J. and Kimball, Rebecca T. and Reddy, Sushma and Bowie, Rauri C. K. and Braun, Edward L. and Braun, Michael J. and Chojnowski, Jena L. and Cox, W. Andrew and Han, Kin-Lan and Harshman, John and Huddleston, Christopher J. and Marks, Ben D. and Miglia, Kathleen J. and Moore, William S. and Sheldon, Frederick H. and Steadman, David W. and Witt, Christopher C. and Yuri, Tamaki},
	Date-Added = {2008-07-22 14:02:52 +0100},
	Date-Modified = {2008-07-22 14:03:20 +0100},
	Doi = {10.1126/science.1157704},
	Eprint = {http://www.sciencemag.org/cgi/reprint/320/5884/1763.pdf},
	Journal = {Science},
	Number = {5884},
	Pages = {1763-1768},
	Title = {{A Phylogenomic Study of Birds Reveals Their Evolutionary History}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/320/5884/1763},
	Volume = {320},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/320/5884/1763},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1157704}}

@article{Clauset.Erwin.2008.a,
	Abstract = {The distribution of species body size within taxonomic groups exhibits a heavy right tail extending over many orders of magnitude, where most species are much larger than the smallest species. We provide a simple model of cladogenetic diffusion over evolutionary time that omits explicit mechanisms for interspecific competition and other microevolutionary processes, yet fully explains the shape of this distribution. We estimate the model's parameters from fossil data and find that it robustly reproduces the distribution of 4002 mammal species from the late Quaternary. The observed fit suggests that the asymmetric distribution arises from a fundamental trade-off between the short-term selective advantages (Cope's rule) and long-term selective risks of increased species body size in the presence of a taxon-specific lower limit on body size.
},
	Author = {Clauset, Aaron and Erwin, Douglas H.},
	Date-Added = {2008-07-22 13:33:49 +0100},
	Date-Modified = {2008-07-22 13:34:24 +0100},
	Doi = {10.1126/science.1157534},
	Eprint = {http://www.sciencemag.org/cgi/reprint/321/5887/399.pdf},
	Journal = {Science},
	Number = {5887},
	Pages = {399-401},
	Title = {{The Evolution and Distribution of Species Body Size}},
	Url = {http://www.sciencemag.org/cgi/content/abstract/321/5887/399},
	Volume = {321},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencemag.org/cgi/content/abstract/321/5887/399},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1157534}}

@article{Gotelli.Graves.1990.a,
	Address = {OSNEY MEAD, OXFORD, OXON, ENGLAND OX2 0EL},
	Author = {Gotelli, Nicholas J. and Graves, Gary R.},
	Date = {MAY 1990},
	Date-Added = {2008-07-13 16:31:21 +0100},
	Date-Modified = {2008-07-13 16:33:41 +0100},
	Journal = {Journal of Biogeography},
	Pages = {315-325},
	Publisher = {BLACKWELL SCIENCE LTD},
	Timescited = {25},
	Title = {Body size and the occurrence of avian species on land-bridge islands},
	Volume = {17},
	Year = {1990},
	Bdsk-File-1 = { }}

@article{Vincenty.1975.a,
	Author = {Vincenty, T},
	Date-Added = {2008-07-08 13:43:19 +0100},
	Date-Modified = {2008-07-08 13:44:49 +0100},
	Journal = {Survey Review},
	Number = {176},
	Pages = {88-93},
	Title = {Direct and inverse solutions of geodesics on the ellipsoid with application of nested equations},
	Volume = {22},
	Year = {1975},
	Bdsk-File-1 = { }}

@article{McDonald.McKnight.ea.2005.a,
	Abstract = {The concept of an ecoregion, a discrete spatial area where species composition is presumed to be relatively homogeneous compared to that between areas, has become an increasingly common conservation tool, We test the effectiveness of one ecoregion delineation (World Wildlife Fund) in capturing patterns of change in species composition of birds. mammals, and trees across the United States (excluding Hawaii) and Canada, and describe the extent to which each ecoregion boundary is concurrent with relatively large changes in species composition. Digitized range maps were used to record presence/absence in 50 x 50 km equal-area grid cells covering the study area. Jaccard's index or similarity was calculated for all pairs of cells in the same or adjacent ecoregions. The average rate at which similarity declined with geographic distance was calculated using pairs of cells within the same ecoregion (intra-ecoregion turnover) or using pairs of cells in adjacent ecoregions (inter-ecoregion turnover). The intra-ecoregion rate varies widely among ecoregions and between taxa, with trees having a faster rate of similarity decline than mammals or birds. For all three species groups, most ecoregion boundaries have similar rates across them (inter-ecoregion) than that within each adjacent ecoregion (intra-ecoregion), with the exception of zones of transition between biomes and major geographical features. Although the ecoregion concept is useful for many other conservation applications, the lack of systematic, high turnover rates along ecoregion boundaries suggests that ecoregions should not be used as a quantitative basis for delineating geographic areas of a particular taxonomic group, (c) 2005 Elsevier Ltd. All rights reserved.},
	Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
	Author = {McDonald, Robert I and McKnight, Meghan W. and Weiss, Dan and Selig, Elizabeth and O'Connor, Mary and Violin, Christy and Moody, Aaron},
	Date = {NOV 2005},
	Date-Added = {2008-07-02 15:21:22 +0100},
	Date-Modified = {2008-07-02 15:24:01 +0100},
	Doi = {DOI 10.1016/j.biocon.2005.05.008},
	Journal = {Biological Conservation},
	Keywords = {biodiversity; species turnover; distance decay; Jaccard's similarity index; ranges},
	Pages = {24-40},
	Publisher = {ELSEVIER SCI LTD},
	Timescited = {9},
	Title = {Species compositional similarity and ecoregions: Do ecoregion boundaries represent zones of high species turnover?},
	Volume = {126},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.biocon.2005.05.008}}

@article{Mace.Balmford.ea.2000.a,
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Mace, Georgina M. and Balmford, Andrew and Boitani, Luigi and Cowlishaw, Guy and Dobson, Andrew P. and Faith, D P and Gaston, Kevin J. and Humphries, C J and Vane-Wright, Richard I and Williams, Peter H and Lawton, John H and Margules, C R and May, Robert M and Nicholls, A O and Possingham, Hugh P and Rahbek, Carsten and van Jaarsveld, A S},
	Date = {MAY 25 2000},
	Date-Added = {2008-07-02 14:47:57 +0100},
	Date-Modified = {2008-07-02 14:49:53 +0100},
	Journal = {Nature},
	Note = {Nature},
	Pages = {393-393},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Timescited = {42},
	Title = {It's time to work together and stop duplicating conservation efforts ...},
	Volume = {405},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Olson.Dinerstein.ea.2001.a,
	Address = {1444 EYE ST, NW, STE 200, WASHINGTON, DC 20005 USA},
	Author = {Olson, David M. and Dinerstein, Eric and Wikramanayake, Eric D and Burgess, Neil D and Powell, George V N and Underwood, Emma C. and D'Amico, Jennifer A and Itoua, Illanga and Strand, Holly E and Morrison, John C and Loucks, Colby J and Allnutt, Thomas F and Ricketts, Taylor H. and Kura, Yumiko and Lamoreux, John F. and Wettengel, Wesley W and Hedao, Prashant and Kassem, Kenneth R},
	Date = {NOV 2001},
	Date-Added = {2008-06-18 15:26:09 +0100},
	Date-Modified = {2008-06-18 15:32:59 +0100},
	Journal = {Bioscience},
	Pages = {933-938},
	Publisher = {AMER INST BIOLOGICAL SCI},
	Timescited = {186},
	Title = {Terrestrial ecoregions of the worlds: A new map of life on Earth},
	Volume = {51},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Sutherland.2003.a,
	Abstract = {There are global threats to biodiversity with current extinction rates well above background levels(1). Although less well publicized, numerous human languages have also become extinct, and others are threatened with extinction(2,3). However, estimates of the number of threatened languages vary considerably owing to the wide range of criteria used. For example, languages have been classified as threatened if the number of speakers is less than 100, 500, 1,000, 10,000, 20,000 or 100,000 (ref. 3). Here I show, by applying internationally agreed criteria for classifying species extinction risk(4), that languages are more threatened than birds or mammals. Rare languages are more likely to show evidence of decline than commoner ones. Areas with high language diversity also have high bird and mammal diversity and all three show similar relationships to area, latitude, area of forest and, for languages and birds, maximum altitude. The time of human settlement has little effect on current language diversity. Although similar factors explain the diversity of languages and biodiversity, the factors explaining extinction risk for birds and mammals ( high altitude, high human densities and insularity) do not explain the numbers of endangered languages.},
	Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Sutherland, William J.},
	Date = {MAY 15 2003},
	Date-Added = {2008-06-09 16:53:00 +0100},
	Date-Modified = {2008-06-09 16:59:08 +0100},
	Doi = {DOI 10.1038/nature01607},
	Journal = {Nature},
	Pages = {276-279},
	Publisher = {NATURE PUBLISHING GROUP},
	Timescited = {37},
	Title = {Parallel extinction risk and global distribution of languages and species},
	Volume = {423},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature01607}}

@article{Suttle.Thomsen.ea.2007.a,
	Abstract = {Predictions of ecological response to climate change are based largely on direct climatic effects on species. We show that, in a California grassland, species interactions strongly influence responses to changing climate, overturning direct climatic effects within 5 years. We manipulated the seasonality and intensity of rainfall over large, replicate plots in accordance with projections of leading climate models and examined responses across several trophic levels. Changes in seasonal water availability had pronounced effects on individual species, but as precipitation regimes were sustained across years, feedbacks and species interactions overrode autecological responses to water and reversed community trajectories. Conditions that sharply increased production and diversity through 2 years caused simplification of the food web and deep reductions in consumer abundance after 5 years. Changes in these natural grassland communities suggest a prominent role for species interactions in ecosystem response to climate change.},
	Address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA},
	Author = {Suttle, K. Blake and Thomsen, Meredith A. and Power, Mary E.},
	Date = {FEB 2 2007},
	Date-Added = {2008-06-04 13:47:36 +0100},
	Date-Modified = {2008-06-04 13:48:26 +0100},
	Doi = {DOI 10.1126/science.1136401},
	Journal = {Science},
	Pages = {640-642},
	Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
	Timescited = {11},
	Title = {Species interactions reverse grassland responses to changing climate},
	Volume = {315},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1136401}}

@article{Myers.Mittermeier.ea.2000.a,
	Abstract = {Consenrationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44\% of all species of vascular plants and 35\% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4\% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.},
	Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	Author = {Myers, Norman and Mittermeier, Russell A. and Mittermeier, Cristina G and da Fonseca, Gustavo A B and Kent, Jennifer},
	Date = {FEB 24 2000},
	Date-Added = {2008-06-03 12:20:40 +0100},
	Date-Modified = {2008-06-03 12:25:43 +0100},
	Journal = {Nature},
	Pages = {853-858},
	Publisher = {MACMILLAN MAGAZINES LTD},
	Timescited = {1771},
	Title = {Biodiversity hotspots for conservation priorities},
	Volume = {403},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Elith.Graham.ea.2006.a,
	Abstract = {Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Elith, Jane and Graham, C H and Anderson, R P and Dudik, M and Ferrier, S and Guisan, A and Hijmans, R J and Huettmann, F and Leathwick, J R and Lehmann, A and Li, J and Lohmann, L G and Loiselle, B A and Manion, G and Moritz, C and Nakamura, M and Nakazawa, Y and Overton, J M and Peterson, A T and Phillips, S J and Richardson, K and Scachetti-Pereira, R and Schapire, R E and Soberon, J and Williams, S and Wisz, M S and Zimmermann, N E},
	Date = {APR 2006},
	Date-Added = {2008-06-03 10:15:18 +0100},
	Date-Modified = {2008-06-03 10:17:04 +0100},
	Journal = {Ecography},
	Pages = {129-151},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {143},
	Title = {Novel methods improve prediction of species' distributions from occurrence data},
	Volume = {29},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Hamilton.1961.a,
	Author = {Hamilton, T H},
	Date-Added = {2008-05-16 11:54:54 +0100},
	Date-Modified = {2008-05-16 11:55:44 +0100},
	Journal = {Evolution},
	Pages = {180-195},
	Title = {The adaptive significance of intraspecific trends of variation in wing length and body size among bird species.},
	Volume = {15},
	Year = {1961}}

@article{Liow.Fortelius.ea.2008.a,
	Abstract = {Do large mammals evolve faster than small mammals or vice versa? Because the answer to this question contributes to our understanding of how life-history affects long-term and large-scale evolutionary patterns, and how microevolutionary rates scale-up to macroevolutionary rates, it has received much attention. A satisfactory or consistent answer to this question is lacking, however. Here, we take a fresh look at this problem using a large fossil dataset of mammals from the Neogene of the Old World (NOW). Controlling for sampling biases, calculating per capita origination and extinction rates of boundary-crossers and estimating survival probabilities using capture-mark-recapture (CMR) methods, we found the recurring pattern that large mammal genera and species have higher origination and extinction rates, and therefore shorter durations. This pattern is surprising in the light of molecular studies, which show that smaller animals, with their shorter generation times and higher metabolic rates, have greater absolute rates of evolution. However, higher molecular rates do not necessarily translate to higher taxon rates because both the biotic and physical environments interact with phenotypic variation, in part fueled by mutations, to affect origination and extinction rates. To explain the observed pattern, we propose that the ability to evolve and maintain behavior such as hibernation, torpor and burrowing, collectively termed "sleep-or-hide" (SLOH) behavior, serves as a means of environmental buffering during expected and unexpected environmental change. SLOH behavior is more common in some small mammals, and, as a result, SLOH small mammals contribute to higher average survivorship and lower origination probabilities among small mammals.
},
	Author = {Liow, Lee Hsiang and Fortelius, Mikael and Bingham, Ella and Lintulaakso, Kari and Mannila, Heikki and Flynn, Larry and Stenseth, Nils Chr.},
	Date-Added = {2008-05-14 09:25:38 +0100},
	Date-Modified = {2008-05-14 09:30:35 +0100},
	Doi = {10.1073/pnas.0709763105},
	Eprint = {http://www.pnas.org/cgi/reprint/105/16/6097.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {16},
	Pages = {6097-6102},
	Title = {{Higher origination and extinction rates in larger mammals}},
	Url = {http://www.pnas.org/cgi/content/abstract/105/16/6097},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/cgi/content/abstract/105/16/6097},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0709763105}}

@article{Felsenstein.2008.a,
	Author = {Felsenstein,Joseph},
	Date-Added = {2008-05-13 15:51:31 +0100},
	Date-Modified = {2008-05-13 15:52:17 +0100},
	Doi = {10.1086/587525},
	Eprint = {http://www.journals.uchicago.edu/doi/pdf/10.1086/587525},
	Journal = {The American Naturalist},
	Number = {6},
	Pages = {713-725},
	Title = {Comparative Methods with Sampling Error and Within-Species Variation: Contrasts Revisited and Revised.},
	Url = {http://www.journals.uchicago.edu/doi/abs/10.1086/587525},
	Volume = {171},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.journals.uchicago.edu/doi/abs/10.1086/587525},
	Bdsk-Url-2 = {http://dx.doi.org/10.1086/587525}}

@article{Arita.Vazquez-Dominguez.2008.a,
	Author = {Arita,Hector T. and Vazquez-Dominguez,Ella},
	Date-Added = {2008-05-13 15:45:43 +0100},
	Date-Modified = {2008-05-13 15:49:42 +0100},
	Doi = {10.1111/j.1461-0248.2008.01197.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1461-0248.2008.01197.x},
	Journal = {Ecology Letters},
	Number = {0},
	Pages = {???-???},
	Title = {The tropics: cradle, museum or casino? A dynamic null model for latitudinal gradients of species diversity},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2008.01197.x},
	Volume = {0},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2008.01197.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01197.x}}

@article{Nogues-Bravo.Araujo.ea.2008.a,
	Annote = {10.1038/nature06812},
	Author = {Nogues-Bravo, David and Araujo, Miguel B. and Romdal, T. and Rahbek, Carsten},
	Date-Added = {2008-05-13 15:37:45 +0100},
	Date-Modified = {2008-05-13 15:38:37 +0100},
	Isbn = {0028-0836},
	Journal = {Nature},
	L3 = {http://www.nature.com/nature/journal/v453/n7192/suppinfo/nature06812_S1.html},
	M3 = {10.1038/nature06812},
	Number = {7192},
	Pages = {216--219},
	Publisher = {Nature Publishing Group},
	Title = {Scale effects and human impact on the elevational species richness gradients},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nature06812},
	Volume = {453},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature06812}}

@article{Rabosky.2006.a,
	Abstract = {Maximum likelihood is a potentially powerful approach for investigating the tempo of diversification using molecular phylogenetic data. Likelihood methods distinguish between rate-constant and rate-variable models of diversification by fitting birth-death models to phylogenetic data. Because model selection in this context is a test of the null hypothesis that diversification rates have been constant over time, strategies for selecting best-fit models must minimize Type I error rates while retaining power to detect rate variation when it is present. Here I examine model selection, parameter estimation, and power to reject the null hypothesis using likelihood models based on the birth-death process. The Akaike information criterion (AIC) has often been used to select among diversification models; however, I find that selecting models based on the lowest AIC score leads to a dramatic inflation of the Type I error rate. When appropriately corrected to reduce Type I error rates, the birth-death likelihood approach performs as well or better than the widely used gamma statistic, at least when diversification rates have shifted abruptly over time. Analyses of datasets simulated under a range of rate-variable diversification scenarios indicate that the birth-death likelihood method has much greater power to detect variation in diversification rates when extinction is present. Furthermore, this method appears to be the only approach available that can distinguish between a temporal increase in diversification rates and a rate-constant model with nonzero extinction. I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards.},
	Address = {810 E 10TH STREET, LAWRENCE, KS 66044 USA},
	Author = {Rabosky, Daniel L.},
	Date = {JUN 2006},
	Date-Added = {2008-05-13 14:55:30 +0100},
	Date-Modified = {2008-05-13 14:58:46 +0100},
	Journal = {Evolution},
	Keywords = {diversification rates; macroevolution; maximum likelihood; phylogeny; speciation},
	Pages = {1152-1164},
	Publisher = {SOC STUDY EVOLUTION},
	Rating = {0},
	Timescited = {4},
	Title = {Likelihood methods for detecting temporal shifts in diversification rates},
	Volume = {60},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Rabosky.Donnellan.ea.2007.a,
	Abstract = {The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesistesting framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Rabosky, Daniel L. and Donnellan, Stephen C. and Talaba, Amanda L. and Lovette, Irby J.},
	Date = {DEC 7 2007},
	Date-Added = {2008-05-13 14:55:30 +0100},
	Date-Modified = {2008-05-13 14:58:45 +0100},
	Doi = {DOI 10.1098/rspb.2007.0924},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {diversification rates; phylogeny; key innovation; speciation; scincid lizards},
	Pages = {2915-2923},
	Publisher = {ROYAL SOC},
	Rating = {0},
	Timescited = {0},
	Title = {Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.0924}}

@unpublished{Bolker.2007.a,
	Author = {Bolker, Ben},
	Date-Added = {2008-05-13 14:44:22 +0100},
	Date-Modified = {2008-05-13 14:51:02 +0100},
	Title = {Ecological models and data in R},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Yom-Tov.1997.a,
	Author = {Yom-Tov, Yoram},
	Date-Added = {2008-05-13 14:41:08 +0100},
	Date-Modified = {2008-05-13 14:42:02 +0100},
	Journal = {Israel Journal of Zoology},
	Pages = {217-218},
	Title = {The evolution of two-dimensional vertebrates},
	Volume = {43},
	Year = {1997},
	Bdsk-File-1 = { }}

@article{Araujo.Nogues-Bravo.ea.2008.a,
	Abstract = {It is widely believed that contemporary climate determines large-scale patterns of species richness. An alternative view proposes that species richness reflects biotic responses to historic climate changes. These competing "contemporary climate" vs "historic climate" hypotheses have been vigorously debated without reaching consensus. Here, we test the proposition that European species richness of reptiles and amphibians is driven by climate changes in the Quaternary. We find that climate stability between the Last Glacial Maximum (LGM) and the present day is a better predictor of species richness than contemporary climate; and that the 0 degrees C isotherm of the LGM delimits the distributions of narrow-ranging species, whereas the current 0 degrees C isotherm limits the distributions of wide-ranging species. Our analyses contradict previous studies of large-scale species richness patterns and support the view that "historic climate" can contribute to current species richness independently of and at least as much as contemporary climate.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2ZG, OXON, ENGLAND},
	Author = {Araujo, Miguel B. and Nogues-Bravo, David and Diniz-Filho, Jose Alexandre F. and Haywood, Alan M. and Valdes, Paul J. and Rahbek, Carsten},
	Date = {FEB 2008},
	Date-Added = {2008-05-13 14:32:51 +0100},
	Date-Modified = {2008-05-13 14:33:09 +0100},
	Doi = {DOI 10.1111/j.2007.0906-7590.05318.x},
	Journal = {Ecography},
	Pages = {8-15},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {1},
	Title = {Quaternary climate changes explain diversity among reptiles and amphibians},
	Volume = {31},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.2007.0906-7590.05318.x}}

@article{Mayhew.Jenkins.ea.2008.a,
	Abstract = {The past relationship between global temperature and levels of biological diversity is of increasing concern due to anthropogenic climate warming. However, no consistent link between these variables has yet been demonstrated. We analysed the fossil record for the last 520 Myr against estimates of low latitude sea surface temperature for the same period. We found that global biodiversity (the richness of families and genera) is related to temperature and has been relatively low during warm 'greenhouse' phases, while during the same phases extinction and origination rates of taxonomic lineages have been relatively high. These findings are consistent for terrestrial and marine environments and are robust to a number of alternative assumptions and potential biases. Our results provide the first clear evidence that global climate may explain substantial variation in the fossil record in a simple and consistent manner. Our findings may have implications for extinction and biodiversity change under future climate warming.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Mayhew, Peter J. and Jenkins, Gareth B. and Benton, Timothy G.},
	Date = {JAN 7 2008},
	Date-Added = {2008-05-13 14:24:04 +0100},
	Date-Modified = {2008-05-13 14:24:09 +0100},
	Doi = {DOI 10.1098/rspb.2007.1302},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {fossil record; global biodiversity; global climate change; global temperature; macroevolution; mass extinction},
	Pages = {47-53},
	Publisher = {ROYAL SOC},
	Timescited = {0},
	Title = {A long-term association between global temperature and biodiversity, origination and extinction in the fossil record},
	Volume = {275},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.1302}}

@article{Kozak.Wiens.2007.a,
	Abstract = {Many groups of organisms show greater species richness in the tropics than in the temperate zone, particularly in tropical montane regions. Forty years ago, Janzen suggested that more limited temperature seasonality in the tropics leads to greater climatic zonation and more climatic barriers to organismal dispersal along elevational gradients in the tropics relative to temperate regions. These factors could lead to differences in how species arise in tropical versus temperate regions and possibly contribute to greater tropical diversity. However, no studies have compared the relationships among climate, elevational distribution and speciation in a group inhabiting both tropical and temperate regions. Here, we compare elevational and climatic divergence among 30 sister-species pairs (14 tropical, 16 temperate) within a single family of salamanders (Plethodontidae) that reaches its greatest species richness in montane Mesoamerica. In support of Janzen's hypothesis, we find that sister species are more elevationally and climatically divergent in the tropics than in the temperate zone. This pattern seemingly reflects regional variation in the role of climate in speciation, with niche conservatism predominating in the temperate zone and niche divergence in the tropics. Our study demonstrates how latitudinal differences in elevational climatic zonation may increase opportunities for geographical isolation, speciation and the associated build-up of species diversity in the tropics relative to the temperate zone.},
	Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
	Author = {Kozak, Kenneth H. and Wiens, John J.},
	Date = {DEC 7 2007},
	Date-Added = {2008-05-13 14:23:17 +0100},
	Date-Modified = {2008-05-13 14:23:21 +0100},
	Doi = {DOI 10.1098/rspb.2007.1106},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {elevation; climate; latitude; niche evolution; speciation; species richness},
	Pages = {2995-3003},
	Publisher = {ROYAL SOC},
	Timescited = {2},
	Title = {Climatic zonation drives latitudinal variation in speciation mechanisms},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.1106}}

@article{Thomas.Orme.ea.2008.a,
	Abstract = {Aim Using a global data base of the distribution of extant bird species, we examine the evidence for spatial variation in the evolutionary origins of contemporary avian diversity. In particular, we assess the possible role of the timing of mountain uplift in promoting diversification in different regions.

Location Global.

Methods We mapped the distribution of avian richness at four taxonomic levels on an equal-area 1 degrees grid. We examined the relationships between richness at successive taxonomic levels (e.g. species richness vs. genus richness). We mapped the residuals from linear regressions of these relationships to identify areas that are exceptional in the number of lower taxa relative to the number of higher taxa. We use generalized least squares models to test the influence of elevation range and temperature on lower-taxon richness relative to higher-taxon richness.

Results Peaks of species richness in the Neotropics were congruent with patterns of generic richness, whilst peaks in Australia and the Himalayas were congruent with patterns of both genus and family richness. Hotspots in the Afrotropics did not reflect higher-taxon patterns. Regional differences in the relationship between richness at successive taxonomic levels revealed variation in patterns of taxon co-occurrence. Species and genus co-occurrence was positively associated with elevational range across much of the world. Taxon occurrence in the Neotropics was associated with a positive interaction between elevational range and temperature.

Conclusions These results demonstrate that contemporary patterns of richness show different associations with higher-taxon richness in different regions, which implies that the timing of historical effects on these contemporary patterns varies across regions. We suggest that this is due to dispersal limitation and phylogenetic constraints on physiological tolerance limits promoting diversification. We speculate that diversification rates respond to long-term changes in the Earth's topography, and that the role of tropical mountain ranges is implicated as a correlate of contemporary diversity, and a source of diversification across avian evolutionary history.},
	Address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND},
	Author = {Thomas, Gavin H. and Orme, C. David L. and Davies, Richard G. and Olson, Valerie A. and Bennett, Peter M. and Gaston, Kevin J. and Owens, Ian P. F. and Blackburn, Tim M.},
	Date = {MAY 2008},
	Date-Added = {2008-05-13 14:15:09 +0100},
	Date-Modified = {2008-05-13 14:15:23 +0100},
	Doi = {DOI 10.1111/j.1466-8238.2008.00384.x},
	Journal = {Global Ecology and Biogeography},
	Keywords = {biodiversity; birds; orogeny; species richness; taxon ratios; topography},
	Pages = {340-351},
	Publisher = {BLACKWELL PUBLISHING},
	Timescited = {0},
	Title = {Regional variation in the historical components of global avian species richness},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2008.00384.x}}

@article{Phillimore.Orme.ea.2008.a,
	Abstract = {Sympatric speciation is now accepted as theoretically plausible and a likely explanation for divergence in a handful of taxa, but its contribution to large-scale patterns of speciation remains contentious. A major problem is that it is difficult to differentiate between alternate scenarios of geographic speciation when species ranges have shifted substantially in the past. Previous studies have searched for a signal of the geographic mode of speciation by testing for a correlation between time since speciation and range overlap. Here we use simulations to show that the proportion of species showing zero or complete range overlap are more reliable indicators of the geography of speciation than is the correlation between time since speciation and overlap. We then apply these findings to the distributions of 291 pairs of avian sister species. Although 49\% of pairs show some overlap in their ranges, our simulations show that this is not surprising under allopatric models of speciation. More revealingly, less than 2\% show complete range overlap. Our simulations demonstrate that the observed patterns are most consistent with a model in which allopatric speciation is dominant but in which sympatric speciation is also present and contributes 5\% of speciation events.},
	Address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA},
	Author = {Phillimore, Albert B. and Orme, C. David L. and Thomas, Gavin H. and Blackburn, Tim M. and Bennett, Peter M. and Gaston, Kevin J. and Owens, Ian P. F.},
	Date = {MAY 2008},
	Date-Added = {2008-05-13 14:15:09 +0100},
	Date-Modified = {2008-05-13 14:15:16 +0100},
	Doi = {DOI 10.1086/587074},
	Journal = {American Naturalist},
	Keywords = {speciation; allopatric; sympatric; geographic range; birds; phylogeny},
	Pages = {646-657},
	Publisher = {UNIV CHICAGO PRESS},
	Timescited = {0},
	Title = {Sympatric speciation in birds is rare: Insights from range data and simulations},
	Volume = {171},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1086/587074}}

@article{Richards.Carstens.ea.2007.a,
	Abstract = { Abstract Statistical phylogeographic studies contribute to our understanding of the factors that influence population divergence and speciation, and that ultimately generate biogeographical patterns. The use of coalescent modelling for analyses of genetic data provides a framework for statistically testing alternative hypotheses about the timing and pattern of divergence. However, the extent to which such approaches contribute to our understanding of biogeography depends on how well the alternative hypotheses chosen capture relevant aspects of species histories. New modelling techniques, which explicitly incorporate spatio-geographic data external to the gene trees themselves, provide a means for generating realistic phylogeographic hypotheses, even for taxa without a detailed fossil record. Here we illustrate how two such techniques - species distribution modelling and its historical extension, palaeodistribution modelling - in conjunction with coalescent simulations can be used to generate and test alternative hypotheses. In doing so, we highlight a few key studies that have creatively integrated both historical geographic and genetic data and argue for the wider incorporation of such explicit integrations in biogeographical studies. },
	Author = {Richards,Corinne L. and Carstens,Bryan C. and Lacey Knowles,L.},
	Date-Added = {2008-05-13 14:10:01 +0100},
	Date-Modified = {2008-05-13 14:10:35 +0100},
	Doi = {10.1111/j.1365-2699.2007.01814.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-2699.2007.01814.x},
	Journal = {Journal of Biogeography},
	Number = {11},
	Pages = {1833-1845},
	Rating = {0},
	Title = {Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2699.2007.01814.x},
	Volume = {34},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2699.2007.01814.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2699.2007.01814.x}}

@article{McKnight.White.ea.2007.a,
	Abstract = {Beta-diversity, the change in species composition between places, is a critical but poorly understood component of biological diversity. Patterns of beta-diversity provide information central to many ecological and evolutionary questions, as well as to conservation planning. Yet beta-diversity is rarely studied across large extents, and the degree of similarity of patterns among taxa at such scales remains untested. To our knowledge, this is the first broad-scale analysis of cross-taxon congruence in beta-diversity, and introduces a new method to map beta-diversity continuously across regions. Congruence between amphibian, bird, and mammal beta-diversity in the Western Hemisphere varies with both geographic location and spatial extent. We demonstrate that areas of high beta-diversity for the three taxa largely coincide, but areas of low beta-diversity exhibit little overlap. These findings suggest that similar processes lead to high levels of differentiation in amphibian, bird, and mammal assemblages, while the ecological and biogeographic factors influencing homogeneity in vertebrate assemblages vary. Knowledge of beta-diversity congruence can help formulate hypotheses about the mechanisms governing regional diversity patterns and should inform conservation, especially as threat from global climate change increases. },
	Annote = {Reviewed this},
	Author = {McKnight, Meghan W. and White, Peter S. and McDonald, Robert I. and Lamoreux, John F. and Sechrest, Wes and Ridgely, Robert S. and Stuart, Simon N.},
	Date-Added = {2008-05-13 14:01:19 +0100},
	Date-Modified = {2008-05-13 14:02:19 +0100},
	Journal = {PLoS Biology},
	Number = {10},
	Sp = {e272 EP -},
	Title = {Putting Beta-Diversity on the Map: Broad-Scale Congruence and Coincidence in the Extremes},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050272},
	Volume = {5},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pbio.0050272}}

@article{Lima.Ribeiro.ea.2007.a,
	Abstract = { Abstract A climate envelope approach was used to model the distributions of the intertidal gastropod Patella rustica, to test the robustness of forecast responses to climate change. The model incorporated variables that were likely to determine the abundance and the northern range limit of this species in the NE Atlantic. The model was built using classification and regression tree analysis (CART) trained with historical distribution data from the mid 1950s and a set of corresponding climatic and oceanographic variables. Results indicated air and sea temperature, in particular during the reproductive and settlement periods, as the main determinants of the Atlantic distribution of P. rustica. The model was subsequently fed with contemporary climatic data and its output was compared with the current distribution and abundance of P. rustica, assessed during a 2002-2003 survey. The model correctly hindcasted the recent collapse of a distributional gap in northern Portugal, as well as an increase in abundance at locations within its range. The predicted northward expansion of the northern range limit did not occur because the absence of the species was confirmed in a survey encompassing the whole Atlantic French coast up to Brest. Stretches of unsuitable habitat too long to be overcome by dispersal are the likely mechanism controlling the northern limit of the distribution of this intertidal species. },
	Author = {Lima, Fernando P. and Ribeiro, Pedro A. and Queiroz, Nuno and Xavier, Raquel and Tarroso, Pedro and Hawkins, Stephen J. and Santos, Antonio M.},
	Date-Added = {2008-05-13 13:54:14 +0100},
	Date-Modified = {2008-05-13 13:55:36 +0100},
	Doi = {10.1111/j.1365-2486.2007.01424.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-2486.2007.01424.x},
	Journal = {Global Change Biology},
	Number = {10},
	Pages = {2065-2077},
	Title = {Modelling past and present geographical distribution of the marine gastropod Patella rustica as a tool for exploring responses to environmental change},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2486.2007.01424.x},
	Volume = {13},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2486.2007.01424.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2486.2007.01424.x}}

@article{Dormann.2007.a,
	Abstract = {Summary Projections of species' distribution under global change (climatic and environmental) are of great scientific and societal relevance. They rely on a proper understanding of how environmental drivers determine species occurrence patterns. This understanding is usually derived from an analysis of the species' present distribution by statistical means (species distribution models). Projections based on species distribution models make several assumptions (such as constancy of limiting factors, no evolutionary adaptation to drivers, global dispersal), some of which are ecologically untenable. Also, methodological issues muddy the waters (e.g. spatial autocorrelation, collinearity of drivers). Here, I review the main shortcomings of species distribution models and species distribution projections, identify limits to their use and open a perspective on how to overcome some current obstacles. As a consequence, I caution biogeographers against making projections too light-heartedly and conservation ecologists and policy makers to be aware that there are several unresolved problems.},
	Author = {Dormann, Carsten F.},
	Date-Added = {2008-05-13 13:52:00 +0100},
	Date-Modified = {2008-05-13 13:52:00 +0100},
	Journal = {Basic and Applied Ecology},
	Keywords = {Climate change; Conservation management; Environmental change; Extrapolation; Prediction; Spatial statistics; Species distribution model},
	Number = {5},
	Pages = {387--397},
	Title = {Promising the future? Global change projections of species distributions},
	Ty = {JOUR},
	Url = {http://www.sciencedirect.com/science/article/B7GVS-4MY6NG9-1/1/4aedd8cb341014732eaba0927ec9511b},
	Volume = {8},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B7GVS-4MY6NG9-1/1/4aedd8cb341014732eaba0927ec9511b}}

@article{Soberon.2007.a,
	Abstract = { Abstract In the recent past, availability of large data sets of species presences has increased by orders of magnitude. This, together with developments in geographical information systems and statistical methods, has enabled scientists to calculate, for thousands of species, the environmental conditions of their distributional areas. The profiles thus obtained are obviously related to niche concepts in the Grinnell tradition, and separated from those in Elton's tradition. I argue that it is useful to define Grinnellian and Eltonian niches on the basis of the types of variables used to calculate them, the natural spatial scale at which they can be measured, and the dispersal of the individuals over the environment. I use set theory notation and analogies derived from population ecology theory to obtain formal definitions of areas of distribution and several types of niches. This brings clarity to several practical and fundamental questions in macroecology and biogeography. },
	Author = {Soberon,Jorge},
	Date-Added = {2008-05-13 13:51:37 +0100},
	Date-Modified = {2009-02-19 07:01:15 +0000},
	Doi = {10.1111/j.1461-0248.2007.01107.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1461-0248.2007.01107.x},
	Journal = {Ecology Letters},
	Number = {12},
	Pages = {1115-1123},
	Title = {{Grinnellian and Eltonian niches and geographic distributions of species}},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2007.01107.x},
	Volume = {10},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2007.01107.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2007.01107.x}}

@article{Freckleton.Phillimore.ea.200.a,
	Annote = {Manuscript in preparation - don't know status [13/5/2008]},
	Author = {Freckleton, Robert P. and Phillimore, Albert B. and Pagel, Mark},
	Date-Added = {2008-05-13 13:43:24 +0100},
	Date-Modified = {2011-02-08 10:22:20 +0000},
	Journal = {American Naturalist},
	Month = {July},
	Number = {1},
	Title = {Relating traits to diversification: a test and the limits to inference},
	Volume = {172},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-File-3 = { }}

@unpublished{Freckleton.2007.a,
	Annote = {Was called pgls3.R},
	Author = {Freckleton, Robert P.},
	Date-Added = {2008-05-13 13:34:24 +0100},
	Date-Modified = {2008-05-13 13:35:57 +0100},
	Month = {March},
	Title = {Phylogenetic generalized linear model},
	Year = {2007},
	Bdsk-File-1 = { }}

@unpublished{Hadfield.2008.a,
	Annote = {Jarrod's exposistion of the problems of using lmer (rather than ASREML) to fit models with heterogenous variance in a grouping factor},
	Author = {Hadfield, Jarrod D.},
	Date-Added = {2008-05-13 12:54:52 +0100},
	Date-Modified = {2008-05-13 12:56:54 +0100},
	Month = {April},
	Title = {How to Measure Genotype X Treatment Interactions},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Scotese.2004.a,
	Abstract = {Forty-six miniature plate tectonic reconstructions are presented that can be assembled into a "flipbook" that illustrates the movement of the continents since the Late Precambrian, 750 m. yr. ago. Six principal lines of evidence have been used to reconstruct the past positions of the continents: ( 1) linear magnetic anomalies produced by sea floor spreading, ( 2) paleomagnetism, ( 3) hotspot tracks and large igneous provinces, ( 4) the tectonic fabric of the ocean floor mapped by satellite altimetry, ( 5) lithologic indicators of climate (e.g., coals, salt deposits, tillites), and (6) the geologic record of plate tectonic history. I discuss the probable uncertainties associated with the plate tectonic reconstructions and give an estimate of the uncertainty in the positions of the continents back through time.},
	Address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA},
	Author = {Scotese, Christopher R.},
	Date = {NOV 2004},
	Date-Added = {2008-05-13 11:53:30 +0100},
	Date-Modified = {2008-05-13 11:54:02 +0100},
	Journal = {Journal of Geology},
	Pages = {729-741},
	Publisher = {UNIV CHICAGO PRESS},
	Timescited = {15},
	Title = {A continental drift flipbook},
	Volume = {112},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Scholze.Knorr.ea.2006.a,
	Abstract = {We quantify the risks of climate-induced changes in key ecosystem processes during the 21st century by forcing a dynamic global vegetation model with multiple scenarios from 16 climate models and mapping the proportions of model runs showing forest/nonforest shifts or exceedance of natural variability in wildfire frequency and freshwater supply. Our analysis does not assign probabilities to scenarios or weights to models. Instead, we consider distribution of outcomes within three sets of model runs grouped by the amount of global warming they simulate: <2{degrees}C (including simulations in which atmospheric composition is held constant, i.e., in which the only climate change is due to greenhouse gases already emitted), 2-3{degrees}C, and >3{degrees}C. High risk of forest loss is shown for Eurasia, eastern China, Canada, Central America, and Amazonia, with forest extensions into the Arctic and semiarid savannas; more frequent wildfire in Amazonia, the far north, and many semiarid regions; more runoff north of 50{degrees}N and in tropical Africa and northwestern South America; and less runoff in West Africa, Central America, southern Europe, and the eastern U.S. Substantially larger areas are affected for global warming >3{degrees}C than for <2{degrees}C; some features appear only at higher warming levels. A land carbon sink of {approx}1 Pg of C per yr is simulated for the late 20th century, but for >3{degrees}C this sink converts to a carbon source during the 21st century (implying a positive climate feedback) in 44% of cases. The risks continue increasing over the following 200 years, even with atmospheric composition held constant.
},
	Author = {Scholze, Marko and Knorr, Wolfgang and Arnell, Nigel W. and Prentice, I. Colin},
	Date-Added = {2008-05-13 11:49:40 +0100},
	Date-Modified = {2008-05-13 11:50:02 +0100},
	Doi = {10.1073/pnas.0601816103},
	Eprint = {http://www.pnas.org/cgi/reprint/103/35/13116.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {35},
	Pages = {13116-13120},
	Title = {{A climate-change risk analysis for world ecosystems}},
	Url = {http://www.pnas.org/cgi/content/abstract/103/35/13116},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/cgi/content/abstract/103/35/13116},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0601816103}}

@article{Zhou.Zhang.2008.a,
	Abstract = {S. P. Hubbell's unified neutral theory of biodiversity has stimulated much new thinking about biodiversity. However, empirical support for the neutral theory is limited, and several observations are inconsistent with the predictions of the theory, including positive correlations between traits associated with competitive ability and species abundance and correlations between species diversity and ecosystem functioning. The neutral theory can be extended to explain these observations by allowing species to differ slightly in their competitive ability (fitness). Here, we show that even slight differences in fecundity can greatly reduce the time to extinction of competitors even when the community size is large and dispersal is spatially limited. In this case, species richness is dramatically reduced, and a markedly different species abundance distribution is predicted than under pure neutrality. In the nearly neutral model, species co-occur in the same community not because of, but in spite of, ecological differences. The more competitive species with higher fecundity tend to have higher abundance both in the metacommunity and in local communities. The nearly neutral perspective provides a theoretical framework that unites the sampling model of the neutral theory with theory of biodiversity affecting ecosystem function. },
	Author = {Zhou, Shu-Rong and Zhang, Da-Yong},
	Date-Added = {2008-05-07 10:23:55 +0100},
	Date-Modified = {2008-05-07 10:23:55 +0100},
	Journal = {Ecology},
	Number = {1},
	Pages = {248--258},
	Title = {A NEARLY NEUTRAL MODEL OF BIODIVERSITY},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1890%2F06-1817.1},
	Volume = {89},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1890/06-1817.1}}

@article{Deutsch.Tewksbury.ea.2008.a,
	Abstract = {The impact of anthropogenic climate change on terrestrial organisms is often predicted to increase with latitude, in parallel with the rate of warming. Yet the biological impact of rising temperatures also depends on the physiological sensitivity of organisms to temperature change. We integrate empirical fitness curves describing the thermal tolerance of terrestrial insects from around the world with the projected geographic distribution of climate change for the next century to estimate the direct impact of warming on insect fitness across latitude. The results show that warming in the tropics, although relatively small in magnitude, is likely to have the most deleterious consequences because tropical insects are relatively sensitive to temperature change and are currently living very close to their optimal temperature. In contrast, species at higher latitudes have broader thermal tolerance and are living in climates that are currently cooler than their physiological optima, so that warming may even enhance their fitness. Available thermal tolerance data for several vertebrate taxa exhibit similar patterns, suggesting that these results are general for terrestrial ectotherms. Our analyses imply that, in the absence of ameliorating factors such as migration and adaptation, the greatest extinction risks from global warming may be in the tropics, where biological diversity is also greatest.
},
	Author = {Deutsch, Curtis A. and Tewksbury, Joshua J. and Huey, Raymond B. and Sheldon, Kimberly S. and Ghalambor, Cameron K. and Haak, David C. and Martin, Paul R.},
	Date-Added = {2008-05-07 10:11:26 +0100},
	Date-Modified = {2008-05-07 10:12:10 +0100},
	Doi = {10.1073/pnas.0709472105},
	Eprint = {http://www.pnas.org/cgi/reprint/105/18/6668.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {18},
	Pages = {6668-6672},
	Title = {{Impacts of climate warming on terrestrial ectotherms across latitude}},
	Url = {http://www.pnas.org/cgi/content/abstract/105/18/6668},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/cgi/content/abstract/105/18/6668},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0709472105}}

@article{Joppa.Loarie.ea.2008.a,
	Abstract = {Tropical moist forests contain the majority of terrestrial species. Human actions destroy between 1 and 2 million km2 of such forests per decade, with concomitant carbon release into the atmosphere. Within these forests, protected areas are the principle defense against forest loss and species extinctions. Four regions--the Amazon, Congo, South American Atlantic Coast, and West Africa--once constituted about half the world's tropical moist forest. We measure forest cover at progressively larger distances inside and outside of protected areas within these four regions, using datasets on protected areas and land-cover. We find important geographical differences. In the Amazon and Congo, protected areas are generally large and retain high levels of forest cover, as do their surroundings. These areas are protected de facto by being inaccessible and will likely remain protected if they continue to be so. Deciding whether they are also protected de jure--that is, whether effective laws also protect them--is statistically difficult, for there are few controls. In contrast, protected areas in the Atlantic Coast forest and West Africa show sharp boundaries in forest cover at their edges. This effective protection of forest cover is partially offset by their very small size: little area is deep inside protected area boundaries. Lands outside protected areas in the Atlantic Coast forest are unusually fragmented. Finally, we ask whether global databases on protected areas are biased toward highly protected areas and ignore "paper parks." Analysis of a Brazilian database does not support this presumption.
},
	Author = {Joppa, Lucas N. and Loarie, Scott R. and Pimm, Stuart L.},
	Date-Added = {2008-05-07 10:11:21 +0100},
	Date-Modified = {2008-05-07 10:12:16 +0100},
	Doi = {10.1073/pnas.0802471105},
	Eprint = {http://www.pnas.org/cgi/reprint/105/18/6673.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {18},
	Pages = {6673-6678},
	Title = {{On the protection of "protected areas"}},
	Url = {http://www.pnas.org/cgi/content/abstract/105/18/6673},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/cgi/content/abstract/105/18/6673},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0802471105}}

@article{Burnham.Anderson.2004.a,
	Abstract = {The model selection literature has been generally poor at reflecting the deep foundations of the Akaike information criterion (AIC) and at making appropriate comparisons to the Bayesian information criterion (BIC). There is a clear philosophy, a sound criterion based in information theory, and a rigorous statistical foundation for AIC. AIC can be justified as Bayesian using a "savvy" prior on models that is a function of sample size and the number of model parameters. Furthermore, BIC can be derived as a non-Bayesian result. Therefore, arguments about using AIC versus BIC for model selection cannot be from a Bayes versus frequentist perspective. The philosophical context of what is assumed about reality, approximating models, and the intent of model-based inference should determine whether AIC or BIC is used. Various facets of such multimodel inference are presented here, particularly methods of model averaging.
},
	Author = {Burnham, Kenneth P. and Anderson, David R.},
	Date-Added = {2008-05-06 14:23:28 +0100},
	Date-Modified = {2008-05-06 14:23:34 +0100},
	Doi = {10.1177/0049124104268644},
	Eprint = {http://smr.sagepub.com/cgi/reprint/33/2/261.pdf},
	Journal = {Sociological Methods Research},
	Number = {2},
	Pages = {261-304},
	Title = {{Multimodel Inference: Understanding AIC and BIC in Model Selection}},
	Url = {http://smr.sagepub.com/cgi/content/abstract/33/2/261},
	Volume = {33},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://smr.sagepub.com/cgi/content/abstract/33/2/261},
	Bdsk-Url-2 = {http://dx.doi.org/10.1177/0049124104268644}}

@book{Hedges.Olkin.1985.a,
	Address = {San Diego},
	Author = {Hedges, L.V. and Olkin, I.},
	Date-Added = {2008-05-06 11:33:25 +0100},
	Date-Modified = {2008-05-06 11:34:28 +0100},
	Publisher = {Academic Press},
	Title = {Statistical Methods for Meta- Analysis},
	Year = {1985}}

@techreport{USGS.2003.a,
	Author = {{United Stated Geological Survey}},
	Date-Added = {2008-05-06 10:31:54 +0100},
	Date-Modified = {2008-05-06 10:59:09 +0100},
	Institution = {National Center for Earth Resources Observation and Science},
	Title = {Global 30-arc-second elevation data set (GTOPO30)},
	Url = {http://edcdaac.usgs.gov/gtopo30/gtopo30.asp},
	Year = {2003},
	Bdsk-Url-1 = {http://edcdaac.usgs.gov/gtopo30/gtopo30.asp}}

@techreport{USGS.2003.b,
	Author = {{United States Geological Survey}},
	Date-Added = {2008-05-06 10:30:54 +0100},
	Date-Modified = {2008-05-06 10:59:14 +0100},
	Institution = {National Center for Earth Resources Observation and Science},
	Title = {Global land cover characterisation},
	Url = {http://edcdaac.usgs.gov/glcc/glcc.asp},
	Year = {2003},
	Bdsk-Url-1 = {http://edcdaac.usgs.gov/glcc/glcc.asp}}

@url{ISLSCP.2004.a,
	Annote = {Author is data provider},
	Author = {{The International Satellite Land-Surface Climatology Project Initiative II}},
	Date-Added = {2008-05-06 10:26:05 +0100},
	Date-Modified = {2008-05-06 11:00:50 +0100},
	Title = {Fourier-adjusted, Sensor and Solar zenith angle corrected, Interpolated,Reconstructed (FASIR) adjusted Normalised Difference Vegetation Index (NDVI)},
	Url = {http://islscp2.sesda.com/ISLSCP2_1/html_pages/groups/veg/fasir_ndvi_monthly_xdeg.html},
	Year = {2004},
	Bdsk-Url-1 = {http://islscp2.sesda.com/ISLSCP2_1/html_pages/groups/veg/fasir_ndvi_monthly_xdeg.html}}

@article{New.Lister.ea.2002.a,
	Abstract = {We describe the construction of a 10' latitude/longitude data set of mean monthly surface climate over global land areas, excluding Antarctica. The climatology includes 8 climate elements-precipitation, wet-day frequency, temperature, diurnal temperature range, relative humidity, sunshine duration, ground frost frequency and windspeed-and was interpolated from a data set of station means for the period centred on 1961 to 1990. Precipitation was first defined in terms of the parameters of the Gamma distribution, enabling the calculation of monthly precipitation at any given return period. The data are compared to an earlier data set at 0.5degrees latitude/longitude resolution and show added value over most regions. The data will have many applications in applied climatology, biogeochemical modelling, hydrology and agricultural meteorology and are available through the International Water Management Institute World Water and Climate Atlas (http://www.iwmi.org) and the Climatic Research Unit (littp://www.cru,uea.ac.uk).},
	Author = {New, Mark and Lister, David and Hulme, Mike and Makin, Ian},
	Date-Added = {2008-05-06 10:23:17 +0100},
	Date-Modified = {2008-05-06 10:25:40 +0100},
	Journal = {Climate Research},
	Keywords = {high resolution data set; surface climate; applied climatology; precipitation probability; IWMI Climate Atlas; CRU},
	Pages = {1-25},
	Timescited = {0},
	Title = {A high-resolution data set of surface climate over global land areas},
	Volume = {21},
	Year = {2002},
	Bdsk-File-1 = { }}

@book{Steadman.2006.a,
	Address = {Chicago},
	Author = {Steadman, D.W.},
	Date-Added = {2008-05-06 10:14:50 +0100},
	Date-Modified = {2008-05-06 10:15:18 +0100},
	Publisher = {University of Chicago Press},
	Title = {Extinction and biogeography of tropical Pacific birds},
	Year = {2006}}

@article{Clegg.Owens.2002.a,
	Abstract = {Do birds show a different pattern of insular evolution from mammals? Mammals follow the 'island rule', with large-bodied species getting smaller on islands and small-bodied species getting bigger. By contrast, the traditional view on birds is that they follow no general island rule for body size, but that there is an insular trend for large bills. Insular shifts in feeding ecology are, therefore, widely assumed to be the primary cause of divergence in island birds. We use a comparative approach to test these ideas. Contrary to the traditional view, we find no evidence for increased bill size in insular populations. Instead, changes in both bill size and body size obey the 'island rule'. The differences between our results and the traditional view arise because previous analyses were based largely on passerines. We also investigate some ecological factors that are thought to influence island evolution. As predicted by the traditional view, shifts in bill size are associated with feeding ecology. By contrast, shifts in body size are associated with the potential for intraspecific competition and thermal ecology. All these results remain qualitatively unchanged when we use different methods to score the ecological factors and restrict our analyses to taxa showing pronounced morphological divergence. Because of strong covariation between ecological factors, however, we cannot estimate the relative importance of each ecological factor. Overall, our results show that the island rule is valid for both body size and bill length in birds and that, in addition to feeding ecology, insular shifts in the level of intraspecific competition and the abiotic environment also have a role.},
	Author = {Clegg, Sonya M. and Owens, Ian P. F.},
	Date-Added = {2008-05-06 10:10:09 +0100},
	Date-Modified = {2008-05-06 10:11:23 +0100},
	Doi = {DOI 10.1098/rspb.2002.2024},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {bill size; birds; body size; ecology; evolution; islands},
	Pages = {1359-1365},
	Timescited = {0},
	Title = {The 'island rule' in birds: medium body size and its ecological explanation},
	Volume = {269},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2002.2024}}

@article{Brown.Nicoletto.1991.a,
	Author = {Brown,James H. and Nicoletto,Paul F.},
	Date-Added = {2008-05-06 10:01:11 +0100},
	Date-Modified = {2008-05-06 10:01:13 +0100},
	Doi = {10.1086/285297},
	Eprint = {http://www.journals.uchicago.edu/doi/pdf/10.1086/285297},
	Journal = {The American Naturalist},
	Number = {6},
	Pages = {1478},
	Title = {Spatial Scaling of Species Composition: Body Masses of North American Land Mammals},
	Url = {http://www.journals.uchicago.edu/doi/abs/10.1086/285297},
	Volume = {138},
	Year = {1991},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.journals.uchicago.edu/doi/abs/10.1086/285297},
	Bdsk-Url-2 = {http://dx.doi.org/10.1086/285297}}

@article{Blackburn.Gaston.ea.1999.a,
	Author = {Blackburn, Tim M. and Gaston, Kevin J. and Loder, Natasha},
	Date-Added = {2008-05-06 09:01:55 +0100},
	Date-Modified = {2009-06-18 10:11:45 +0100},
	Doi = {10.1046/j.1472-4642.1999.00046.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1046/j.1472-4642.1999.00046.x},
	Journal = {Diversity and Distributions},
	Number = {4},
	Pages = {165-174},
	Title = {{Geographic gradients in body size: a clarification of Bergmann's rule.}},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1046/j.1472-4642.1999.00046.x},
	Volume = {5},
	Year = {1999},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1046/j.1472-4642.1999.00046.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1046/j.1472-4642.1999.00046.x}}

@book{Quinn.Keough.2002.a,
	Address = {Cambridge, U.K},
	Author = {Quinn, G. P. and Keough, M. J.},
	Date-Added = {2008-05-02 16:43:43 +0100},
	Date-Modified = {2008-05-02 16:44:16 +0100},
	Publisher = {Cambridge University Press},
	Title = {Experimental design and data analysis for biologists},
	Year = {2002}}

@incollection{Marsh.1989.a,
	Address = {New York},
	Author = {Marsh, R.L. and Dawson, W.R.},
	Booktitle = {Animal adaptation to cold},
	Date-Added = {2008-05-02 16:40:17 +0100},
	Date-Modified = {2008-05-07 10:14:59 +0100},
	Editor = {Wang, L. C. H.},
	Pages = {206-253},
	Publisher = {Springer-Verlag},
	Series = {Advances in Comparative and Environmental Physiology},
	Title = {Avian adjustments to cold},
	Volume = {4},
	Year = {1989}}

@article{McKechnie.Lovegrove.2002.a,
	Abstract = {Recent evidence suggests that avian facultative hypothermic responses are more common, and occur in a wider variety of ecological contexts, than previously thought. The capacity for shallow hypothermia (rest-phase hypothermia) occurs throughout the avian phylogeny, but the capacity for pronounced hypothermia (torpor) appears to be restricted to certain taxa. Families in which torpor has been reported include the Todidae, Coliidae, Trochilidae, Apodidae, Caprimulgidae, and Columbidae. Facultative hypothermia occurs in species ranging in body mass (M-b) from <3 g to ca. 6500 g. Minimum body temperature (T-b) during hypothermia is continuously distributed from 4.3degreesC to ca. 38degreesC. The physiological distinction between torpor and rest-phase hypothermia is unclear. Whereas these two responses have traditionally been distinguished on the basis of T-b we find little support for the biological reality of specific T-b limits. Instead, we argue that emphasis should be placed on understanding the relationship between metabolic and T-b reduction and the capacity to respond to external stimuli. Patterns of thermoregulation during avian hypothermic responses are relatively variable, and do not necessarily follow the entry-maintenance-arousal patterns that characterize mammalian responses. Avian hypothermic responses are determined by a suite of ecological and physiological determinants including food availability, ambient temperature, hormone levels, and breeding cycle.},
	Author = {McKechnie, Andrew E. and Lovegrove, Barry G.},
	Date-Added = {2008-05-02 16:39:45 +0100},
	Date-Modified = {2008-05-02 16:51:13 +0100},
	Journal = {Condor},
	Keywords = {body size; body temperature; ecological determinants; hypothermia; phylogeny; torpor},
	Pages = {705-724},
	Timescited = {0},
	Title = {Avian facultative hypothermic responses: A review},
	Volume = {104},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Cartron.Kelly.ea.2000.a,
	Abstract = {In a system of intercorrelated variables, the sign and strength of pairwise relationships must conform to a mathematical constraint affecting the entire system. The constraint exists as a property of all correlation matrices, the positive semi-definite (PSD) criterion. We illustrate its implications with a case study of covariation among clutch size, body size, and latitude in the Strigidae. Our analyses indicate that clutch size and body size among strigid owls increase with latitude, while clutch size decreases with body size. The PSD provides a framework to explain the existence of this apparent macroevolutionary paradox. It also shows why the three relationships are never detected concurrently when using simple regressions or independent contrasts. In a system with three intercorrelated variables, the PSD criterion may allow one pairwise relationship to be negative even if the other two relationships are positive. However, the correlation coefficients cannot all be strong. Whenever the PSD criterion may constrain covariation, care should be exercised in inferring evolutionary or ecological processes from patterns of correlation.},
	Author = {Cartron, Jean-Luc E. and Kelly, Jeffrey F and Brown, James H},
	Date-Added = {2008-05-02 16:39:12 +0100},
	Date-Modified = {2008-05-02 16:52:11 +0100},
	Journal = {Oikos},
	Pages = {381-389},
	Rating = {0},
	Timescited = {0},
	Title = {Constraints on patterns of covariation: a case study in strigid owls},
	Volume = {90},
	Year = {2000},
	Bdsk-File-1 = { }}

@book{Burnham.Anderson.2002.a,
	Address = {New York},
	Author = {Burnham, K. P. and Anderson, D. R.},
	Date-Added = {2008-05-02 16:35:15 +0100},
	Date-Modified = {2008-05-02 16:36:13 +0100},
	Edition = {2nd},
	Publisher = {Springer},
	Title = {Model selection and multi-model inference},
	Year = {2002}}

@manual{Littell.Wolfinger.1996.a,
	Address = {Cary},
	Author = {Littell, R. C. and Milliken, G. A. and Stroup, W. W. and Wolfinger, R. D.},
	Date-Added = {2008-05-02 16:33:34 +0100},
	Date-Modified = {2008-05-02 16:52:49 +0100},
	Organization = {SAS Institute},
	Rating = {0},
	Title = {SAS system for mixed models},
	Year = {1996}}

@book{Cressie.1991.a,
	Address = {New York.},
	Author = {Cressie, N},
	Date-Added = {2008-05-02 16:32:51 +0100},
	Date-Modified = {2008-05-02 16:33:16 +0100},
	Publisher = {Wiley},
	Title = {Statistics for spatial data},
	Year = {1991}}

@article{Clifford.Richardson.ea.1989.a,
	Abstract = {Modified tests of association based on the correlation coefficient or the covariance between two spatially autocorrelated processes are presented. These tests can be used both for lattice and nonlattice data. They are based on the evaluation of an effective sample size that takes into account the spatial structure. For positively autocorrelated processes, the effective sample size is reduced. A method for evaluating this reduction via an approximation of the variance of the correlation coefficient is developed. The performance of the tests is assessed by Monte Carlo simulations. The method is illustrated by examples from geographical epidemiology. 
},
	Author = {Clifford, Peter and Richardson, Sylvia and Hemon, Denis},
	Date-Added = {2008-05-02 16:32:28 +0100},
	Date-Modified = {2011-01-11 15:21:59 +0000},
	Journal = {Biometrics},
	Pages = {123-134},
	Rating = {0},
	Timescited = {0},
	Title = {Assessing the Significance of the Correlation Between Two Spatial Processes},
	Volume = {45},
	Year = {1989},
	Bdsk-File-1 = { }}

@book{Sibley.Monroe.1990.a,
	Address = {New Haven},
	Author = {Sibley, C. G. and Monroe, B. L},
	Date-Added = {2008-05-02 16:31:22 +0100},
	Date-Modified = {2008-05-02 16:31:50 +0100},
	Publisher = {Yale University Press},
	Title = {Distribution and taxonomy of birds of the world},
	Year = {1990}}

@book{Del-Hoyo.Sargatal.1992.a,
	Address = {Barcelona},
	Author = {Del Hoyo, J. and Elliott, A. and Sargatal, J.},
	Date-Added = {2008-05-02 16:29:08 +0100},
	Date-Modified = {2008-05-02 16:29:59 +0100},
	Publisher = {Lynx Edicions},
	Title = {Handbook of the birds of the world},
	Year = {1992}}

@incollection{Zeveloff.Boyce.1988.a,
	Address = {New Haven},
	Author = {Zeveloff, S. I. and Boyce, M. S.},
	Booktitle = {Evolution of life histories of mammals theory and pattern},
	Date-Added = {2008-05-02 16:27:21 +0100},
	Date-Modified = {2008-05-02 16:28:46 +0100},
	Editor = {Boyce, M. S.},
	Pages = {123-146},
	Publisher = {Yale University Press},
	Title = {Body size patterns in North American mammal faunas},
	Year = {1988}}

@article{YOMTOV.NIX.1986.a,
	Annote = {No subscription to pre-1997 },
	Author = {Yom-Tov, Yoram and Nix, Henry},
	Date-Added = {2008-05-02 16:26:44 +0100},
	Date-Modified = {2008-05-02 17:29:24 +0100},
	Journal = {Biological Journal of the Linnean Society},
	Pages = {245-262},
	Timescited = {0},
	Title = {Climatological correlates for body size of five species of Australian mammals},
	Url = {http://www.blackwell-synergy.com/toc/bij/29/4},
	Volume = {29},
	Year = {1986},
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/toc/bij/29/4}}

@article{Rosenzweig.1968.a,
	Author = {Rosenzweig, Michael L},
	Date-Added = {2008-05-02 16:25:12 +0100},
	Date-Modified = {2008-05-02 17:31:01 +0100},
	Journal = {American Midland Naturalist},
	Pages = {299-315},
	Title = {The strategy of body size in mammalian carnivores.},
	Volume = {80},
	Year = {1968},
	Bdsk-File-1 = { }}

@article{Ramirez.Diniz-Filho.ea.2008.b,
	Abstract = {Aim To evaluate seasonal body-size patterns for New World birds in geographical space, to develop environmental models to explain the gradients, and to estimate phylogenetic and adaptive contributions.

Location The Western Hemisphere.

Methods We used range maps to generate gridded geometric mean body masses. Summer and winter patterns were distinguished based on breeding and non-breeding ranges. We first generated the geographical gradients, followed by phylogenetic eigenvector regression to generate body sizes predicted by the birds' positions in a phylogenetic tree, which were used to generate the expected phylogenetic gradient. Subtracting the expected pattern from the observed pattern isolated the adaptive component. Ordinary least squares multiple-regression models examined factors influencing the phylogenetic, adaptive and combined components of the seasonal body-size patterns, and non-spatial and spatial models were compared.

Results Birds are larger in the temperate zones than in the tropics. The gradient is quantitatively stronger in winter than in summer. Regression models explained 66.6\% of the variance in summer mass and 45.9\% of the variance in winter mass. In summer, phylogenetic and adaptive responses of birds contribute equally to the gradient. In winter, the gradient in North America is much stronger than that expected by taxonomic turnover, and responses of species independent of their family membership drive the overall pattern.

Main conclusions We confirm Bergmann's rule in New World birds and conclude that winter temperatures ultimately drive the pattern, exerting selection pressures on birds that overwhelm patterns expected by phylogenetic inertia at the family level. However, in summer, the movement of migratory species into the temperate zone weakens the gradient and generates a pattern more congruent with that expected from the taxonomic composition of the fauna. The analytical method we develop here represents a useful tool for partitioning the phylogenetic and non-phylogenetic components of spatially explicit macroecological data.},
	Author = {Ramirez,Lizabeth and Diniz-Filho,Jose Alexandre Felizola and Hawkins,Bradford A.},
	Date-Added = {2008-05-02 16:24:28 +0100},
	Date-Modified = {2008-08-21 09:38:11 +0100},
	Doi = {10.1111/j.1466-8238.2007.00346.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1466-8238.2007.00346.x},
	Journal = {Global Ecology and Biogeography},
	Keywords = {body size; Bergmann's rule; climatic gradients; macroecology; New World birds; phylogenetic eigenvector regression},
	Number = {1},
	Pages = {100-110},
	Title = {Partitioning phylogenetic and adaptive components of the geographical body-size pattern of {N}ew {W}orld birds},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1466-8238.2007.00346.x},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1466-8238.2007.00346.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00346.x},
	Bdsk-Url-3 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00346.x}}

@article{Rahbek.Graves.2000.a,
	Abstract = {Scale is widely recognized as a fundamental conceptual problem in biology, but the question of whether species-richness patterns var) with scale is often ignored in macro-ecological analyses, despite the increasing application of such data in international conservation programmes. We tested for scaling effects in species-richness gradients with spatially scaled data for 241 species of South American hummingbirds (Trochilidae). Analyses revealed that scale matters above and beyond the effect of quadrat area. Species richness was positively correlated with latitude and topographical relief at ten different spatial scales spanning two orders of magnitude (ca. 12 300 tu ra. 1 225 000 km(2)). Surprisingly, when the influence of topography was removed, the conditional variation in species richness explained by latitude fell Precipitously to insignificance at coarser spatial scales. The perception of macro-ecological pattern thus depends directly upon the scale of analysis. Although our results suggest there is no single correct scale For macro-ecological analyses, the averaging effect of quadrat sampling at coarser geographical scales obscures the fine structure of species-richness gradients and localized richness peaks, decreasing the power of statistical tests to discriminate the causal agents of regional richness gradients. Ideally the scale of analysis should be varied systematically to provide the optimal resolution of macro-ecological pattern.},
	Author = {Rahbek, Carsten and Graves, Gary R.},
	Date-Added = {2008-05-02 16:20:29 +0100},
	Date-Modified = {2008-05-04 09:28:19 +0100},
	Journal = {Proceedings of the Royal Society of London Series B - Biological Sciences},
	Keywords = {hummingbirds; latitude; scaling; species-richness gradients; topography; Trochilidae},
	Pages = {2259-2265},
	Timescited = {0},
	Title = {Detection of macro-ecological patterns in {S}outh {A}merican hummingbirds is affected by spatial scale},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Newton.Dale.1996.a,
	Abstract = {1. In western Europe, the number of bird species present in summer remains fairly constant at 187-229 between latitudes 35 and 65 degrees N, decreases to 156 by 70 degrees N, and then markedly to 26 and 24 on islands at 75 and 80 degrees N. The number present in winter decreases steadily with latitude from 211 at 35 degrees N to four at 80 degrees N, reflecting the greater withdrawal of species from northern latitudes in winter.

 2. The proportion of summer visitors in the local avifauna in summer also increases with latitude from 29\% of breeding species at 35 degrees N to 83\% of breeding species at 80 degrees N. Conversely, the proportion of winter visitors in the local avifauna in winter decreases with latitude, from 36\% of wintering species at 35 degrees N to 8\% of wintering species (mostly seabirds) at 70 degrees N to none at 80 degrees N.

3. At most latitudes in the range 35-70 degrees N, while some species leave for the winter, a smaller number of other species move in, mostly from further north. About 23\% of breeding species leave western Europe totally in autumn to winter elsewhere, most in Africa south of the Sahara but others in southern Asia and elsewhere. Conversely, 3\% of wintering species leave western Europe totally in spring to breed elsewhere, some to the north-west in Iceland-Greenland-Canada and others to the north-east in northern Siberia.

},
	Author = {Newton, Ian and Dale, L},
	Date-Added = {2008-05-02 16:19:54 +0100},
	Date-Modified = {2008-05-02 17:35:30 +0100},
	Journal = {Journal of Animal Ecology},
	Keywords = {bird migration; geographical range; latitude; species numbers},
	Pages = {137-146},
	Timescited = {0},
	Title = {Relationship between migration and latitude among west European birds},
	Volume = {65},
	Year = {1996},
	Bdsk-File-1 = { }}

@article{Meiri.Dayan.2003.a,
	Abstract = {Aim We reviewed the occurrence of Bergmann's rule in birds (ninety-four species) and mammals (149 species), using only studies where statistical significance of the results was tested. We also tested whether studies using different characters as surrogates of body size have a different tendency to conform to Bergmann's rule, whether body size and nest type (in birds) have an influence on the tendency to conform to the rule, and whether sedentary birds conform to the rule more than migratory birds.

Location Worldwide.

Methods We reviewed published data on geographic and temporal variation in body size, using only studies where the statistical significance of the results was tested. We asked how many species conform to the rule out of all species studied in each order and family.

Results Over 72\% of the birds and 65\% of the mammal species follow Bergmann's rule. An overall tendency to follow the rule occurs also within orders and families. Studies using body mass in mammals show the greatest tendency to adhere to Bergmann's rule (linear measurements and dental measurements show a weaker tendency); while in birds, studies using body mass and other surrogates (linear measurements and egg size) show a similar tendency. Birds of different body mass categories exhibit a similar tendency to follow Bergmann's rule, while in mammals the lower body size categories (4-50 and 50-500 g) show a significantly lower tendency to conform to the rule. Sedentary birds tend to conform to Bergmann's rule more than migratory species. Nest type does not affect the tendency to conform to Bergmann's rule.

Main conclusions Bergmann's rule is a valid ecological generalization for birds and mammals.},
	Author = {Meiri, Shai and Dayan, Tamar},
	Date-Added = {2008-05-02 16:19:13 +0100},
	Date-Modified = {2008-05-04 09:27:54 +0100},
	Journal = {Journal of Biogeography},
	Keywords = {Bergmann's rule; body size; geographic variation; size clines; latitude; temperature; Aves; Mammalia},
	Pages = {331-351},
	Timescited = {0},
	Title = {On the validity of {B}ergmann's rule},
	Volume = {30},
	Year = {2003},
	Bdsk-File-1 = { }}

@article{McNab.1971.a,
	Author = {McNab, Brian K.},
	Date-Added = {2008-05-02 16:18:48 +0100},
	Date-Modified = {2008-05-16 12:20:05 +0100},
	Journal = {Ecology},
	Pages = {845-854},
	Timescited = {0},
	Title = {On the ECOLOGICAL SIGNIFICANCE OF {B}ERGMANN'S RULE},
	Volume = {52},
	Year = {1971},
	Bdsk-File-1 = { }}

@article{Lindsey.1966.a,
	Author = {Lindsey, C. C.},
	Date-Added = {2008-05-02 16:18:01 +0100},
	Date-Modified = {2008-05-02 16:18:25 +0100},
	Journal = {Evolution},
	Pages = {456-465},
	Title = {Body sizes of poikilotherm vertebrates at different latitudes.},
	Volume = {20},
	Year = {1966},
	Bdsk-File-1 = { }}

@article{James.1970.a,
	Author = {James, Frances C.},
	Date-Added = {2008-05-02 16:15:34 +0100},
	Date-Modified = {2008-05-05 12:04:50 +0100},
	Journal = {Ecology},
	Pages = {365-390},
	Timescited = {0},
	Title = {GEOGRAPHIC SIZE VARIATION IN BIRDS AND ITS RELATIONSHIP TO CLIMATE},
	Volume = {51},
	Year = {1970},
	Bdsk-File-1 = { }}

@article{Greve.Gaston.ea.2008.a,
	Author = {Greve,Michelle and Gaston,Kevin J. and van Rensburg,Berndt J. and Chown,Steven L.},
	Date-Added = {2008-05-02 16:14:14 +0100},
	Date-Modified = {2008-05-02 16:14:53 +0100},
	Doi = {10.1111/j.1466-8238.2008.00388.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1466-8238.2008.00388.x},
	Journal = {Global Ecology and Biogeography},
	Number = {0},
	Pages = {???-???},
	Title = {Environmental factors, regional body size distributions and spatial variation in body size of local avian assemblages},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1466-8238.2008.00388.x},
	Volume = {0},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1466-8238.2008.00388.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1466-8238.2008.00388.x},
	Bdsk-Url-3 = {http://dx.doi.org/10.1111/j.1466-8238.2008.00388.x}}

@article{Graves.1991.a,
	Abstract = {Critical correlative support for Bergmann's ecogeographic rule is provided by symmetrical patterns of size variation in Diglossa carbonaria, a tropical passerine bird whose geographic range in the Andes Mountains of South America straddles the equator.  Body size is positively correlated with latitude both north and south of the equator. Moreover, parapatric taxa that exhibit either partial (northwestern Bolivia) or complete (northern Peru) reproductive isolation converge  in body size.  Relative uniformity in the length of the highly modified flower-piercing bill among populations of D. carbonaria that differ significantly in body size suggests that character displacement or interspecific competition is not responsible for these patterns.  These findings support the hypothesis that climate, particularly temperature seasonality, is an important environmental determinant of geographic size variation in homeotherms.  In addition they demonstrate that clinal variation correlated with subtle climatic gradients can occur in tropical environments.},
	Author = {Graves, Gary R.},
	Date-Added = {2008-05-02 16:10:34 +0100},
	Date-Modified = {2008-05-05 12:13:37 +0100},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {CLINAL VARIATION; TEMPERATURE SEASONALITY; DIGLOSSA; FLOWER PIERCER},
	Pages = {2322-2325},
	Timescited = {0},
	Title = {{B}ERGMANN's RULE NEAR THE EQUATOR - LATITUDINAL CLINES IN BODY SIZE OF AN {A}NDEAN PASSERINE BIRD},
	Volume = {88},
	Year = {1991},
	Bdsk-File-1 = { }}

@article{GEIST.1987.a,
	Annote = {Subscription not available},
	Author = {Geist, Volker},
	Date-Added = {2008-05-02 16:09:30 +0100},
	Date-Modified = {2008-05-05 12:17:20 +0100},
	Journal = {Canadian Journal of Zoology},
	Pages = {1035-1038},
	Timescited = {0},
	Title = {BERGMANN's RULE IS INVALID},
	Volume = {65},
	Year = {1987}}

@article{Diniz.2001.a,
	Abstract = {I show how phylogenetic correlograms track distinct microevolutionary processes and can be used as empirical descriptors of the relationship between interspecific covariance (VB) and time since divergence (t). Data were simulated under models of gradual and speciational change, using increasing levels of stabilizing selection in a stochastic Ornstein-Uhlenbeck (O-U) process, an a phylogeny of 42 species. For each simulated dataset, correlograms were constructed using Moran's I coefficients estimated at five time slices, established at constant intervals. The correlograms generated under different evolutionary models differ significantly according to F-values derived from analysis of variance comparing Moran's I at each time slice and based on Wilks' lambda from multivariate analysis of valiance comparing their overall profiles in a two-way design. Under Brownian motion or with small restraining forces in the O-U process, correlograms were better fit by a linear model. However, increasing restraining forces in the O-U process cause a lack of linear fit, and correlograms are better described by exponential medals. These patterns are better fit for gradual than for speciational modes of change. Correlograms can be used as a diagnostic method and to describe the V-B/t relationship before using methods to analyze correlated evolution that assume (or perform statistically better when) this relationship is linear.},
	Author = {Diniz-Filho, Jos{\'e} Alexandre Felizola},
	Date-Added = {2008-05-02 16:08:27 +0100},
	Date-Modified = {2008-05-02 16:09:03 +0100},
	Journal = {Evolution},
	Keywords = {autocorrelation; comparative methods; eigenvector regression; evolutionary processes; phylogenetic correlograms},
	Pages = {1104-1109},
	Timescited = {0},
	Title = {Phylogenetic autocorrelation under distinct evolutionary processes},
	Volume = {55},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{COUSINS.1989.a,
	Author = {COUSINS, SH},
	Date-Added = {2008-05-02 16:06:23 +0100},
	Date-Modified = {2008-05-02 16:07:10 +0100},
	Journal = {Nature},
	Note = {Nature},
	Pages = {350-351},
	Timescited = {0},
	Title = {SPECIES RICHNESS AND THE ENERGY THEORY},
	Volume = {340},
	Year = {1989},
	Bdsk-File-1 = { }}

@article{Cardillo.2002.a,
	Abstract = {Axe latitudinal gradients in regional diversity random or biased with respect to body size? Using data for the New World avifauna, I show that the slope of the increase in regional species richness from the Arctic to the equator is not independent of body size. The increase is steepest among small and medium-sized species, and shallowest among the largest species. This is reflected in latitudinal variation in the shape of frequency distributions of body sizes in regional subsets of the New World avifauna. Because species are added disproportionately in small and medium size classes towards low latitudes, distributions become less widely spread along the body size axis than expected from the number of species. These patterns suggest an interaction between the effects of latitude and body size on species richness, implying that mechanisms which vary with both latitude and body size may be important determinants of high tropical diversity in New World birds.},
	Author = {Cardillo, M},
	Date-Added = {2008-05-02 16:05:43 +0100},
	Date-Modified = {2008-05-02 16:06:08 +0100},
	Journal = {Global Ecology and Biogeography},
	Keywords = {beta-diversity; birds; body size distributions; latitudal gradients; macroecology; New World avifauna; species richness},
	Pages = {59-65},
	Timescited = {0},
	Title = {Body size and latitudinal gradients in regional diversity of New World birds},
	Volume = {11},
	Year = {2002},
	Bdsk-File-1 = { }}

@incollection{Calder.1974.a,
	Address = {Cambridge, Mass.},
	Author = {Calder, III, W. A.},
	Booktitle = {Avian energetics},
	Date-Added = {2008-05-02 16:01:16 +0100},
	Date-Modified = {2008-05-02 16:05:00 +0100},
	Editor = {Paynter, Jr, R.A.},
	Pages = {86-151},
	Publisher = {Nuttall Ornithological Club},
	Title = {Consequences of body size for avian energetics},
	Year = {1974}}

@article{Boyce.1978.a,
	Author = {Boyce, Mark S.},
	Date-Added = {2008-05-02 16:00:19 +0100},
	Date-Modified = {2008-05-05 12:11:33 +0100},
	Journal = {Oecologia},
	Pages = {1-19},
	Timescited = {0},
	Title = {CLIMATIC VARIABILITY AND BODY SIZE VARIATION IN {M}USKRATS (\textit{Ondatra zibethicus}) OF {N}ORTH {A}MERICA},
	Volume = {36},
	Year = {1978},
	Bdsk-File-1 = { }}

@article{Boyce.1979.a,
	Author = {Boyce, Mark S.},
	Date-Added = {2008-05-02 16:00:19 +0100},
	Date-Modified = {2008-05-05 12:07:19 +0100},
	Journal = {American Naturalist},
	Number = {4},
	Pages = {569-583},
	Timescited = {0},
	Title = {SEASONALITY AND PATTERNS OF NATURAL-SELECTION FOR LIFE HISTORIES},
	Volume = {114},
	Year = {1979},
	Bdsk-File-1 = { }}

@article{Blackburn.Gaston.1996.a,
	Abstract = {Spatial patterns in animal body sizes have primarily been studied with the aim of evaluating Bergmann's rule, which states that body size is inversely related to ambient temperature, and hence increases with latitude across closely related species. However, geographic range sizes and species richness also show spatial variation, and there is evidence that both are correlated with body size. It is surprising, therefore, that there has been no attempt to examine covariation in body size, species richness and geographic range size patterns simultaneously in a single assemblage. Here, we do so, using the assemblage of birds in the New World. The mean body mass of New World birds is lowest in equatorial areas, and increases with latitude either side of the equator, as expected from Bergmann's rule. However, this pattern closely miners that in species richness, and there is a strong inverse correlation between the number of species in an area and their mean body mass. This correlation is stronger than that of either variable with latitude, and hints al a common underlying cause. In contrast, the relationship between the mean body size and the mean geographic range size of species in an area is very weak. Nevertheless, the spatial patterns mean that the interspecific relationship between range size and body size varies across latitudes, which has important consequences for conservation assessments based on species' range sizes. If there is an ecological reason why larger body size is favoured at high latitudes, where energy availability is lower, this could in part explain the coincidence of spatial patterns in body size and species richness. Spatial patterns in range size also may in part be mediated through a weak correlation with body size. Thus, spatial patterns in all three variables may be inter-related.},
	Annote = {No subscription},
	Author = {Blackburn, TM and Gaston, KJ},
	Date-Added = {2008-05-02 15:55:04 +0100},
	Date-Modified = {2008-05-05 12:22:26 +0100},
	Journal = {Oikos},
	Pages = {436-446},
	Timescited = {0},
	Title = {Spatial patterns in the body sizes of bird species in the New World},
	Volume = {77},
	Year = {1996}}

@article{Bergmann.1847.a,
	Annote = {Concerning the relationship of heat conservation of animals to their size.},
	Author = {Bergmann, Karl},
	Date-Added = {2008-05-02 15:52:12 +0100},
	Date-Modified = {2008-05-02 15:53:36 +0100},
	Journal = {Gottinger studien},
	Pages = {595-708},
	Title = {Ueber die verhaltnisse der warmeokonomie der thiere zu ihrer grosse},
	Volume = {3},
	Year = {1847}}

@article{Ashton.2001.a,
	Author = {Ashton, Kyle G},
	Date-Added = {2008-05-02 15:49:33 +0100},
	Date-Modified = {2008-05-05 12:23:42 +0100},
	Journal = {Evolution},
	Pages = {2523-2533},
	Title = {Body size variation among mainland populations of the western rattlesnake (Crotalus viridis).},
	Volume = {55},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Weir.Schluter.2008.a,
	Abstract = { Abstract Molecular clocks are widely used to date phylogenetic events, yet evidence supporting the rate constancy of molecular clocks through time and across taxonomic lineages is weak. Here, we present 90 candidate avian clock calibrations obtained from fossils and biogeographical events. Cross-validation techniques were used to identify and discard 16 inconsistent calibration points. Molecular evolution occurred in an approximately clock-like manner through time for the remaining 74 calibrations of the mitochondrial gene, cytochrome b. A molecular rate of approximately 2.1% (+- 0.1%, 95% confidence interval) was maintained over a 12-million-year interval and across most of 12 taxonomic orders. Minor but significant variance in rates occurred across lineages but was not explained by differences in generation time, body size or latitudinal distribution as previously suggested. },
	Author = {Weir, Jason T. and Schluter, Dolph},
	Date-Added = {2008-04-30 10:46:53 +0100},
	Date-Modified = {2008-04-30 10:47:13 +0100},
	Doi = {10.1111/j.1365-294X.2008.03742.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-294X.2008.03742.x},
	Journal = {Molecular Ecology},
	Number = {10},
	Pages = {2321-2328},
	Title = {Calibrating the avian molecular clock},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-294X.2008.03742.x},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-294X.2008.03742.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-294X.2008.03742.x},
	Bdsk-Url-3 = {http://dx.doi.org/10.1111/j.1365-294X.2008.03742.x}}

@article{Bode.Wilson.ea.2008.a,
	Abstract = {Priorities for conservation investment at a global scale that are based on a single taxon have been criticized because geographic richness patterns vary taxonomically. However, these concerns focused only on biodiversity patterns and did not consider the importance of socioeconomic factors, which must also be included if conservation funding is to be allocated efficiently. In this article, we create efficient global funding schedules that use information about conservation costs, predicted habitat loss rates, and the endemicity of seven different taxonomic groups. We discover that these funding allocation schedules are less sensitive to variation in taxon assessed than to variation in cost and threat. Two-thirds of funding is allocated to the same regions regardless of the taxon, compared with only one-fifth if threat and cost are not included in allocation decisions. Hence, if socioeconomic factors are considered, we can be more confident about global-scale decisions guided by single taxonomic groups.
},
	Author = {Bode, Michael and Wilson, Kerrie A. and Brooks, Thomas M. and Turner, Will R. and Mittermeier, Russell A. and McBride, Marissa F. and Underwood, Emma C. and Possingham, Hugh P.},
	Date-Added = {2008-04-30 09:49:52 +0100},
	Date-Modified = {2008-04-30 09:50:14 +0100},
	Doi = {10.1073/pnas.0710705105},
	Eprint = {http://www.pnas.org/cgi/reprint/105/17/6498.pdf},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {17},
	Pages = {6498-6501},
	Title = {{Cost-effective global conservation spending is robust to taxonomic group}},
	Url = {http://www.pnas.org/cgi/content/abstract/105/17/6498},
	Volume = {105},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.pnas.org/cgi/content/abstract/105/17/6498},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0710705105},
	Bdsk-Url-3 = {http://dx.doi.org/10.1073/pnas.0710705105}}

@article{West.Brown.ea.1997.a,
	Abstract = {Allometric scaling relations, including the 3/4 power law for metabolic rates, are characteristic of all organisms and are here derived from a general model that describes how essential materials are transported through space-filling fractal networks of branching tubes. The model assumes that the energy dissipated is minimized and that the terminal tubes do not vary with body size. It provides a complete analysis of scaling relations for mammalian circulatory systems that are in agreement with data. More generally, the model predicts structural and functional properties of vertebrate cardiovascular and respiratory systems, plant vascular systems, insect tracheal tubes, and other distribution networks.},
	Annote = {[See notes on talk by Richard Sibly]},
	Author = {West, Geoff B and Brown, James H and Enquist, Brian J},
	Date-Added = {2008-04-28 16:05:29 +0100},
	Date-Modified = {2008-04-28 16:09:01 +0100},
	Journal = {Science},
	Pages = {122-126},
	Timescited = {0},
	Title = {A general model for the origin of allometric scaling laws in biology},
	Volume = {276},
	Year = {1997},
	Bdsk-File-1 = { }}

@article{Qian.Ricklefs.2008.a,
	Abstract = { Abstract The factors that determine large-scale patterns of species richness are poorly understood. In particular, biologists have not determined the relative roles of taxon-specific characteristics that influence diversification and distribution, and region-specific features that promote and constrain diversity. We show that the numbers of species of vascular plants and of four terrestrial vertebrate taxa (mammals, birds, reptiles and amphibians) vary in parallel across 296 geographic areas covering most of the globe, even after accounting for sample area, climate, topographic heterogeneity and differences between continents. Thus, a common set of regional characteristics and processes appears to shape patterns of species richness in a diverse set of taxa, despite substantial differences in their biological traits. },
	Author = {Qian,Hong and Ricklefs,Robert E.},
	Date-Added = {2008-04-16 13:42:19 +0100},
	Date-Modified = {2008-04-16 13:43:14 +0100},
	Doi = {10.1111/j.1461-0248.2008.01168.x},
	Eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1461-0248.2008.01168.x},
	Journal = {Ecology Letters},
	Number = {0},
	Pages = {???-???},
	Title = {Global concordance in diversity patterns of vascular plants and terrestrial vertebrates},
	Url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2008.01168.x},
	Volume = {11},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2008.01168.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01168.x},
	Bdsk-Url-3 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01168.x}}

@article{Garant.Hadfield.ea.2008.a,
	Abstract = {Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long-term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an `animal model' approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40-year period (1965--1988 [cooler] vs. 1989--2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied. },
	Author = {Garant, Dany and Hadfield, Jarrod D. and Kruuk, Loeske E. B. and Sheldon, Ben},
	Date-Added = {2008-04-16 12:06:11 +0100},
	Date-Modified = {2008-04-16 12:10:00 +0100},
	Doi = {10.1111/j.1365-294X.2007.03436.x},
	Journal = {Molecular Ecology},
	Keywords = {animal model, climate change, genetic correlation, heritability, Parus major, quantitative genetic},
	Pages = {179--188},
	Title = {Stability of genetic variance and covariance for reproductive characters in the face of climate change in a wild bird population},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-294X.2007.03436.x}}

@article{Rodrigues.2007.a,
	Abstract = {Using data on the global distribution of mammal, bird and amphibian species, Grenyer et al. conclude that planning based on individual taxa does not provide efficient solutions for the conservation of other taxa. They also report that the performance of existing global conservation strategies---endemic bird areas, biodiversity hotspots and global 200 ecoregions---in representing those taxa is often no better (and in some cases worse) than random. I argue here that the methodology used by Grenyer et al. was not appropriate for purported globally comprehensive analyses. Focusing on analyses of rare species as an example, I demonstrate how the data actually reveal substantial cross-taxon surrogacy and good performance of existing global conservation strategies},
	Author = {Rodrigues, Ana S L},
	Date-Added = {2008-04-14 16:46:17 +0100},
	Date-Modified = {2008-04-14 16:51:16 +0100},
	Journal = {Nature},
	Pages = {E19},
	Title = {Effective global conservation strategies},
	Volume = {450},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Kremen.Cameron.ea.2008.a,
	Abstract = {Globally, priority areas for biodiversity are relatively well known, yet few detailed plans exist to direct conservation action within them, despite urgent need. Madagascar, like other globally recognized biodiversity hot spots, has complex spatial patterns of endemism that differ among taxonomic groups, creating challenges for the selection of within-country priorities. We show, in an analysis of wide taxonomic and geographic breadth and high spatial resolution, that multitaxonomic rather than single-taxon approaches are critical for identifying areas likely to promote the persistence of most species. Our conservation prioritization, facilitated by newly available techniques, identifies optimal expansion sites for the Madagascar government's current 
goal of tripling the land area under protection. Our findings further suggest that high-resolution multitaxonomic approaches to prioritization may be necessary to ensure protection for biodiversity in other global hot spots.},
	Author = {Kremen, C and Cameron, A and Moilanen, A. and Phillips, S. J. and Thomas, C D and Beentje, H and Dransfield, J. and Fisher, B L and Glaw, F and Good, T C and Harper, G. J. and Hijmans, R. J. and Lees, D. C. and Louis , Jr., E. and Nussbaum, R. A. and Raxworthy, C. J. and Razafimpahanana, A. and Schatz, G. E. and Vences, M. and Vieites, David R. and Wright, P. C. and Zjhra, M. L.},
	Date-Added = {2008-04-11 10:22:39 +0100},
	Date-Modified = {2008-04-11 10:31:00 +0100},
	Journal = {Science},
	Pages = {222-226},
	Title = {Aligning Conservation Priorities Across Taxa in Madagascar with High-Resolution Planning Tools},
	Volume = {320},
	Year = {2008},
	Bdsk-File-1 = { }}

@article{Chown.Sinclair.ea.2004.a,
	Author = {Chown, Steven L. and Sinclair, Brent J. and Leinaas, Hans P. and Gaston, Kevin J.},
	Date-Added = {2008-04-10 12:12:40 +0100},
	Date-Modified = {2008-04-10 12:15:50 +0100},
	Doi = {ARTN e406},
	Journal = {Plos Biology},
	Number = {11},
	Pages = {1701-1707},
	Timescited = {0},
	Title = {Hemispheric asymmetries in biodiversity - A serious matter for ecology},
	Volume = {2},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/406},
	Bdsk-Url-2 = {http://dx.doi.org/406}}

@article{Rohlf.2006.a,
	Abstract = {Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to phylogeny and there is an expectation that the corrected regression or correlation coefficients will usually be closer to zero. It is shown here that this is not an accurate way to interpret these methods. The effect of taking phylogeny into account is to reduce the variance of the estimated regression or correlation coefficients. Their means are not because since estimates of regression coefficients are unbiased whether or not the correct phylogeny is taken into account. Estimates of correlations are only slightly biased (and in the opposite direction that many expect).},
	Author = {Rohlf, F. James},
	Date-Added = {2008-04-10 10:32:44 +0100},
	Date-Modified = {2008-04-10 10:33:39 +0100},
	Journal = {Evolution},
	Keywords = {bias; comparative methods; generalized least-squares; independent contrasts},
	Pages = {1509-1515},
	Timescited = {0},
	Title = {A comment on phylogenetic correction},
	Volume = {60},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Cassey.Blackburn.ea.2005.a,
	Abstract = {1. The establishment of species outside their natural geographical ranges is an important driver of changes in global biodiversity. This creates an imperative to understand why some species are more successful than others at establishing viable populations following introduction.

2. Historical data are particularly useful in this regard, and those for birds especially comprehensive. This has resulted in the publication of regional-scale studies that have used these data to attempt to quantify relationships between establishment success and characteristics of bird introductions.

3. We use a meta-analytical approach to summarize quantitatively the results of these studies, and to assess the influence of variables invoked to explain the variation in establishment success in birds.

4. We find that variables describing characteristics specific to the individual introduction event (i.e. event-level variables), such as introduction effort (or 'propagule pressure'), are the most consistent predictors of establishment success.},
	Author = {Cassey, P and Blackburn, TM and Duncan, RP and Lockwood, JL},
	Date-Added = {2008-04-03 12:13:01 +0100},
	Date-Modified = {2008-04-03 12:13:17 +0100},
	Doi = {DOI 10.1111/j.1365-2656.2004.00918.x},
	Journal = {Journal of Animal Ecology},
	Keywords = {birds; introductions; meta-analysis; propagule pressure},
	Pages = {250-258},
	Timescited = {0},
	Title = {Lessons from the establishment of exotic species: a meta-analytical case study using birds},
	Volume = {74},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2656.2004.00918.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2656.2004.00918.x}}

@article{Valentine.Jablonski.1986.a,
	Author = {Valentine, James W. and Jablonski, David},
	Date-Added = {2008-03-27 21:16:54 +0000},
	Date-Modified = {2008-03-28 10:11:16 +0000},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Pages = {6912-6914},
	Timescited = {0},
	Title = {MASS EXTINCTIONS - SENSITIVITY OF MARINE LARVAL TYPES},
	Volume = {83},
	Year = {1986},
	Bdsk-File-1 = { }}

@article{Roy.Jablonski.ea.2000.a,
	Abstract = {The latitudinal diversity gradient, with maximum taxonomic richness in the tropics, is widely accepted as being pervasive on land, but the existence of this pattern in the sea has been surprisingly controversial. This is partly due to Thorson's influential claim that the normal latitudinal diversity gradient occurs in marine epifauna (taxa living on the surface of the substratum) but not in infauna (burrowing or boring into the substratum), a contrast he attributed to the greater spatial and temporal environmental homogeneity of infaunal habitats. In an analysis of 930 species of north-eastern Pacific marine shelf bivalves, we found that bivalves as a whole, and both infauna and epifauna separately, show a strong latitudinal diversity gradient (measured as number of species per degree latitude) that is closely related to mean sea surface temperature (SST), even in analyses of residuals and first differences. This agrees with results for marine gastropods, but contradicts Thorson's environmental homogeneity hypothesis. The relationship between SST and diversity is consistent with a species-energy hypothesis, but the linkages from SST to diversity remain unclear. Most bivalve clades within broad functional groups conform to the general latitudinal trend, except for the deposit-feeding protobranchs. This group's non-directional pattern may be related to its mode of development, because a similar effect is seen in several other groups locked into this low-fecundity, non-feeding larval mode.},
	Author = {Roy, Kaustuv and Jablonski, David and Valentine, James W.},
	Date-Added = {2008-03-27 21:16:54 +0000},
	Date-Modified = {2008-03-27 21:21:05 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {latitudinal diversity gradient; marine bivalves; species-energy hypothesis},
	Pages = {293-299},
	Timescited = {0},
	Title = {Dissecting latitudinal diversity gradients: functional groups and clades of marine bivalves},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Mittelbach.Schemske.ea.2007.a,
	Abstract = {A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.},
	Author = {Mittelbach, Gary G. and Schemske, Douglas W. and Cornell, Howard V. and Allen, Andrew P. and Brown, Jonathan M. and Bush, Mark B. and Harrison, Susan P. and Hurlbert, Allen H. and Knowlton, Nancy and Lessios, Harilaos A. and McCain, Christy M. and McCune, Amy R. and McDade, Lucinda A. and McPeek, Mark A. and Near, Thomas J. and Price, Trevor D. and Ricklefs, Robert E. and Roy, Kaustuv and Sax, Dov F. and Schluter, Dolph and Sobel, James M. and Turelli, Michael},
	Date-Added = {2008-03-27 20:09:55 +0000},
	Date-Modified = {2008-03-27 20:14:43 +0000},
	Journal = {Ecology Letters},
	Number = {4},
	Pages = {315-331},
	Title = {Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography},
	Volume = {10},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Triantis.Mylonas.ea.2003.a,
	Author = {Triantis, K A and Mylonas, M and Lika, K and Vardinoyannis, K},
	Date-Added = {2008-03-27 20:07:40 +0000},
	Date-Modified = {2008-03-27 20:07:50 +0000},
	Journal = {Journal of Biogeography},
	Keywords = {species-area, choros model, habitat diversity, area per se, habitat hypothesis, species richness, islands, small island effect},
	Pages = {19-27},
	Title = {A model for the species-area-habitat relationship},
	Volume = {30},
	Year = {2003},
	Bdsk-File-1 = { }}

@article{Jablonski.2001.a,
	Author = {Jablonski, David},
	Date-Added = {2008-03-27 20:03:44 +0000},
	Date-Modified = {2008-03-27 20:05:09 +0000},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Note = {13/8/06 (PSAR family-level paper): clades that are widespread persist better at times of mass extinction, and this is a pretty robust pattern.},
	Pages = {5393-5398},
	Title = {Lessons from the past: Evolutionary impacts of mass extinctions},
	Volume = {98},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Foote.2000.a,
	Abstract = {Changes in genus diversity within higher taxa of marine animals on the temporal scale of a few million years are more strongly correlated with changes in extinction rate than with changes in origination rate during the Paleozoic. After the Paleozoic the relative roles of origination and extinction in diversity dynamics are reversed, Metazoa as well as individual higher taxa shift from one mode of diversity dynamics to the other The magnitude of taxonomic rates, the relative variance of origination and extinction rates, and the presence or absence of a long-term secular increase in diversity all fail to account fur the shift in importance of origination and extinction in diversity changes. Origination and extinction rates both tend to be diversity-dependent, but different modes of diversity-dependence may contribute to the change in diversity dynamics from the Paleozoic to the post-Paleozoic. During the Paleozoic, there is a weak tendency for extinction rates to be more diversity-dependent than origination rates, whereas after the Paleozoic the two rates are about equally diversity-dependent on average.},
	Author = {Foote, Mike},
	Date-Added = {2008-03-27 20:01:55 +0000},
	Date-Modified = {2008-03-27 20:02:42 +0000},
	Journal = {Paleobiology},
	Number = {4},
	Pages = {578-605},
	Title = {Origination and extinction components of taxonomic diversity: Paleozoic and post-Paleozoic dynamics},
	Volume = {26},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Shmida.Wilson.1985.a,
	Author = {Shmida, Avi and Wilson, Mark V.},
	Date-Added = {2008-03-27 19:57:23 +0000},
	Date-Modified = {2008-03-27 20:00:12 +0000},
	Journal = {Journal of Biogeography},
	Note = {12-6-06: Brief notes for PSAR family-level paper in lab-book; basic gist is that the only driver of species richness vs area that is increasingly important at larger scales is ecological equivalence, i.e., multiple species occupying the same niche in different parts of the world. Habitat diversity has its maximum importance at a meso scale, which provides a testable prediction for PSAR analyses: habitat diversity might do a better job of explaining residual variance below the breakpoint rather than above.},
	Pages = {1-20},
	Title = {Biological determinants of species diversity},
	Volume = {12},
	Year = {1985},
	Bdsk-File-1 = { }}

@book{Brown.1995.a,
	Address = {Chicago},
	Author = {Brown, Jim H.},
	Date-Added = {2008-03-27 19:56:32 +0000},
	Date-Modified = {2008-03-27 19:56:42 +0000},
	Publisher = {Chicago University Press},
	Title = {Macroecology},
	Year = {1995}}

@book{Gaston.Blackburn.2000.a,
	Address = {Oxford},
	Author = {Gaston, Kevin J. and Blackburn, Tim M.},
	Date-Added = {2008-03-27 19:55:55 +0000},
	Date-Modified = {2008-03-27 19:56:12 +0000},
	Publisher = {Blackwell Scientific},
	Title = {Pattern and Process in Macroecology},
	Year = {2000}}

@book{Schluter.2000.a,
	Address = {Oxford},
	Author = {Schluter, Dolph},
	Date-Added = {2008-03-27 19:54:22 +0000},
	Date-Modified = {2008-03-27 19:54:41 +0000},
	Publisher = {Oxford University Press},
	Title = {The Ecology of Adaptive Radiation},
	Year = {2000}}

@book{MacArthur.Wilson.1967.a,
	Address = {Princeton},
	Author = {MacArthur, Robert H. and Wilson, Ed O.},
	Date-Added = {2008-03-27 19:51:54 +0000},
	Date-Modified = {2008-03-27 19:52:17 +0000},
	Publisher = {Princeton University Press},
	Title = {The Equilibrium Theory of Island Biogeography},
	Year = {1967}}

@article{Ricklefs.Lovette.1999.a,
	Abstract = {1. We analysed the relationships between species richness, island area, and habitat diversity for birds, bats, butterflies, and reptiles and amphibians on 19 islands in the Lesser Antilles. Habitat diversity was quantified by Simpson's index based on the total areas of five vegetation types on each island. Island area varied over two orders of magnitude (13-1510 km(2)) and habitat diversity varied between 1 and 3.7 equivalents of equally abundant habitat types.
2. Because the Lesser Antilles consist of an inner are of high, volcanic islands and an outer are of low-lying islands formed of uplifted marine sediments, correlations between area and elevation (r(2) = 0.32) and between area and habitat diversity (r(2) = 0.40) were weak. Habitat diversity was, however, strongly correlated with maximum island elevation (r(2) = 0.85).
3. Simple correlations of species richness with island area were significant for all four faunal groups, and simple correlations of species richness with elevation and habitat were significant for all groups except bats. In multiple regressions of species richness on area and habitat diversity together, area was a significant effect for birds and bats, and habitat diversity was a significant effect for birds, butterflies, and reptiles and amphibians.
4. These results suggest that the four Lesser Antillean taxonomic groups differ in their responses to area and habitat diversity. For butterflies and for reptiles and amphibians, the relationship of species richness to area is probably a fortuitous consequence of a relationship between habitat diversity and area. Bird species richness responds independently to both habitat diversity and area, and bat species richness is influenced by area but not by habitat diversity.
5. We suggest that this variation is related to differences in several biological traits of the different faunal groups. Strong habitat-diversity effects are likely in taxa with high degrees of habitat specialization, populations large enough to have a low probability of stochastic extinction, life-cycles that include a resistant resting stage that reduces vulnerability to catastrophic extinction, or a combination of these traits. In contrast, strong: area effects are likely in taxa with weak habitat specialization, low population density, or both.
6. At least in Lesser Antillean birds, it is unlikely that immigration depends on island size. Therefore, the species-area relationship for birds is probably generated by island-size-dependent extinction. Among the four taxonomic groups we studied, only butterflies are likely to show a 'rescue effect' stemming from frequent between-island movement of individuals, as only butterflies exhibited low levels of endemism and lacked a unique area effect for species richness.
7. Considered in concert, these taxon-specific differences demonstrate that both biological characteristics of organisms and geographical features of island groups mediate the relative contribution of island area and habitat diversity to variation in species richness.},
	Author = {Ricklefs, Robert E. and Lovette, Irby J.},
	Date-Added = {2008-03-27 19:49:13 +0000},
	Date-Modified = {2008-03-27 19:50:54 +0000},
	Journal = {Journal of Animal Ecology},
	Keywords = {area effects; habitat diversity; island biogeography; Lesser Antilles; species-area relationship},
	Pages = {1142-1160},
	Title = {The roles of island area per se and habitat diversity in the species-area relationships of four Lesser Antillean fanual groups},
	Volume = {68},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Simberloff.1974.a,
	Author = {Simberloff, Daniel S},
	Date-Added = {2008-03-27 15:43:04 +0000},
	Date-Modified = {2008-03-27 16:01:50 +0000},
	Journal = {Annual Review of Ecology and Systematics},
	Month = {November},
	Pages = {161-182},
	Title = {Equilibrium Theory of Island Biogeography and Ecology},
	Volume = {5},
	Year = {1974},
	Bdsk-File-1 = { }}

@article{Losos.Schluter.2000.a,
	Abstract = {Large islands typically have more species than comparable smaller islands. Ecological theories, the most influential being the equilibrium theory of island biogeography(1), explain the species-area relationship as the outcome of the effect of area on immigration and extinction rates. However, these theories do not apply to taxa on land masses, including continents and large islands, that generate most of their species in situ. In this case, species-area relationships should be driven by higher speciation rates in larger areas(2-6), a theory that has never been quantitatively tested. Here we show that Anolis lizards on Caribbean islands meet several expectations of the evolutionary theory. Within-island speciation exceeds immigration as a source of new species on all islands larger than 3,000 km(2), whereas speciation is rare on smaller islands. Above this threshold island size, the rate of species proliferation increases with island area, a process that results principally from the positive effects of area on speciation rate. Also as expected, the slope of the species-area relationship jumps sharply above the threshold. Although Anolis lizards have been present on large Caribbean islands for over 30 million years, there are indications that the current number of species still falls below the speciation-extinction equilibrium.},
	Author = {Losos, Jonathan B. and Schluter, Dolph},
	Date-Added = {2008-03-27 15:37:42 +0000},
	Date-Modified = {2008-03-27 15:38:19 +0000},
	Journal = {Nature},
	Pages = {847-850},
	Timescited = {0},
	Title = {Analysis of an evolutionary species-area relationship},
	Volume = {408},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Ricklefs.Losos.ea.2007.a,
	Abstract = {We analysed the diversification of squamate reptiles (7488 species) based on a new molecular phylogeny, and compared the results to similar estimates for passerine birds (5712 species). The number of species in each of 36 squamate lineages showed no evidence of phylogenetic conservatism. Compared with a random speciation-extinction process with parameters estimated from the size distribution of clades, the alethinophidian snakes (2600 species) were larger than expected and 13 clades, each having fewer than 20 species, were smaller than expected, indicating rate heterogeneity. From a lineage-through-time plot, we estimated that a provisional rate of lineage extinction (0.66 per Myr) was 94\% of the rate of lineage splitting (0.70 per Myr). Diversification in squamate lineages was independent of their stem age, but strongly related to the area of the region within which they occur. Tropical vs. temperate latitude exerted a marginally significant influence on species richness. In comparison with passerine birds, squamates share several clade features, including: (1) independence of species richness and age; (2) lack of phylogenetic signal with respect to clade size; (3) general absence of exceptionally large clades; (4) over-representation of small clades; (5) influence of region size on clade size; and (6) similar rates of speciation and extinction. The evidence for both groups suggests that clade size has achieved long-term equilibrium, suggesting negative feedback of species richness on the rate of diversification.},
	Author = {Ricklefs, Robert E. and Losos, Jonathan B. and Townsend, T. M.},
	Date-Added = {2008-03-27 15:34:43 +0000},
	Date-Modified = {2008-03-27 15:37:17 +0000},
	Doi = {DOI 10.1111/j.1420-9101.2007.01388.x},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {alethinophidian snakes; extinction; key innovation; lineage-through-time plot; mass extinction; passerine birds; phylogenetic independence; speciation; squamate reptiles},
	Pages = {1751-1762},
	Timescited = {0},
	Title = {Evolutionary diversification of clades of squamate reptiles},
	Volume = {20},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1420-9101.2007.01388.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1420-9101.2007.01388.x}}

@article{Gaston.Blackburn.1997.a,
	Abstract = {Using coarse resolution data on the spatial distribution of the entire New World avifauna, we test fbr phylogenetic patterns in the mean and total geographic range sizes of taxa. The analyses reveal that (i) the species-range size distribution is only approximately normalized, and remains significantly left-skewed, under logarithmic transformation. Most variance in range sixes is explained at the level of species within genera; (ii) there is no effect of the age of taxa on mean clade range size, although older taxa are more likely to have larger total range sizes; (iii) there is some evidence that taxa comprising more species have larger total range sizes; (iv) there is little or no evidence for a relationship between rate of cladogenesis and range size. The results suggest that geographic range size is a labile trait, at least for New World birds, and that the influence of evolutionary history is only weakly detectable in the range size variation of extant taxa; at least at the scale of analysis used here. In addition to these conclusions, two general and important procedural issues emerge. (C) 1997 The Linnean Society of London.},
	Author = {Gaston, Kevin J. and Blackburn, Tim M.},
	Date-Added = {2008-03-27 15:31:00 +0000},
	Date-Modified = {2008-03-27 15:31:48 +0000},
	Journal = {Biological Journal of the Linnean Society},
	Keywords = {birds; cladogenesis; distribution; macroecology; range size},
	Pages = {239-253},
	Timescited = {0},
	Title = {Age, area and avian diversification},
	Volume = {62},
	Year = {1997},
	Bdsk-File-1 = { }}

@book{Rosenzweig.1995.a,
	Address = {Cambridge},
	Author = {Rosenzweig, Michael L},
	Date-Added = {2008-03-27 15:28:15 +0000},
	Date-Modified = {2008-03-27 19:52:51 +0000},
	Publisher = {Cambridge University Press},
	Title = {Species Diversity in Space and Time},
	Year = {1995}}

@article{Davies.Savolainen.ea.2005.a,
	Abstract = {Phylogenetic analyses provide a means to explore evolutionary explanations for regional variation in species richness. The environment might also explain much of the previously unexplained imbalance of phylogenetic trees. We use data on geographic distribution and phylogenetic affinity to examine correlates of species richness among genera of irises (family: Iridaceae). Irises display strong phylogenetic imbalance, with a few clades containing a disproportionate number of species, most notably those found in the dry Mediterranean climate of the Cape of South Africa. The abiotic environment and area are strong predictors of iris species richness, but environment alone is insufficient to explain the high diversity of Cape clades. One possible explanation is that the interaction between biological traits and environment resulted in the unusually high diversification rates in the region.},
	Author = {Davies, T. Jonathan and Savolainen, Vincent and Chase, Mark W and Goldblatt, Peter and Barraclough, Timothy G.},
	Date-Added = {2008-03-27 15:22:32 +0000},
	Date-Modified = {2008-03-27 15:27:46 +0000},
	Journal = {American Naturalist},
	Keywords = {species richness; environment; diversification rates; Iridaceae; Cape of South Africa},
	Number = {3},
	Pages = {418-425},
	Timescited = {0},
	Title = {Environment, area, and diversification in the species-rich flowering plant family Iridaceae},
	Volume = {166},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Revell.Harrison.2008.a,
	Abstract = {Summary: PCCA (phylogenetic canonical correlation analysis) is a new program for canonical correlation analysis of multivariate, continuously valued data from biological species. Canonical correlation analysis is a technique in which derived variables are obtained from two sets of original variables whereby the correlations between corresponding derived variables are maximized. It is a very useful multivariate statistical method for the calculation and analysis of correlations between character sets. The program controls for species non-independence due to phylogenetic history and computes canonical coefficients, correlations and scores; and conducts hypothesis tests on the canonical correlations. It can also compute a multivariate version of Pagel's {lambda}, which can then be used in the phylogenetic transformation.  Availability: PCCA is distributed as DOS/Windows, Mac OS X and Linux/Unix executables with a detailed program manual and is freely available on the World Wide Web at:  http://anolis.oeb.harvard.edu/~liam/programs/.  Contact: lrevell@fas.harvard.edu 10.1093/bioinformatics/btn065},
	Author = {Revell, Liam J. and Harrison, Alexis S.},
	Citeulike-Article-Id = {2600060},
	Date-Added = {2008-03-27 15:01:30 +0000},
	Date-Modified = {2008-03-27 15:01:50 +0000},
	Doi = {10.1093/bioinformatics/btn065},
	Journal = {Bioinformatics},
	Keywords = {furuya, matrixdecomposition},
	Month = {April},
	Number = {7},
	Pages = {1018--1020},
	Priority = {4},
	Title = {PCCA: a program for phylogenetic canonical correlation analysis},
	Url = {http://dx.doi.org/10.1093\%2Fbioinformatics\%2Fbtn065},
	Volume = {24},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1093%5C/bioinformatics%5C/btn065},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btn065},
	Bdsk-Url-3 = {http://dx.doi.org/10.1093/bioinformatics/btn065}}

@article{Price.Wagner.2004.a,
	Abstract = {The biota of Hawaiian Islands is derived entirely from long distance dispersal, often followed by ill situ speciation. Species descended from each colonist constitute monophyletic lineages that have diverged to varying degrees under similar spatial and temporal constraints. We partitioned the Hawaiian angiosperm flora into lineages and assessed morphological, ecological, and biogeographic characteristics to examine their relationships to variation in species number (S). Lineages with external bird dispersal (through adhesion) were significantly more species-rich than those with abiotic dispersal, but only weakly more species-rich than lineages with internal bird dispersal (involving fleshy fruits). Pollination mode and growth form (woody vs. herbaceous) had no significant effect on S, in contrast to studies of angiosperm families. S relates positively to the geographic and ecological range size of whole lineages, but negatively to local abundance and mean range sizes of constituent species. Species-rich lineages represent a large proportion of major adaptive shifts, although this appears to be all artifact of having more species. Examination of 52 sister species pairs in numerous lineages provides evidence for allopatric (including peripheral isolates) and parapatric (ecological) modes, with 15 cases of each. Although postspeciational dispersal may obscure these modes in many of the remaining cases, instances of sympatric and hybrid speciation are also discussed. Because speciation is both a consequence and a cause of ecological and biogeographic traits, speciation mode may be integral to relationships between traits. We discuss the role of speciation in shaping the regional species pool.},
	Author = {Price, JP and Wagner, WL},
	Date-Added = {2008-03-27 13:58:54 +0000},
	Date-Modified = {2008-03-27 13:59:12 +0000},
	Journal = {Evolution},
	Keywords = {adaptive radiation; dispersal; Hawaii; pollination; speciation},
	Pages = {2185-2200},
	Timescited = {0},
	Title = {Speciation in Hawaiian angiosperm lineages: Cause, consequence, and mode},
	Volume = {58},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Valentine.1980.a,
	Author = {Valentine, James W.},
	Date-Added = {2008-03-27 13:54:39 +0000},
	Date-Modified = {2008-03-27 20:21:50 +0000},
	Journal = {Paleobiology},
	Pages = {444-450},
	Timescited = {0},
	Title = {DETERMINANTS OF DIVERSITY IN HIGHER TAXONOMIC CATEGORIES},
	Volume = {6},
	Year = {1980},
	Bdsk-File-1 = { }}

@book{Coyne.Orr.2004.a,
	Address = {Sunderland MA},
	Author = {Coyne, Jerry A and Orr, H A},
	Date-Added = {2008-03-27 13:52:49 +0000},
	Date-Modified = {2008-03-27 19:53:08 +0000},
	Publisher = {Sinauer},
	Title = {Speciation},
	Year = {2004}}

@article{Owens.Bennett.ea.1999.a,
	Abstract = {Why do some avian families contain so many more species than other families? We use comparisons between sister taxa to test predictions arising from six explanations to this puzzle: that differences between families are due to chance, body size, life history, sexual selection, intrinsic ecological factors or extrinsic abiotic factors, respectively. In agreement with previous analyses, we find no support for the idea that differences in species richness are simply due to chance. However, contrary to most previous work, we also find no support for the hypotheses that high species richness is correlated with small body size and fast life history. Rather, high species diversity is strongly associated with pronounced plumage dichromatism, generalist feeding habits and good dispersal capabilities as well as large and fragmented geographical ranges. In addition, all of these relationships are robust to the removal of the two most speciose avian lineages, the Ciconiiformes and the Passeriformes. The supposed relationships between species richness and both body size and life history are, however, due to phylogenetic non-independence. Together with previous work showing that differences between avian lineages in extinction risk are associated with variation in body size and life history, these results indicate that extinction rates and speciation rates are not necessarily determined by the same factors. Hence, high extinction rates are not inevitably associated with low speciation rates. Extinction-prone. lineages may, in fact, have a high rate of speciation. In such lineages a high proportion of 'vulnerable' species would be a natural, ongoing phenomenon.},
	Author = {Owens, Ian P. F. and Bennett, Peter M. and Harvey, Paul H.},
	Date-Added = {2008-03-27 13:52:15 +0000},
	Date-Modified = {2008-04-09 17:11:46 +0100},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {species richness; body size; life history; sexual selection; speciation; birds},
	Pages = {933-939},
	Timescited = {0},
	Title = {Species richness among birds: body size, life history, sexual selection or ecology?},
	Volume = {266},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Barraclough.Harvey.ea.1995.a,
	Abstract = {Many authors have suggested that sexual selection by female choice may increase the speciation rate and hence generate taxonomic diversity. Using sister taxa comparisons, we find a significant positive correlation between the proportion of sexually dichromatic species within taxa of passerine birds, and the number of species in those taxa. Theory predicts this result if sexual dichromatism in passerines has evolved through the action of female choice.},
	Author = {Barraclough, Timothy G. and Harvey, Paul H. and Nee, Sean},
	Date-Added = {2008-03-27 13:48:08 +0000},
	Date-Modified = {2008-03-27 20:22:38 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Pages = {211-215},
	Timescited = {0},
	Title = {SEXUAL SELECTION AND TAXONOMIC DIVERSITY IN PASSERINE BIRDS},
	Volume = {259},
	Year = {1995},
	Bdsk-File-1 = { }}

@incollection{Purvis.1996.a,
	Author = {Purvis, Andy},
	Booktitle = {New uses for new phylogenies},
	Crossref = {Harvey.LeighBrown.ea.1996.a},
	Date-Added = {2008-03-27 13:42:05 +0000},
	Date-Modified = {2008-11-16 17:28:39 +0000},
	Pages = {153 - 168},
	Title = {Testing macroevolutionary hypotheses}}

@book{Harvey.LeighBrown.ea.1996.a,
	Address = {Oxford},
	Author = {Harvey, Paul H. and Leigh Brown, A J and Maynard Smith, John and Nee, Sean},
	Date-Added = {2008-03-27 13:34:21 +0000},
	Date-Modified = {2008-11-16 17:33:57 +0000},
	Editor = {Harvey, Paul H. and Leigh Brown, A J and Maynard Smith, John and Nee, Sean},
	Publisher = {Oxford University Press},
	Title = {New uses for new phylogenies},
	Year = {1996}}

@article{Slowinski.Guyer.1993.a,
	Author = {Slowinski, Joseph B and Guyer, Craig},
	Date-Added = {2008-03-27 13:30:44 +0000},
	Date-Modified = {2008-03-27 15:07:02 +0000},
	Journal = {American Naturalist},
	Pages = {1019-1024},
	Timescited = {0},
	Title = {TESTING WHETHER CERTAIN TRAITS HAVE CAUSED AMPLIFIED DIVERSIFICATION - AN IMPROVED METHOD BASED ON A MODEL OF RANDOM SPECIATION AND EXTINCTION},
	Volume = {142},
	Year = {1993},
	Bdsk-File-1 = { }}

@article{GUYER.SLOWINSKI.1993.a,
	Abstract = {The idea that some organisms possess adaptive features that make them more likely to speciate and/or less likely to go extinct than closely related groups, suggests that large phylogenetic trees should be unbalanced (more species should occur in the group possessing the adaptive features than in the sister group lacking such features). Several methods have been used to document this type of adaptive radiation. One problem with these attempts is that evolutionary biologists may overlook balanced phylogenies while focusing on a few impressively unbalanced ones. To overcome this potential bias, we sampled published large phylogenies without regard to tree shape. These were used to test whether or not such trees are consistently unbalanced. We used recently developed null models to demonstrate that the shapes of large phylogenetic trees: 1) are similar among angiosperms, insects, and tetrapods; 2) differ from those expected due to random selection of a phylogeny from the pool of all trees of similar size; and 3) are significantly more unbalanced than expected if species diverge at random, therefore, conforming to one prediction of adaptive radiation. This represents an important first step in documenting whether adaptive radiation has been a general feature of evolution.},
	Author = {Guyer, Craig and Slowinski, Joseph B},
	Date-Added = {2008-03-27 13:30:44 +0000},
	Date-Modified = {2008-03-27 15:08:05 +0000},
	Journal = {Evolution},
	Keywords = {ADAPTIVE RADIATION; DIVERSIFICATION; NULL MODELS; PHYLOGENY; TOPOLOGY},
	Pages = {253-263},
	Timescited = {0},
	Title = {ADAPTIVE RADIATION AND THE TOPOLOGY OF LARGE PHYLOGENIES},
	Volume = {47},
	Year = {1993},
	Bdsk-File-1 = { }}

@article{McPeek.Brown.2007.a,
	Abstract = {Animal taxa show remarkable variability in species richness across phylogenetic groups. Most explanations for this disparity postulate that taxa with more species have phenotypes or ecologies that cause higher diversification rates (i.e., higher speciation rates or lower extinction rates). Here we show that clade longevity, and not diversification rate, has primarily shaped patterns of species richness across major animal clades: more diverse taxa are older and thus have had more time to accumulate species. Diversification rates calculated from 163 species-level molecular phylogenies were highly consistent within and among three major animal phyla ( Arthropoda, Chordata, Mollusca) and did not correlate with species richness. Clades with higher estimated diversification rates were younger, but species numbers increased with increasing clade age. A fossil-based data set also revealed a strong, positive relationship between total extant species richness and crown group age across the orders of insects and vertebrates. These findings do not negate the importance of ecology or phenotype in influencing diversification rates, but they do show that clade longevity is the dominant signal in major animal biodiversity-patterns. Thus, some key innovations may have acted through fostering clade longevity and not by heightening diversification rate.},
	Author = {McPeek, Mark A. and Brown, Jonathan M.},
	Date-Added = {2008-03-27 13:18:18 +0000},
	Date-Modified = {2008-03-27 13:18:32 +0000},
	Journal = {American Naturalist},
	Keywords = {biodiversity patterns; clade age; diversification rate; metazoa; species richness},
	Pages = {E97-E106},
	Timescited = {0},
	Title = {Clade age and not diversification rate explains species richness among animal taxa},
	Volume = {169},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Scotland.Sanderson.2004.a,
	Author = {Scotland, Robert W and Sanderson, Michael J},
	Date-Added = {2008-03-27 13:15:53 +0000},
	Date-Modified = {2008-08-21 09:42:10 +0100},
	Journal = {Science},
	Pages = {643-643},
	Timescited = {0},
	Title = {The significance of few versus many in the tree of life},
	Volume = {303},
	Year = {2004},
	Bdsk-File-1 = { }}

@book{Willis.1922.a,
	Address = {Cambridge},
	Author = {Willis, J C},
	Date-Added = {2008-03-27 13:13:30 +0000},
	Date-Modified = {2008-03-27 19:53:55 +0000},
	Publisher = {Cambridge University Press},
	Title = {Age and Area},
	Year = {1922}}

@article{Meiri.Thomas.2007.a,
	Abstract = {Recent compilations of large-scale data bases on the geographical distributions and body sizes of animals, coupled with developments in spatial statistics, have led to renewed interest in the geographical distribution of animal body sizes and the interspecific version of Bergmann's rule. Standard practice seems to be an examination of mean body sizes within higher taxa on gridded maps, with little regard to species richness or phylogeny. However, because the frequency distribution of body sizes is typically highly skewed, average size within grid cells may differ significantly between species-rich and species-poor cells even when the median and modal sizes remain constant. Species richness influences body size patterns because species are not added to communities at random in relation to their size: areas of low diversity are characterized by a higher range of body sizes than is expected by chance. Finally, a consideration of phylogenetic structure within taxa is necessary to elucidate whether patterns in the geography of size result from turnover between or within intermediate taxonomic levels. We suggest that the highest and lowest quantiles of body size distribution be mapped in order to expose possible physiological or ecological limitations on body size.},
	Author = {Meiri, Shai and Thomas, Gavin H.},
	Date-Added = {2008-03-20 11:45:46 +0000},
	Date-Modified = {2008-03-20 11:45:57 +0000},
	Doi = {DOI 10.1111/j.1466-8238.2007.00343.x},
	Journal = {Global Ecology and Biogeography},
	Keywords = {Bergmann's rule; body size; climate; community assembly; geographical variation; species richness; taxon replacement},
	Pages = {689-693},
	Timescited = {0},
	Title = {The geography of body size - challenges of the interspecific approach},
	Volume = {16},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00343.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00343.x}}

@article{Kembel.Hubbell.2006.a,
	Abstract = {Numerous ecological and evolutionary processes are thought to play a role in maintaining the high plant species diversity of tropical forests. An understanding of the phylogenetic structure of an ecological community can provide insights into the relative importance of different processes structuring that community. The objectives of this study were to measure the phylogenetic structure of Neotropical forest tree communities in the Forest Dynamics Plot (FDP) on Barro Colorado Island, Panama, to determine how the phylogenetic structure of tree communities varied among spatial scales and habitats within the FDP, and to study the effects of null-model choice on estimates of community phylogenetic structure. We measured community phylogenetic structure for tree species occurring together in quadrats ranging in size from 10 X 10 m to 100 X 100 m in the FDP. We estimated phylogenetic structure by comparing observed phylogenetic distances among species to the distribution of phylogenetic distances for null communities generated using two different null models. A null model that did not maintain observed species occurrence frequencies tended to find nonrandom community phylogenetic structure, even for random data. Using a null model that maintained observed species frequencies in null communities, the average phylogenetic structure of tree communities in the FDP was close to random at all spatial scales examined, but more quadrats than expected contained species that were phylogenetically clustered or overdispersed, and phylogenetic structure varied among habitats. In young forests and plateau habitats, communities were phylogenetically clustered, meaning that trees were more closely related to their neighbors than expected, while communities in swamp and slope habitats were phylogenetically overdispersed, meaning that trees were more distantly related to their neighbors than expected. Phylogenetic clustering suggests the importance of environmental filtering of phylogenetically conserved traits in young forests and plateau habitats, but the phylogenetic overdispersion observed in other habitats has several possible explanations, including variation in the strength of ecological processes among habitats or the phylogenetic history of niches, traits, and habitat associations. Future studies will need to include information on species traits in order to explain the variation in phylogenetic structure among habitats in tropical forests.},
	Author = {Kembel, Steven W. and Hubbell, Stephen P.},
	Date-Added = {2008-02-19 10:50:06 +0000},
	Date-Modified = {2008-02-19 10:50:10 +0000},
	Journal = {Ecology},
	Keywords = {community phylogenetic structure; environmental filtering; Forest Dynamics Plot; null models; Panama; phylogenetic clustering; phylogenetic overdispersion},
	Pages = {S86-S99},
	Timescited = {0},
	Title = {The phylogenetic structure of a neotropical forest tree community},
	Volume = {87},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Hardy.Senterre.2007.a,
	Abstract = {1 Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities.

2 Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. I-ST, P-ST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. F-ST, N-ST).

3 Two coefficients which express community differentiation among sites from species identity (I-ST) or species phylogeny (P-ST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (Pi(ST)) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site).

4 We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (P-ST > I-ST or Pi(ST) > 0) or phylogenetic overdispersion (P-ST < I-ST or Pi(ST) < 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations.

5 I-ST, P-ST or Pi(ST) can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears.

6 We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions.

7 The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species).},
	Author = {Hardy, Olivier J. and Senterre, Bruno},
	Date-Added = {2008-02-19 10:49:23 +0000},
	Date-Modified = {2008-02-19 10:49:30 +0000},
	Doi = {DOI 10.1111/j.1365-2745.2007.01222.x},
	Journal = {Journal of Ecology},
	Keywords = {additive partitioning of diversity; community ecology; Equatorial Guinea; neutral community; phylogenetic structure of communities; phylogeny; rain forest; randomization test; species assemblage; tropical trees},
	Pages = {493-506},
	Timescited = {0},
	Title = {Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity},
	Volume = {95},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2745.2007.01222.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2745.2007.01222.x}}

@article{Ackerly.Schwilk.ea.2006.a,
	Abstract = {In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (a niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (beta niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This a niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (beta niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the beta niche might have taken place. throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of a niche traits might be a common feature of niche evolution in many adaptive radiations.},
	Author = {Ackerly, D. D. and Schwilk, D. W. and Webb, C. O.},
	Date-Added = {2008-02-19 10:44:18 +0000},
	Date-Modified = {2008-02-19 10:46:55 +0000},
	Journal = {Ecology},
	Keywords = {adaptive radiation; Ceanothus; Cerastes; Coast Range; community assembly; Euceanothus; habitat; niche conservatism; phylogenetic comparative methods; specific leaf area; Sierra Nevada; trait divergence; Transverse Range},
	Pages = {S50-S61},
	Timescited = {0},
	Title = {Niche evolution and adaptive radiation: Testing the order of trait divergence},
	Volume = {87},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Strauss.Webb.ea.2006.a,
	Abstract = {Some species introduced into new geographical areas from their native ranges wreak ecological and economic havoc in their new environment. Although many studies have searched for either species or habitat characteristics that predict invasiveness of exotic species, the match between characteristics of the invader and those of members of the existing native community may be essential to understanding invasiveness. Here, we find that one metric, the phylogenetic relatedness of an invader to the native community, provides a predictive tool for invasiveness. Using a phylogenetic supertree of all grass species in California, we show that highly invasive grass species are, on average, significantly less related to native grasses than are introduced but noninvasive grasses. The match between the invader and the existing native community may explain why exotic pest species are not uniformly noxious in all novel habitats. Relatedness of invaders to the native biota may be one useful criterion for prioritizing management efforts of exotic species.},
	Author = {Strauss, SY and Webb, CO and Salamin, N},
	Date-Added = {2008-02-19 10:44:18 +0000},
	Date-Modified = {2008-02-19 10:45:51 +0000},
	Doi = {DOI 10.1073/pnas.0508073103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {biological invasions; community phylogenetics; grass; novel weapons; supertree},
	Pages = {5841-5845},
	Timescited = {0},
	Title = {Exotic taxa less related to native species are more invasive},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0508073103},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0508073103}}

@article{Webb.2000.a,
	Abstract = {Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees (greater than or equal to 10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.},
	Author = {Webb, Campbell O.},
	Date-Added = {2008-02-19 10:44:18 +0000},
	Date-Modified = {2011-05-18 12:01:51 +0100},
	Journal = {American Naturalist},
	Keywords = {phylogenetic conservatism; net ecological similarity; supertree; tropical rain forest; taxonomic diversity},
	Pages = {145-155},
	Timescited = {0},
	Title = {Exploring the phylogenetic structure of ecological communities: An example for rain forest trees},
	Volume = {156},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Ceballos.Ehrlich.2006.a,
	Abstract = {Hotspots, which have played a central role in the selection of sites for reserves, require careful rethinking. We carried out a global examination of distributions of all nonmarine mammals to determine patterns of species richness, endemism, and endangerment, and to evaluate the degree of congruence among hotspots of these three measures of diversity in mammals. We then compare congruence of hotspots in two animal groups (mammals and birds) to assess the generality of these patterns. We defined hotspots as the richest 2.5\% of cells in a global equal-area grid comparable to V latitude x 1 degrees longitude. Hotspots of species richness, "endemism," and extinction threat were noncongruent. Only 1\% of cells and 16\% of species were common to the three types of mammalian hotspots. Congruence increased with increases in both the geographic scope of the analysis and the percentage of cells defined as being hotspots. The within-mammal hotspot noncongruence was similar to the pattern recently found for birds. Thus, assigning global conservation priorities based on hotspots is at best a limited strategy.},
	Author = {Ceballos, Gerardo and Ehrlich, Paul R.},
	Date-Added = {2008-02-18 15:56:03 +0000},
	Date-Modified = {2008-02-18 15:56:11 +0000},
	Doi = {DOI 10.1073/pnas.0609334103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {hotspot congruence; birds; patterns of species distribution; endemism; threatened species},
	Pages = {19374-19379},
	Timescited = {0},
	Title = {Global mammal distributions, biodiversity hotspots, and conservation},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0609334103},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0609334103}}

@article{Pagel.Venditti.ea.2006.a,
	Abstract = {A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22\% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.},
	Author = {Pagel, Mark and Venditti, Chris and Meade, Andrew},
	Date-Added = {2008-02-18 15:52:04 +0000},
	Date-Modified = {2008-02-18 15:53:25 +0000},
	Doi = {DOI 10.1126/science.1129647},
	Journal = {Science},
	Pages = {119-121},
	Timescited = {0},
	Title = {Large punctuational contribution of speciation to evolutionary divergence at the molecular level},
	Volume = {314},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1129647},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1129647}}

@article{Jablonski.Roy.ea.2006.a,
	Abstract = {The evolutionary dynamics underlying the latitudinal gradient in biodiversity have been controversial for over a century. Using a spatially explicit approach that incorporates not only origination and extinction but immigration, a global analysis of genera and subgenera of marine bivalves over the past 11 million years supports an "out of the tropics'' model, in which taxa preferentially originate in the tropics and expand toward the poles without losing their tropical presence. The tropics are thus both a cradle and a museum of biodversity, contrary to the conceptual dichotomy dominant since 1974; a tropical diversity crisis would thus have profound evolutionary effects at all latitudes.},
	Author = {Jablonski, David and Roy, Kaustuv and Valentine, James W.},
	Date-Added = {2008-02-18 15:51:16 +0000},
	Date-Modified = {2008-02-18 15:51:19 +0000},
	Doi = {DOI 10.1126/science.1130880},
	Journal = {Science},
	Pages = {102-106},
	Timescited = {0},
	Title = {Out of the tropics: Evolutionary dynamics of the latitudinal diversity gradient},
	Volume = {314},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1130880},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1130880}}

@misc{Araujo.Rahbek.2006.a,
	Author = {Araujo, Miguel B. and Rahbek, Carsten},
	Date-Added = {2008-02-18 15:48:30 +0000},
	Date-Modified = {2008-02-18 15:49:05 +0000},
	Doi = {DOI 10.1126/science.1131758},
	Journal = {Science},
	Pages = {1396-1397},
	Timescited = {0},
	Title = {How does climate change affect biodiversity?},
	Volume = {313},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1131758},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1131758}}

@article{Gotelli.2000.a,
	Abstract = {The analysis of presence-absence matrices with "null model" randomization tests has been a major source of controversy in community ecology for over two decades. In this paper, I systematically compare the performance of nine null model algorithms and four co-occurrence indices with respect to Type I and Type II errors. The nine algorithms differ in whether rows and columns are treated as fixed sums, equiprobable, or proportional. The three models that maintain fixed row sums are invulnerable to Type I errors (false positives). One of these three is a modified version of the original algorithm of E. F. Conner and D. Simberloff. Of the four co-occurrence indices, the number of checkerboard combinations and the number of species combinations may be prone to Type II errors (false negatives), and may not reveal significant patterns in noisy data sets. L. Stone and A. Robert's checkerboard score has good power for detecting species pairs that do nut co-occur together frequently, whereas D. Schluter's V ratio reveals nonrandom patterns in the row and column totals of the matrix. Degenerate matrices (matrices with empty rows or columns) do not. greatly alter the outcome of null model analyses. The choice of an appropriate null model and index may depend on whether the data represent classic "island lists" of species in an archipelago or standardized "sample lists" of species collected with equal sampling effort. Systematic examination of a set of related null models can pinpoint how violation of the assumptions of the model contributes to nonrandom patterns.},
	Author = {Gotelli, Nicholas J},
	Date-Added = {2008-02-18 15:13:47 +0000},
	Date-Modified = {2008-02-18 15:16:41 +0000},
	Journal = {Ecology},
	Keywords = {assembly rules; checkerboard distribution; coexistence; community structure; competition; co-occurrence; Monte Carlo simulation; null model; presence-absence matrix; randomization test; species combinations},
	Number = {9},
	Pages = {2606-2621},
	Timescited = {0},
	Title = {Null model analysis of species co-occurrence patterns},
	Volume = {81},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Huntley.Collingham.ea.2008.a,
	Author = {Huntley, Brian and Collingham, Yvonne C and Willis, Stephen G and Green, Rhys E},
	Date-Added = {2008-02-18 14:22:44 +0000},
	Date-Modified = {2008-02-18 14:25:39 +0000},
	Doi = {10.1371/journal.pone.0001439},
	Journal = {PLoS One},
	Number = {1},
	Pages = {e1439},
	Title = {Potential Impacts of Climatic Change on European Breeding Birds},
	Volume = {3},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0001439%20}}

@article{Vieites.Min.ea.2007.a,
	Abstract = {A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continental-wide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene-Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter- and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution.},
	Author = {Vieites, David R. and Min, Mi-Sook and Wake, David B.},
	Date-Added = {2008-02-18 14:21:06 +0000},
	Date-Modified = {2008-02-18 14:21:10 +0000},
	Doi = {DOI 10.1073/pnas.0705056104},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {historical biogeography; paleogeography; plethodontidae dispersal; salamander phylogeny; phylogeny},
	Pages = {19903-19907},
	Timescited = {0},
	Title = {Rapid diversification and dispersal during periods of global warming by plethodontid salamanders},
	Volume = {104},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0705056104},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0705056104}}

@article{Hunt.Bergsten.ea.2007.a,
	Abstract = {Beetles represent almost one- fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80\% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre- Cretaceous origin of more than 100 present- day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.},
	Author = {Hunt, Toby and Bergsten, Johannes and Levkanicova, Zuzana and Papadopoulou, Anna and John, Oliver St. and Wild, Ruth and Hammond, Peter M. and Ahrens, Dirk and Balke, Michael and Caterino, Michael S. and Gomez-Zurita, Jesus and Ribera, Ignacio and Barraclough, Timothy G. and Bocakova, Milada and Bocak, Ladislav and Vogler, Alfried P.},
	Date-Added = {2008-02-18 14:19:40 +0000},
	Date-Modified = {2008-02-18 14:19:50 +0000},
	Doi = {DOI 10.1126/science.1146954},
	Journal = {Science},
	Pages = {1913-1916},
	Timescited = {0},
	Title = {A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation},
	Volume = {318},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1146954},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1146954}}

@article{Bininda-Emonds.Cardillo.ea.2007.a,
	Abstract = {Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.},
	Author = {Bininda-Emonds, Olaf R. P. and Cardillo, Marcel and Jones, Kate E. and MacPhee, Ross D. E. and Beck, Robin M. D. and Grenyer, Richard and Price, Samantha A. and Vos, Rutger A. and Gittleman, John L. and Purvis, Andy},
	Date-Added = {2008-02-15 16:30:33 +0000},
	Date-Modified = {2008-02-15 16:30:48 +0000},
	Doi = {DOI 10.1038/nature05634},
	Journal = {Nature},
	Pages = {507-512},
	Timescited = {0},
	Title = {The delayed rise of present-day mammals},
	Volume = {446},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature05634},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature05634}}

@article{Ricklefs.2006.a,
	Abstract = {Net diversification rates were estimated for samples of primarily tribe-to-family-level clades of passerine birds, taking into account extinction as well as speciation. Two samples were used. The first consisted of 37 clades of primarily temperate North American and primarily tropical South American passerines; the second comprised a global set of 90 clades, each distributed within one or more zoogeographic regions. Circumscription and ages of clades were taken from Sibley and Ahlquist's phylogeny based on DNA hybridization, with updates from more recent sequence analysis. Under a homogeneous speciation (rate = lambda) and extinction (rate = p) process, the expected number of species (N) after t units of time can be described by the expression, N(t) = [exp(lambda 1 - kappa)t - kappa]/(1 - kappa), where kappa = mu/lambda. A nonlinear least-squares regression for the temperate and tropical American clades with more than one species estimated kappa = 0.938 +/- 0.076 (mean +/- SE), suggesting a high rate of turnover of lineages within clades. Because of the broad confidence limits in kappa, I used values ranging from 0.80 to 0.98 to calculate speciation rates in subsequent analyses, assuming that kappa is uniform among clades and does not vary with latitude. Speciation rate among South American clades exceeded that among North American clades for all kappa, whether monophyletic lineages were included or not. The estimated speciation rate was negatively related to clade age, suggesting that proliferation within clades slows with time. In the global data set, rate of speciation decreased with clade age and increased with the area of the region or regions within which a clade is distributed, and for any given value of kappa the speciation rate was significantly higher in tropical than in temperate regions. Relaxing the assumption of latitude independence in kappa, larger clade size in the tropics could be achieved by various combinations of relative speciation and extinction rates that obscure the underlying causes of global biodiversity patterns. Nonetheless, the results of this analysis clearly indicate that a higher rate of diversification in the tropics contributes to the pervasive latitudinal gradient in diversity observed in passerine birds.},
	Author = {Ricklefs, Robert E.},
	Date-Added = {2008-02-15 13:44:03 +0000},
	Date-Modified = {2008-02-15 13:44:14 +0000},
	Journal = {Ecology},
	Keywords = {clades; diversification; extinction; global variation; latitudinal diversity gradient; passerine birds; speciation; species richness},
	Pages = {2468-2478},
	Timescited = {0},
	Title = {Global variation in the diversification rate of passerine birds},
	Volume = {87},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Weir.Schluter.2007.a,
	Abstract = {Although the tropics harbor greater numbers of species than do temperate zones, it is not known whether the rates of speciation and extinction also follow a latitudinal gradient. By sampling birds and mammals, we found that the distribution of the evolutionary ages of sister species-pairs of species in which each is the other's closest relative-adheres to a latitudinal gradient. The time to divergence for sister species is shorter at high latitudes and longer in the tropics. Birth-death models fitting these data estimate that the highest recent speciation and extinction rates occur at high latitudes and decline toward the tropics. These results conflict with the prevailing view that links high tropical diversity to elevated tropical speciation rates. Instead, our findings suggest that faster turnover at high latitudes contributes to the latitudinal diversity gradient.},
	Author = {Weir, Jason T. and Schluter, Dolph},
	Date-Added = {2008-02-15 10:53:19 +0000},
	Date-Modified = {2008-02-15 10:53:33 +0000},
	Doi = {DOI 10.1126/science.1135590},
	Journal = {Science},
	Pages = {1574-1576},
	Timescited = {0},
	Title = {The latitudinal gradient in recent speciation and extinction rates of birds and mammals},
	Volume = {315},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1135590},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1135590}}

@misc{Losos.Glor.2003.a,
	Abstract = {The geography of speciation has long been contentious. In recent years, phylogenetic approaches have been proposed to determine the geographical mode of speciation. If reliable, these methods not only provide a means of settling the debate about the geography of speciation, but also indicate that sympatric speciation is surprisingly common and that peripatric speciation is relatively rare. Similar to any phylogenetic inference, reconstructions of speciation mode are only useful if the underlying assumptions of the method are met. In this case, the key assumption is that the geographical range of both extant and ancestral species at the time of speciation can be inferred from present-day distributions. We discuss whether, and under what circumstances, such assumptions could be met. We conclude that interspecific phylogenies are unable to test alternative hypotheses concerning the geography of speciation rigorously because of the lability of geographical ranges and the lack of correlation between the role of adaptive processes and geographical mode of speciation.},
	Author = {Losos, Jonathan B. and Glor, Richard E.},
	Date-Added = {2008-02-14 14:31:09 +0000},
	Date-Modified = {2008-03-27 15:37:04 +0000},
	Doi = {DOI 10.1016/S0169-5347(03)00037-5},
	Journal = {Trends In Ecology \& Evolution},
	Pages = {220-227},
	Timescited = {0},
	Title = {Phylogenetic comparative methods and the geography of speciation},
	Volume = {18},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0169-5347(03)00037-5},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0169-5347(03)00037-5}}

@article{Sekercioglu.Daily.ea.2004.a,
	Abstract = {We present a general framework for characterizing the ecological and societal consequences of biodiversity loss and applying it to the global avifauna. To investigate the potential ecological consequences of avian declines, we developed comprehensive databases of the status and functional roles of birds and a stochastic model for forecasting change. Overall, 21\% of bird species are currently extinction-prone and 6.5\% are functionally extinct, contributing negligibly to ecosystem processes. We show that a quarter or more of frugivorous and omnivorous species and one-third or more of herbivorous, piscivorous, and scavenger species are extinction-prone. Furthermore, our projections indicate that by 2100, 6-14\% of all bird species will be extinct, and 7-25\% (28-56\% on oceanic islands) will be functionally extinct. Important ecosystem processes, particularly decomposition, pollination, and seed dispersal, will likely decline as a result.},
	Author = {Sekercioglu, Cagan H and Daily, Gretchen C and Ehrlich, Paul R},
	Date-Added = {2008-02-11 10:23:46 +0000},
	Date-Modified = {2008-08-21 09:42:41 +0100},
	Doi = {DOI 10.1073/pnas.0408049101},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {ecosystem services; functional extinctions; trophic cascades; community disassembly; ecological redundancy},
	Pages = {18042-18047},
	Timescited = {0},
	Title = {Ecosystem consequences of bird declines},
	Volume = {101},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0408049101},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0408049101}}

@article{Zink.Klicka.ea.2004.a,
	Abstract = {It is generally assumed that the Quaternary was a period of heightened diversification in temperate vertebrate organisms. Previous molecular systematics studies have challenged this assertion. We re-examined this issue in north temperate birds using log-lineage plots and distributions of sister-taxon distances. Log-lineage plots support earlier conclusions that avian diversification slowed during the Quaternary. To test plots of empirical sister-taxon distances we simulated three sets of phylogenies: constant speciation and extinction, a pulse of recent speciation, and a pulse of recent extinction. Previous opinions favour the model of recent speciation although our empirical dataset on 74 avian comparisons failed to reject a distribution derived from the constant and extinction models. Hence, it does not appear that the Quaternary was a period of exceptional rates of diversification, relative to the background rate.},
	Author = {Zink, RM and Klicka, J and Barber, BR},
	Date-Added = {2008-02-11 10:22:34 +0000},
	Date-Modified = {2008-02-11 10:22:42 +0000},
	Doi = {DOI 10.1098/rstb.2003.1392},
	Journal = {Philosophical Transactions of the Royal Society of London Series B-Biological Sciences},
	Keywords = {Quaternary; log-lineage plots; sister taxa; simulated phylogenies; diversification rates},
	Pages = {215-219},
	Timescited = {0},
	Title = {The tempo of avian diversification during the Quaternary},
	Volume = {359},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rstb.2003.1392},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rstb.2003.1392}}

@article{Zink.2004.a,
	Abstract = {Subspecies are often used in ways that require their evolutionary independence, for example as proxies for units of conservation. Mitochondrial DNA sequence data reveal that 97\% of continentally distributed avian subspecies lack the population genetic structure indicative of a distinct evolutionary unit. Subspecies considered threatened or endangered, some of which have been targets of expensive restoration efforts, also generally lack genetic distinctiveness. Although sequence data show that species include 1.9 historically significant units on average, these units are not reflected by current subspecies nomenclature. Yet, it is these unnamed units and not named subspecies that should play a major role in guiding conservation efforts and in identifying biological diversity. Thus, a massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.},
	Author = {Zink, RM},
	Date-Added = {2008-02-11 10:22:34 +0000},
	Date-Modified = {2008-02-11 10:22:36 +0000},
	Doi = {DOI 10.1098/rspb.2003.2617},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {mitochondrial DNA; subspecies; reciprocal monophyly; conservation},
	Pages = {561-564},
	Timescited = {0},
	Title = {The role of subspecies in obscuring avian biological diversity and misleading conservation policy},
	Volume = {271},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2003.2617},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2003.2617}}

@article{Whitlock.2005.a,
	Abstract = {The most commonly used method in evolutionary biology for combining information across multiple tests of the same null hypothesis is Fisher's combined probability test. This note shows that an alternative method called the weighted Z-test has more power and more precision than does Fisher's test. Furthermore, in contrast to some statements in the literature, the weighted Z-method is superior to the unweighted Z-transform approach. The results in this note show that, when combining P-values from multiple tests of the same hypothesis, the weighted Z-method should be preferred.},
	Author = {Whitlock, MC},
	Date-Added = {2008-02-11 10:21:55 +0000},
	Date-Modified = {2008-02-11 10:21:58 +0000},
	Doi = {DOI 10.1111/j.1420-9101.2005.00917.x},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {combined probabilities; Fisher's procedure; meta-analysis; multiple comparisons; Stouffer's method; weighted Z},
	Pages = {1368-1373},
	Timescited = {0},
	Title = {Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach},
	Volume = {18},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1420-9101.2005.00917.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1420-9101.2005.00917.x}}

@article{Sutherland.Armstrong-Brown.ea.2006.a,
	Abstract = {1. Evidence-based policy requires researchers to provide the answers to ecological questions that are of interest to policy makers. To find out what those questions are in the UK, representatives from 28 organizations involved in policy, together with scientists from 10 academic institutions, were asked to generate a list of questions from their organizations.

2. During a 2-day workshop the initial list of 1003 questions generated from consulting at least 654 policy makers and academics was used as a basis for generating a short list of 100 questions of significant policy relevance. Short-listing was decided on the basis of the preferences of the representatives from the policy-led organizations.

3. The areas covered included most major issues of environmental concern in the UK, including agriculture, marine fisheries, climate change, ecosystem function and land management.

4. The most striking outcome was the preference for general questions rather than narrow ones. The reason is that policy is driven by broad issues rather than specific ones. In contrast, scientists are frequently best equipped to answer specific questions. This means that it may be necessary to extract the underpinning specific question before researchers can proceed.

5. Synthesis and applications. Greater communication between policy makers and scientists is required in order to ensure that applied ecologists are dealing with issues in a way that can feed into policy. It is particularly important that applied ecologists emphasize the generic value of their work wherever possible.},
	Author = {Sutherland, WJ and Armstrong-Brown, S and Armsworth, PR and Brereton, T and Brickland, J and Campbell, CD and Chamberlain, DE and Cooke, AI and Dulvy, NK and Dusic, NR and Fitton, M and Freckleton, RP and Godfray, HCJ and Grout, N and Harvey, HJ and Hedley, C and Hopkins, JJ and Kift, NB and Kirby, J and Kunin, WE and Macdonald, DW and Marker, B and Naura, M and Neale, AR and Oliver, T and Osborn, D and Pullin, AS and Shardlow, MEA and Showler, DA and Smith, PL and Smithers, RJ and Solandt, JL and Spencer, J and Spray, CJ and Thomas, CD and Thompson, J and Webb, SE and Yalden, DW and Watkinson, AR},
	Date-Added = {2008-02-11 10:21:07 +0000},
	Date-Modified = {2008-02-11 10:21:13 +0000},
	Doi = {DOI 10.1111/j.1365-2664.2006.01188.x},
	Journal = {Journal of Applied Ecology},
	Keywords = {agricultural reform; biodiversity; conservation; fisheries; land management; restoration ecology},
	Pages = {617-627},
	Timescited = {0},
	Title = {The identification of 100 ecological questions of high policy relevance in the UK},
	Volume = {43},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2664.2006.01188.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2664.2006.01188.x}}

@article{Sarkar.Pappas.ea.2004.a,
	Abstract = {We analyse optimal and heuristic place prioritization algorithms for biodiversity conservation area network design which can use probabilistic data on the distribution of surrogates for biodiversity. We show how an Expected Surrogate Set Covering Problem (ESSCP) and a Maximal Expected Surrogate Covering Problem (MESCP) can be linearized for computationally efficient solution. For the ESSCP, we study the performance of two optimization software packages (XPRESS and CPLEX) and five heuristic algorithms based on traditional measures of complementarity and rarity as well as the Shannon and Simpson indices of alpha-diversity which are being used in this context for the first time. On small artificial data sets the optimal place prioritization algorithms often produced more economical solutions than the heuristic algorithms, though not always ones guaranteed to be optimal. However, with large data sets, the optimal algorithms often required long computation times and produced no better results than heuristic ones. Thus there is generally little reason to prefer optimal to heuristic algorithms with probabilistic data sets.},
	Author = {Sarkar, Sahotra and Pappas, Christopher and Garson, Justin and Aggarwal, Anshu and Cameron, Susan},
	Date-Added = {2008-02-11 10:19:28 +0000},
	Date-Modified = {2008-08-21 09:41:50 +0100},
	Journal = {Diversity and Distributions},
	Keywords = {area selection; conservation planning; integer programming; linear programming; probabilistic data analysis; reserve network selection; site selection},
	Pages = {125-133},
	Timescited = {0},
	Title = {Place prioritization for biodiversity conservation using probabilistic surrogate distribution data},
	Volume = {10},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Moore.Balmford.ea.2003.a,
	Abstract = {The aim of continental and global identification of priority areas for conservation is to identify particularly valuable areas for conservation on which to focus more-detailed effort. Often, these sets of important areas, referred to as priority sets, have been identified through use of data on a single taxon (e.g., birds), which is assumed to act as an indicator for all biodiversity. Using a database of the distributions of 3882 vertebrate species in sub-Saharan Africa, we conducted one of very few large-scale tests of this assumption. We used six potential indicator groups-birds, mammals, amphibians, snakes, threatened birds, and threatened mammals-to find priority sets of 200 areas that best represent the species in that group. Priority sets of grid cells designed to maximize representation of a single indicator group captured 83-93\% of species in the other groups. This high degree of representation is consistent with observed high levels of overlap in the patterns of distribution of species in different groups. Those species of highest conservation interest were more poorly represented, however, with only 75-88\% of other groups' threatened species and 63-76\% of other groups' narrow-range species represented in the priority sets. We conclude that existing priority sets based on indicator groups provide a pragmatic basis for the immediate assessment of priorities for conservation at a continental scale. However, complete and efficient representation-especially of narrow-range species-will not be achieved through indicator groups alone. Therefore, priority-setting procedures must remain flexible so that new areas important for other taxa can be incorporated as data become available.},
	Author = {Moore, JL and Balmford, A and Brooks, T and Burgess, ND and Hansen, LA and Rahbek, C and Williams, PH},
	Date-Added = {2008-02-11 10:17:41 +0000},
	Date-Modified = {2008-02-11 10:18:01 +0000},
	Journal = {Conservation Biology},
	Pages = {207-218},
	Timescited = {0},
	Title = {Performance of sub-Saharan vertebrates as indicator groups for identifying priority areas for conservation},
	Volume = {17},
	Year = {2003},
	Bdsk-File-1 = { }}

@article{Rodrigues.Cerdeira.ea.2000.a,
	Abstract = {Flexibility, efficiency and accountability are considered key attributes of good reserve selection methods. Flexibility, the ability to incorporate all the diversity of considerations, concerns and information that typically impinge on real conservation problems, is fundamental if the particulars of any given situation are to be addressed and land use conflicts are to be effectively resolved. High efficiency, the representation of the maximum diversity of the relevant Features (e.g. species) at the minimum cost, is important because reserves will commonly be in direct competition with other forms of land use. Accountability means that the solutions are obtained in a transparent way, allowing others to understand why and how the result was arrived at. Because of the robustness of the general integer linear model, a remarkably rich variety of problems concerning the management and efficient use of scarce resources can be represented as problems of this type. This study starts by analysing a simple representation problem and then develops more general problems that can be applied to a variety of conservation planning exercises. It is illustrated how high flexibility can be attained, while simultaneously addressing efficiency and accountability, by modelling reserve selection questions as integer linear problems.},
	Author = {Rodrigues, Ana S and Cerdeira, J Orestes and Gaston, Kevin J.},
	Date-Added = {2008-02-11 10:15:25 +0000},
	Date-Modified = {2008-08-21 09:39:56 +0100},
	Journal = {Ecography},
	Pages = {565-574},
	Timescited = {0},
	Title = {Flexibility, efficiency, and accountability: adapting reserve selection algorithms to more complex conservation problems},
	Volume = {23},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Buckley.Jetz.2007.b,
	Abstract = {Our knowledge of the broad-scale ecology of vertebrate ectotherms remains very limited. Despite ongoing declines and sensitivity to environmental change, amphibian distributions are particularly poorly understood. We present a global analysis of contemporary environmental and historical constraints on amphibian richness, the first for an ectotherm clade at this scale. Amphibians are presumed to experience environmental constraints distinct from those of better studied endothermic taxa due to their stringent water requirements and the temperature dependence of their energetic costs and performance. Single environmental predictors set upper bounds on, but do not exclusively determine, amphibian richness. Accounting for differing regional histories of speciation and extinction helps resolve triangular or scattered relationships between core environmental predictors and amphibian richness, as the relationships' intercepts or slopes can vary regionally. While the magnitude of richness is strongly determined by regional history, within-region patterns are consistently jointly driven by water and temperature. This confirms that ecophysiological constraints extend to the broad scale. This coupling suggests that shifts in climatic regimes will probably have dramatic consequences for amphibians. Our results illustrate how the environmental and historical explanations of species richness gradients can be reconciled and how the perspectives are complements for understanding broad-scale patterns of diversity.},
	Author = {Buckley, Lauren B. and Jetz, Walter},
	Date-Added = {2008-02-11 10:05:58 +0000},
	Date-Modified = {2008-02-11 10:11:44 +0000},
	Doi = {DOI 10.1098//rspb.2006.0436},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {amphibians; biogeography; climate change; diversity gradient; historical contingency; water-temperature hypothesis},
	Pages = {1167-1173},
	Timescited = {0},
	Title = {Environmental and historical constraints on global patterns of amphibian richness},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098//rspb.2006.0436},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098//rspb.2006.0436}}

@article{Hurlbert.Jetz.2007.a,
	Abstract = {Most studies examining continental-to-global patterns of species richness rely on the overlaying of extent-of-occurrence range maps. Because a species does not occur at all locations within its geographic range, range-map-derived data represent actual distributional patterns only at some relatively coarse and undefined resolution. With the increasing availability of high-resolution climate and land-cover data, broad-scale studies are increasingly likely to estimate richness at high resolutions. Because of the scale dependence of most ecological phenomena, a significant mismatch between the presumed and actual scale of ecological data may arise. This may affect conclusions regarding basic drivers of diversity and may lead to errors in the identification of diversity hotspots. Here, we examine avian range maps of 834 bird species in conjunction with geographically extensive survey data sets on two continents to determine the spatial resolutions at which range-map data actually characterize species occurrences and patterns of species richness. At resolutions less than 2 degrees (approximate to 200 km), range maps overestimate the area of occupancy of individual species and mischaracterize spatial patterns of species richness, resulting in up to two-thirds of biodiversity hotspots being misiclentified. The scale dependence of range-map accuracy poses clear limitations on broad-scale ecological analyses and conservation assessments. We suggest that range-map data contain less information than is generally assumed and provide guidance about the appropriate scale of their use.},
	Author = {Hurlbert, Allen H. and Jetz, Walter},
	Date-Added = {2008-02-11 10:05:58 +0000},
	Date-Modified = {2008-02-11 10:06:55 +0000},
	Doi = {DOI 10.1073/pnas.0704469104},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {biodiversity; birds; geographic range; range occupancy; species richness pattern},
	Pages = {13384-13389},
	Timescited = {0},
	Title = {Species richness, hotspots, and the scale dependence of range maps in ecology and conservation},
	Volume = {104},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0704469104},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0704469104}}

@article{Jetz.Rahbek.2002.a,
	Abstract = {Geographic patterns in species richness are mainly based on wide-ranging species because their larger number of distribution records has a disproportionate contribution to the species richness counts. Here we demonstrate how this effect strongly influences our understanding of what determines species richness. Using both conventional and spatial regression models, we show that for sub-Saharan African birds, the apparent role of productivity diminishes with decreasing range size, whereas the significance of topographic heterogeneity increases. The relative importance of geometric constraints from the continental edge is moderate. Our findings highlight the failure of traditional species richness models to account for narrow-ranging species that frequently are also threatened.},
	Author = {Jetz, W and Rahbek, C},
	Date-Added = {2008-02-11 10:05:58 +0000},
	Date-Modified = {2008-02-11 10:06:46 +0000},
	Journal = {Science},
	Pages = {1548-1551},
	Timescited = {0},
	Title = {Geographic range size and determinants of avian species richness},
	Volume = {297},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Kreft.Jetz.2007.a,
	Abstract = {Plants, with an estimated 300,000 species, provide crucial primary production and ecosystem structure. To date, our quantitative understanding of diversity gradients of megadiverse clades such as plants has been hampered by the paucity of distribution data. Here, we investigate the global-scale species-richness pattern of vascular plants and examine its environmental and potential historical determinants. Across 1,032 geographic regions worldwide, potential evapotranspiration, the number of wet days per year, and measurements of topographical and habitat heterogeneity emerge as core predictors of species richness. After accounting for environmental effects, the residual differences across the major floristic kingdoms are minor, with the exception of the uniquely diverse Cape Region, highlighting the important role of historical contingencies. Notably, the South African Cape region contains more than twice as many species as expected by the global environmental model, confirming its uniquely evolved flora. A combined multipreclictor model explains approximate to 70\% of the global variation in species richness and fully accounts for the enigmatic latitudinal gradient in species richness. The models illustrate the geographic interplay of different environmental predictors of species richness. Our findings highlight that different hypotheses about the causes of diversity gradients are not mutually exclusive, but likely act synergistically with water-energy dynamics playing a dominant role. The presented geostatistical approach is likely to prove instrumental for identifying richness patterns of the many other taxa without single-species distribution data that still escape our understanding.},
	Author = {Kreft, Holger and Jetz, Walter},
	Date-Added = {2008-02-11 10:05:58 +0000},
	Date-Modified = {2008-02-11 10:06:32 +0000},
	Doi = {DOI 10.1073/pnas.0608361104},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {biodiversity; historical contingency; latitudinal gradient; macroecology; species richness},
	Pages = {5925-5930},
	Timescited = {0},
	Title = {Global patterns and determinants of vascular plant diversity},
	Volume = {104},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0608361104},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0608361104}}

@article{Jetz.Wilcove.ea.2007.a,
	Abstract = {Over the past few decades, land-use and climate change have led to substantial range contractions and species extinctions. Even more dramatic changes to global land cover are projected for this century. We used the Millennium Ecosystem Assessment scenarios to evaluate the exposure of all 8,750 land bird species to projected land-cover changes due to climate and land-use change. For this first baseline assessment, we assumed stationary geographic ranges that may overestimate actual losses in geographic range. Even under environmentally benign scenarios, at least 400 species are projected to suffer > 50\% range reductions by the year 2050 (over 900 by the year 2100). Although expected climate change effects at high latitudes are significant, species most at risk are predominantly narrow-ranged and endemic to the tropics, where projected range contractions are driven by anthropogenic land conversions. Most of these species are currently not recognized as imperiled. The causes, magnitude and geographic patterns of potential range loss vary across socioeconomic scenarios, but all scenarios (even the most environmentally benign ones) result in large declines of many species. Whereas climate change will severely affect biodiversity, in the near future, land-use change in tropical countries may lead to yet greater species loss. A vastly expanded reserve network in the tropics, coupled with more ambitious goals to reduce climate change, will be needed to minimize global extinctions.},
	Author = {Jetz, Walter and Wilcove, David S. and Dobson, Andrew P.},
	Date-Added = {2008-02-11 10:05:58 +0000},
	Date-Modified = {2008-05-02 10:52:12 +0100},
	Doi = {ARTN e157},
	Journal = {PLoS Biology},
	Pages = {1211-1219},
	Timescited = {0},
	Title = {Projected impacts of climate and land-use change on the global diversity of birds},
	Volume = {5},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/157},
	Bdsk-Url-2 = {http://dx.doi.org/157}}

@article{Freckleton.2000.a,
	Abstract = {1. Phylogenetic methods that account for the degree of relationship between species are increasingly commonly used for cross-species comparisons of ecological data. In particular 'phylogenetic contrasts' are commonly used to generate data for analysis that are phylogenetically independent. The efficacy of this technique for removing phylogenetic correlations is rarely tested, however.

2. For a number of reasons, including non-Brownian modes of evolution, phylogenetic contrasts may not always be phylogenetically independent. This lack of independence defeats the object of phylogenetic analysis and effectively invalidates the results of such analyses. Typically such problems may be overcome using simple data transformations but it is necessary to identify the correct transformation for each analysis variable.

3. Examples are presented for which contrasts have failed to control for phylogenetic correlation. This was because the correct transformation of the data was not identified prior to analysis. It is highlighted that the very act of transformation of data increases our understanding of the ecological variables being studied because the choice of transformation depends on how the character in question evolved.},
	Author = {Freckleton, Rob P.},
	Date-Added = {2008-02-11 10:01:10 +0000},
	Date-Modified = {2011-01-14 14:11:22 +0000},
	Journal = {Functional Ecology},
	Keywords = {comparative method; life histories; phylogenetic correction},
	Pages = {129-134},
	Timescited = {0},
	Title = {Phylogenetic tests of ecological and evolutionary hypotheses: checking for phylogenetic independence},
	Volume = {14},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Freckleton.Harvey.2006.a,
	Abstract = {Many phylogenetic comparative methods that are currently widely used in the scientific literature assume a Brownian motion model for trait evolution, but the suitability of that model is rarely tested, and a number of important factors might affect whether this model is appropriate or not. For instance, we might expect evolutionary change in adaptive radiations to be driven by the availability of ecological niches. Such evolution has been shown to produce patterns of change that are different from those modelled by the Brownian process. We applied two tests for the assumption of Brownian motion that generally have high power to reject data generated under non-Brownian niche-filling models for the evolution of traits in adaptive radiations. As a case study, we used these tests to explore the evolution of feeding adaptations in two radiations of warblers. In one case, the patterns revealed do not accord with Brownian motion but show characteristics expected under certain niche-filling models.},
	Author = {Freckleton, Robert P. and Harvey, Paul H.},
	Date-Added = {2008-02-11 10:01:10 +0000},
	Date-Modified = {2008-05-02 10:52:24 +0100},
	Doi = {ARTN e373},
	Journal = {PLoS Biology},
	Pages = {2104-2111},
	Timescited = {0},
	Title = {Detecting non-Brownian trait evolution in adaptive radiations},
	Volume = {4},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/373},
	Bdsk-Url-2 = {http://dx.doi.org/373}}

@article{Freckleton.Harvey.ea.2002.a,
	Abstract = {The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60\% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16\% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.},
	Author = {Freckleton, Robert P. and Harvey, Paul H. and Pagel, Mark},
	Date-Added = {2008-02-11 10:01:10 +0000},
	Date-Modified = {2008-10-09 11:40:12 +0100},
	Journal = {American Naturalist},
	Keywords = {generalized least squares; maximum likelihood; phylogenetic correction; phylogenetically independent contrasts},
	Pages = {712-726},
	Timescited = {0},
	Title = {Phylogenetic analysis and comparative data: A test and review of evidence},
	Volume = {160},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Dial.Marzluff.1989.a,
	Author = {Dial, Kenneth P. and Marzluff, John M.},
	Date-Added = {2008-02-11 09:57:29 +0000},
	Date-Modified = {2008-04-16 14:01:19 +0100},
	Journal = {Systematic Zoology},
	Pages = {26-37},
	Timescited = {0},
	Title = {NONRANDOM DIVERSIFICATION WITHIN TAXONOMIC ASSEMBLAGES},
	Volume = {38},
	Year = {1989},
	Bdsk-File-1 = { }}

@article{Bokma.2002.a,
	Abstract = {Of the approximately 9500 bird species, the vast majority is small-bodied. That is a general feature of evolutionary lineages, also observed for instance in mammals and plants. The avian interspecific body size distribution is right-skewed even on a logarithmic scale. That has previously been interpreted as evidence that body size evolution has been biased. However, a procedure to test for unbiased evolution from the shape of body size distributions was lacking. In the present paper unbiased body size evolution is defined precisely, and a statistical test is developed based on Monte Carlo simulation of unbiased evolution. Application of the test to birds suggests that it is highly unlikely that avian body size evolution has been unbiased as defined. Several possible explanations for this result are discussed. A plausible explanation is that the general model of unbiased evolution assumes that population size and generation time do not affect the evolutionary variability of body size; that is, that micro- and macroevolution are decoupled, which theory suggests is not likely to be the case.},
	Author = {Bokma, F},
	Date-Added = {2008-02-11 09:56:39 +0000},
	Date-Modified = {2008-02-11 09:56:50 +0000},
	Journal = {Evolution},
	Keywords = {aves; body size evolution; evolutionary trend; extinction; macroevolution; speciation},
	Pages = {2499-2504},
	Timescited = {0},
	Title = {A statistical test of unbiased evolution of body size in birds},
	Volume = {56},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Benton.2001.a,
	Abstract = {Phylogenies, or evolutionary trees, are fundamental to biology. Systematists have laboured since (lie time of Darwin to discover the tree of life. Recent developments in systematics, such as cladistics and molecular sequencing, have led practitioners to believe that their phylogenies are more testable now than equivalent efforts from the 1960s or earlier. Whole trees, and nodes within trees, may be assessed for their robustness. However, these quantitative approaches cannot be used to demonstrate that one tree is more likely to be correct than another. Congruence assessments may help. Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. Controlled comparisons of phylogenies of four major groups Agnatha, Sarcopterygii, Sauria and Mammalia) do not show uniform improvement, or decline, of fit to stratigraphy through the twentieth century. Nor do morphological or molecular trees differ uniformly in their performance.},
	Author = {Benton, MJ},
	Date-Added = {2008-02-11 09:55:44 +0000},
	Date-Modified = {2008-02-11 09:56:05 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {cladistics; phylogeny; fossil record; stratigraphy; tree},
	Pages = {2123-2130},
	Timescited = {0},
	Title = {Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century},
	Volume = {268},
	Year = {2001},
	Bdsk-File-1 = { }}

@misc{Benton.Pearson.2001.a,
	Abstract = {It is easy to claim that the fossil record says nothing about speciation because the biological species concept (which relies on interbreeding) cannot be applied to it and genetic studies cannot be carried out on it. However, fossilized organisms are often preserved in sufficient abundance for populations of intergrading morphs to be recognized, which, by analogy with modern populations, are probably biological species. Moreover, the fossil record is our only reliable documentation of the sequence of past events over long time intervals: the processes of speciation are generally too slow to be observed directly, and permanent reproductive isolation can only be verified with hindsight. Recent work has shown that some parts of the fossil record are astonishingly complete and well documented, and patterns of lineage splitting can be examined in detail. Marine plankton appear to show gradual speciation. with subsequent morphological differentiation of lineages taking up to 500 000 years to occur. Marine invertebrates and vertebrates more commonly show punctuated patterns, with periods of rapid speciation followed by long-term stasis of species lineages.},
	Author = {Benton, MJ and Pearson, PN},
	Date-Added = {2008-02-10 09:22:49 +0000},
	Date-Modified = {2008-02-18 15:49:48 +0000},
	Journal = {Trends In Ecology \& Evolution},
	Pages = {405-411},
	Timescited = {0},
	Title = {Speciation in the fossil record},
	Volume = {16},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Alroy.Marshall.ea.2001.a,
	Abstract = {Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene), Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cretaceous and early Tertiary diversity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine biodiversity. These limitations will be addressed as the database and methods are refined.},
	Author = {Alroy, J and Marshall, CR and Bambach, RK and Bezusko, K and Foote, M and Fursich, FT and Hansen, TA and Holland, SM and Ivany, LC and Jablonski, D and Jacobs, DK and Jones, DC and Kosnik, MA and Lidgard, S and Low, S and Miller, AI and Novack-Gottshall, PM and Olszewski, TD and Patzkowsky, ME and Raup, DM and Roy, K and Sepkoski, JJ and Sommers, MG and Wagner, PJ and Webber, A},
	Date-Added = {2008-02-10 09:21:32 +0000},
	Date-Modified = {2008-02-10 09:21:38 +0000},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Pages = {6261-6266},
	Timescited = {0},
	Title = {Effects of sampling standardization on estimates of Phanerozoic marine diversification},
	Volume = {98},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Alroy.1998.a,
	Abstract = {Body mass estimates for 1534 North American fossil mammal species show that new species are on average 9.1\% larger than older species in the same genera. This within-lineage effect is not a sampling bias. It persists throughout the Cenozoic; accounting for the gradual overall increase in average mass (Cope's rule). The effect is stronger for larger mammals, being near zero for small mammals. This variation partially explains the unwavering lower size limit and the gradually expanding mid-sized gap, but not the sudden large increase in the upper size limit, at the Cretaceous-Tertiary boundary.},
	Author = {Alroy, J},
	Date-Added = {2008-02-10 09:20:39 +0000},
	Date-Modified = {2008-02-15 16:28:53 +0000},
	Journal = {Science},
	Pages = {731-734},
	Rating = {0},
	Timescited = {0},
	Title = {Cope's rule and the dynamics of body mass evolution in North American fossil mammals},
	Volume = {280},
	Year = {1998},
	Bdsk-File-1 = { }}

@article{Ricklefs.2003.a,
	Abstract = {The distribution of species richness in families of passerine birds suggests that the net rate of diversification was significantly higher than average in as many as 7 out of 47 families. However, the absence of excess species richness among the 106 tribes within these families indicates that these high rates were transient, perhaps associated in some cases with tectonic movements or dispersal events that extended geographical ranges. Thus, large clade size among passerine birds need not represent intrinsic key innovations that influence the rate of diversification. Approximately 17 families and 30 tribes have too few species relative to other passerine taxa. Many of these are ecologically or geographically marginal, being especially over-represented in the Australasian region. Observed intervals between lineage splitting suggest that extinction has occurred ca. 90\% as frequently as speciation (waiting times of 1.03 and 0.93 Myr) and that the 47 modern families comprising 5712 species descended from approximately 430 passerine lineages extant 24 Myr ago. Speciation and extinction rates among small, marginal families might be 1-2 orders of magnitude lower.},
	Author = {Ricklefs, Robert E.},
	Date-Added = {2008-02-08 17:11:19 +0000},
	Date-Modified = {2008-03-27 15:33:51 +0000},
	Doi = {DOI 10.1098/rspb.2003.2489},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {cladogenesis; diversification; geometric distribution; key innovation; species richness},
	Pages = {2285-2291},
	Timescited = {0},
	Title = {Global diversification rates of passerine birds},
	Volume = {270},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2003.2489},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2003.2489}}

@article{Rodrigues.Tratt.ea.1999.a,
	Abstract = {It is widely held chat existing reserve systems are inadequate in representing the diversity of biological features of the regions in which they reside. Evidence for this argument has, however, derived principally from analyses of the efficiency of networks when compared with a minimum set that represents each species at least once. Here, we examine the efficiency of the system of Sites of Special Scientific Interest (SSSIs) in representing wetland plants in fen sites in the Scottish Borders, a region where reserve networks might be expected a priori to perform reasonably well in this regard. The results support the general contention that networks have been designated in an inefficient manner. However, examined in terms of effectiveness (measured as the gap between the representation target required and the one attained by the existing network), the SSSI system is actually a rather good way of representing diversity This result is consistent when each of several very different representation targets is evaluated, and suggests that a more balanced approach to evaluating the performance of reserve networks should be employed, and that general statements based on existing analyses should be treated cautiously.},
	Author = {Rodrigues, Ana S L and Tratt, Rosalind and Wheeler, Bryan D and Gaston, Kevin J.},
	Date-Added = {2008-02-08 16:58:50 +0000},
	Date-Modified = {2008-10-30 14:26:35 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {biodiversity; effectiveness; efficiency; minimum set algorithms; nature reserves},
	Pages = {1453-1460},
	Rating = {0},
	Timescited = {0},
	Title = {The performance of existing networks of conservation areas in representing biodiversity},
	Volume = {266},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Lennon.Koleff.ea.2001.a,
	Abstract = {1. Using data on the spatial distribution of the British avifauna, we address three basic questions about the spatial structure of assemblages: (i) Is there a relationship between species richness (alpha diversity) and spatial turnover of species (beta diversity)? (ii) Do high richness locations have fewer species in common with neighbouring areas than low richness locations?, and (iii) Are any such relationships contingent on spatial scale (resolution or quadrat area), and do they reflect the operation of a particular kind of species-area relationship (SAR)?

2. For all measures of spatial turnover, we found a negative relationship with species richness. This held across all scales, with the exception of turnover measured as beta (sim).

3. Higher richness areas were found to have more species in common with neighbouring areas.

4. The logarithmic SAR fitted better than the power SAR overall, and fitted significantly better in areas with low richness and high turnover.

5. Spatial patterns of both turnover and richness vary with scale. The finest scale richness pattern (10 km) and the coarse scale richness pattern (90 km) are statistically unrelated. The same is true of the turnover patterns.

6. With coarsening scale, locations of the most species-rich quadrats move north. This observed sensitivity of richness 'hotspot' location to spatial scale has implications for conservation biology, e.g. the location of a reserve selected on the basis of maximum richness may change considerably with reserve size or scale of analysis.

7. Average turnover measured using indices declined with coarsening scale, but the average number of species gained or lost between neighbouring quadrats was essentially scale invariant at 10-13 species, despite mean richness rising from 80 to 146 species (across an 81-fold area increase). We show that this kind of scale invariance is consistent with the logarithmic SAR.},
	Author = {Lennon, JJ and Koleff, P and Greenwood, JJD and Gaston, KJ},
	Date-Added = {2008-02-08 16:54:38 +0000},
	Date-Modified = {2008-02-08 16:55:23 +0000},
	Journal = {Journal of Animal Ecology},
	Keywords = {diversity hotspots; pattern matching; scale invariance; spatial autocorrelation; species distribution; species turnover},
	Pages = {966-979},
	Timescited = {0},
	Title = {The geographical structure of British bird distributions: diversity, spatial turnover and scale},
	Volume = {70},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{McGill.2003.a,
	Abstract = {Intensively sampled species abundance distributions (SADs) show left-skew on a log scale. That is, there are too many rare species to fit a lognormal distribution. I propose that this log-left-skew might be a sampling artefact. Monte Carlo simulations show that taking progressively larger samples from a log-unskewed distribution (such as the lognormal) causes log-skew to decrease asymptotically (move towards -infinity) until it reaches the level of the underlying distribution (zero in this case). In contrast, accumulating certain types of repeated small samples results in a log-skew that becomes progressively more log-left-skewed to a level well beyond the underlying distribution. These repeated samples correspond to samples from the same site over many years or from many sites in 1 year. Data from empirical datasets show that log-skew generally goes from positive (right-skewed) to negative (left-skewed) as the number of temporally or spatially replicated samples increases. This suggests caution when interpreting log-left-skew as a pattern that needs biological interpretation.},
	Author = {McGill, BJ},
	Date-Added = {2008-02-08 16:53:33 +0000},
	Date-Modified = {2008-02-08 16:53:46 +0000},
	Doi = {DOI 10.1046/j.1461-0248.2003.00491.x},
	Journal = {Ecology Letters},
	Keywords = {left-skew; species abundance distributions; sampling},
	Pages = {766-773},
	Timescited = {0},
	Title = {Does Mother Nature really prefer rare species or are log-left-skewed SADs a sampling artefact?},
	Volume = {6},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1046/j.1461-0248.2003.00491.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1046/j.1461-0248.2003.00491.x}}

@article{La-Sorte.2006.a,
	Abstract = {Aim The assumption that ecological patterns at large spatial scales originate exclusively from non-anthropogenic processes is growing more questionable with the increasing domination of the biosphere by humans. Because common and rare species are known to respond differently to anthropogenic activities at local scales these differential responses could, over time, be reflected in distributional patterns of species richness at larger spatial scales. This work tests the hypothesis that modern processes have played a role in shaping these patterns, by examining recent changes in the structure and composition of assemblages of breeding avifauna over a large geographical extent.

Location The portion of North America containing the contiguous United States and southern Canada.

Methods Changes in the geographical range structure of breeding avifauna in North America from 1968 to 2003 were analysed in regions containing historically moderate levels of anthropogenic activities. Two geographical measures, extent of occurrence and area of occupancy, were used to identify the level of rarity or commonality of individual species and to estimate, based on a vector analysis, patterns of change in geographical range structure for individual species and avian assemblages.

Results More species experienced patterns of geographical range expansion (51\%) than contraction (28\%). The majority of avian assemblages (43\%) displayed patterns of geographical range expansion: common species increased in number and proportion (6\%) in association with reciprocal losses in rare and moderately rare species, resulting in a constant level of species richness. The minority of avian assemblages (21\%) displayed patterns of geographical range contraction: gains occurred for common species as well as for rare and moderately rare species, resulting in substantial increases in species richness and a decline in the proportion of common species (4\%). The remaining avian assemblages presented equivocal patterns characterized by gains in the number and proportion (2\%) of common species and gains in species richness.

Main conclusions Modern processes have played a role in shaping the distribution patterns of species richness at large spatial scales based on the composition of common and rare species. This suggests that anthropogenic activities cannot be ignored as a possible causal factor when considering ecological patterns at large spatial scales.},
	Author = {La Sorte, FA},
	Date-Added = {2008-02-08 16:51:15 +0000},
	Date-Modified = {2008-02-08 16:51:23 +0000},
	Doi = {DOI 10.1111/j.1365-2699.2006.01480.x},
	Journal = {Journal of Biogeography},
	Keywords = {anthropogenic activities; Breeding Bird Survey; commonness; distribution; diversity; geographical range; North America; rarity; species richness},
	Pages = {1183-1191},
	Timescited = {0},
	Title = {Geographical expansion and increased prevalence of common species in avian assemblages: implications for large-scale patterns of species richness},
	Volume = {33},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01480.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01480.x}}

@article{Kissling.Gudrun.2008.a,
	Author = {Kissling, W. Daniel and Gudrun, Carl},
	Date-Added = {2008-02-08 16:35:49 +0000},
	Date-Modified = {2009-06-02 16:27:49 +0100},
	Journal = {Global Ecology and Biogeography},
	Number = {3},
	Pages = {59-71},
	Title = {Spatial autocorrelation and the selection of simultaneous autoregressive models},
	Volume = {17},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-File-3 = { }}

@article{Graham.Moritz.ea.2006.a,
	Abstract = {Patterns of biological diversity should be interpreted in light of both contemporary and historical influences; however, to date, most attempts to explain diversity patterns have largely ignored history or have been unable to quantify the influence of historical processes. The historical effects on patterns of diversity have been hypothesized to be most important for taxonomic groups with poor dispersal abilities. We quantified the relative stability of rainforests over the late Quaternary period by modeling rainforest expansion and contraction in 21 biogeographic subregions in northeast Australia across four time periods. We demonstrate that historical habitat stability can be as important, and in endemic low-dispersal taxa even more important, than current habitat area in explaining spatial patterns of species richness. In contrast, patterns of endemic species richness for taxa with high dispersal capacity are best predicted by using current environmental parameters. We also show that contemporary patterns of species turnover across the region are best explained by historical patterns of habitat connectivity. These results clearly demonstrate that spatially explicit analyses of the historical processes of persistence and colonization are both effective and necessary for understanding observed patterns of biodiversity.},
	Author = {Graham, CH and Moritz, C and Williams, SE},
	Date-Added = {2008-02-08 16:30:48 +0000},
	Date-Modified = {2008-02-08 16:30:56 +0000},
	Doi = {DOI 10.1073/pnas.0505754103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {Australian Wet Tropics; beta-diversity; dispersal; habitat connectivity; historical habitat stability},
	Pages = {632-636},
	Timescited = {0},
	Title = {Habitat history improves prediction of biodiversity in rainforest fauna},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0505754103},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0505754103}}

@misc{Isaac.Mallet.ea.2004.a,
	Abstract = {Species numbers are increasing rapidly. This is due mostly to taxonomic inflation, where known subspecies are raised to species as a result in a change in species concept, rather than to new discoveries. Yet macroecologists and conservation biologists depend heavily on species lists, treating them as accurate and stable measures of biodiversity. Deciding on a standardized, universal species list might ameliorate the mismatch between taxonomy and the uses to which it is put. However, taxonomic uncertainty is ultimately due to the evolutionary nature of species, and is unlikely to be solved completely by standardization. For the moment, at least, users must acknowledge the limitations of taxonomic species and avoid unrealistic expectations of species lists.},
	Author = {Isaac, NJB and Mallet, J and Mace, GM},
	Date-Added = {2008-02-08 16:24:33 +0000},
	Date-Modified = {2008-02-18 15:49:38 +0000},
	Doi = {DOI 10.1016/j.tree.2004.06.004},
	Journal = {Trends In Ecology \& Evolution},
	Pages = {464-469},
	Timescited = {0},
	Title = {Taxonomic inflation: its influence on macroecology and conservation},
	Volume = {19},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tree.2004.06.004},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.tree.2004.06.004}}

@article{Gaston.Davies.ea.2005.a,
	Abstract = {Aims To determine the shape of global species-range size distributions, the influence on these of island species, threatened species and patterns of latitudinal variation in range sizes, and the fit to logit-normal distributions.

Location Global.

Methods We take the spatial distributions of the raptors and owls of the world as exemplar data sets, document the shapes of their species-range size distributions, the influence of particular groups of species and of latitudinal variation in range sizes on these shapes, and the fit of these distributions to a variety of models.

Results The global species-range size distributions of both raptors and owls are extremely right skewed on untransformed axes. They are not lognormally distributed, as has commonly been stated for species-range size distributions, nor logit-normally distributed as has been suggested might be the case. For raptors, departures from either a lognormal or a logit-normal are little mitigated by excluding groups of species that might be thought to distort the observed species-range size distribution, nor by the latitudinal gradient in geographical range size. For owls, the effects of excluding island and threatened species are more marked, with the fit of the species-range size distribution to a lognormal or a logit-normal becoming much closer.

Conclusions A simple general description of the shape of species-range size distributions remains elusive. This constitutes a significant constraint on the development of theory as to how they are determined. Whilst in principle the fit of any given mechanistic model can be tested against one or more empirical data sets, whatever their form, a simple general mathematical description of species-range size distributions would make the process of rapidly testing the appropriateness of mechanistic models more straightforward.},
	Author = {Gaston, K J and Davies, R G and Gascoigne, C E and Williamson, M},
	Date-Added = {2008-02-08 16:23:12 +0000},
	Date-Modified = {2008-03-27 14:02:13 +0000},
	Journal = {Global Ecology and Biogeography},
	Keywords = {logit; lognormal; macroecology; owls; range size; raptors},
	Pages = {67-76},
	Timescited = {0},
	Title = {The structure of global species-range size distributions: raptors \& owls},
	Volume = {14},
	Year = {2005},
	Bdsk-File-1 = { }}

@misc{Colwell.Rahbek.ea.2004.a,
	Abstract = {If species' ranges are randomly shuffled within a bounded geographical domain free of environmental gradients, ranges overlap increasingly toward the center of the domain, creating a "middomain" peak of species richness. This "mid-domain effect" (MDE) has been controversial both in concept and in application. Empirical studies assess the degree to which the evolutionary, ecological, and historical processes that undeniably act on individual species and clades produce geographical patterns that resemble those produced by MDE models. MDE models that resample empirical range size frequency distributions (RSFDs) balance the risk of underestimating and overestimating the role of MDE, whereas theoretical RSFDs are generally biased toward underestimating MDE. We discuss the inclusion of nonendemic species in MDE models, rationales for setting domain limits, and the validity of one- and two-dimensional MDE models. MDE models, though null models, are not null hypotheses to be simplistically rejected or accepted. They are a means of estimating the expected effect of geometric constraints within the context of multiple causality. We call for assessment of MDE on an equal statistical footing with other candidate explanations for richness gradients. Although some critics have categorically dismissed MDE, an overview of the 21 MDE studies published to date reveals a substantial signature of MDE in natural patterns and justifies continued work.},
	Author = {Colwell, RK and Rahbek, C and Gotelli, NJ},
	Date-Added = {2008-02-08 15:49:59 +0000},
	Date-Modified = {2008-02-08 15:51:21 +0000},
	Journal = {American Naturalist},
	Keywords = {diversity and species richness gradients; domain limits; geometric constraints; mid-domain effect; null models; range size frequency distributions},
	Pages = {E1-E23},
	Timescited = {0},
	Title = {The mid-domain effect and species richness patterns: What have we learned so far?},
	Volume = {163},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Emerson.Kolm.2005.a,
	Abstract = {A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas(1,2), and the role of speciation is also recognized as an important factor(3-6). However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number.},
	Author = {Emerson, Brent C and Kolm, Niclas},
	Date-Added = {2008-02-08 15:48:53 +0000},
	Date-Modified = {2008-03-27 15:11:43 +0000},
	Doi = {DOI 10.1038/nature03450},
	Journal = {Nature},
	Pages = {1015-1017},
	Timescited = {0},
	Title = {Species diversity can drive speciation},
	Volume = {434},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature03450},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature03450}}

@misc{Brett.2004.a,
	Abstract = {Correlations which are artifacts of various types of data transformations can be said to be spurious. This study considers four common types of analyses where the X and Y variables are not independent; these include regressions of the form X/Z vs Y/Z, XxZ vs YxZ, X vs Y/X, and X+Y vs Y. These analyses were carried out using a series of Monte Carlo simulations while varying sample size and sample variability. The impact of disparities in variability between the shared and non-shared terms and measurement error for the shared term on the magnitude of the spurious correlations was also considered. The accuracy of equations previously derived to predict the magnitude of spurious correlations was also assessed. These results show the risk of producing spurious correlations when analyzing non-independent variables is very large. Spurious correlations occurred in all cases assessed, the mean spurious coefficient of determination (r(2)) frequently exceeded 0.50, and in some cases the 90\% confidence interval for these simulations included all large r(2) values. The magnitude of spurious correlations was sensitive to differences in the variability of the shared and non-shared terms, with large spurious correlations obtained when the variability for the shared term was larger. Sample size had only a modest impact on the magnitude of spurious correlations. When measurement error for the shared variable was smaller than one half the coefficient of variation for that variable, which is generally the case, the measurement error did not generate large spurious correlations. The equations available to predict expected spurious correlations provided accurate predictions for the case of XxZ vs YxZ, variable predictions for the case of X vs Y/X, and poor predictions for most cases of X/Z vs Y/Z, and X+Y vs Y.},
	Author = {Brett, MT},
	Date-Added = {2008-02-08 15:45:33 +0000},
	Date-Modified = {2008-02-08 15:46:22 +0000},
	Journal = {Oikos},
	Pages = {647-656},
	Timescited = {0},
	Title = {When is a correlation between non-independent variables "spurious"?},
	Volume = {105},
	Year = {2004},
	Bdsk-File-1 = { }}

@article{Ding.Yuan.ea.2006.a,
	Abstract = {Aim To create a map of bird species richness (BSR) in East Asia and to examine the effect of area, isolation, primary productivity, topographic heterogeneity, and human population density on BSR.

Location East Asia (from 70 degrees E to 180 degrees E longitude), including the eastern half of the Palaearctic Region, the entire Oriental Region, and the entire Wallacea Subregion.

Methods The breeding ranges of 2406 terrestrial bird species were mapped and overlaid to create a species richness map. The BSR map was transformed into a 100 x 100 km quadrat system, and BSR was analysed in relation to land area, average normalized difference vegetation index (NDVI), elevation range, and average population density.

Results In general, BSR declined from the Tropics to the Arctic. In mainland East Asia, however, BSR was highest around the Tropic of Cancer, and fluctuated between 30 degrees and 50 degrees N. Islands had lower BSR than adjacent mainland areas. The NDVI was strongly positively correlated with BSR in mainland areas and on islands. For mainland areas, NDVI explained 65\% of the BSR variation, and topographic heterogeneity explained an additional 6\% in ordinary least-squares regression. On islands, NDVI explained 66\% of BSR variation, island area explained 13\%, and distance to mainland accounted for 1\%.

Main conclusions In East Asia, we suggest that primary productivity is the key factor underpinning patterns of BSR. Primary productivity sets the upper limits of the capacity of habitats to support bird species. In isolated areas such as islands and peninsulas, however, BSR might not reach the richness limits set by primary productivity because the degree of isolation and area size also can affect species richness. Other factors, such as spatial heterogeneity, biotic interactions, and perturbations, may also affect species richness. However, their effects are secondary and are not as strong as primary productivity, isolation, and area size.},
	Author = {Ding, Tsung-Su and Yuan, H W and Geng, S and Koh, C N and Lee, P F},
	Date-Added = {2008-02-08 15:40:41 +0000},
	Date-Modified = {2008-10-22 17:43:12 +0100},
	Doi = {DOI 10.1111/j.1365-2699.2006.01419.x},
	Journal = {Journal of Biogeography},
	Keywords = {East Asia; energy availability; energy limitation theory; island biogeography; latitudinal gradient; primary productivity; spatial heterogeneity; species diversity},
	Pages = {683-693},
	Timescited = {0},
	Title = {Macro-scale bird species richness patterns of the East Asian mainland and islands: energy, area and isolation},
	Volume = {33},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01419.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01419.x}}

@misc{Diniz-Filho.2006.a,
	Author = {Diniz-Filho, JA},
	Date-Added = {2008-02-08 15:17:46 +0000},
	Date-Modified = {2008-02-18 15:50:13 +0000},
	Doi = {DOI 10.1111/j.1365-2699.2006.01552.x},
	Journal = {Journal of Biogeography},
	Pages = {1153-1154},
	Timescited = {0},
	Title = {Modern processes drive macroecological patterns in North American avifauna},
	Volume = {33},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01552.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1365-2699.2006.01552.x}}

@misc{Brooks.Mittermeier.ea.2006.a,
	Abstract = {The location of and threats to biodiversity are distributed unevenly, so prioritization is essential to minimize biodiversity loss. To address this need, biodiversity conservation organizations have proposed nine templates of global priorities over the past decade. Here, we review the concepts, methods, results, impacts, and challenges of these prioritizations of conservation practice within the theoretical irreplaceability/vulnerability framework of systematic conservation planning. Most of the templates prioritize highly irreplaceable regions; some are reactive ( prioritizing high vulnerability), and others are proactive ( prioritizing low vulnerability). We hope this synthesis improves understanding of these prioritization approaches and that it results in more efficient allocation of geographically flexible conservation funding.},
	Author = {Brooks, TM and Mittermeier, RA and da Fonseca, GAB and Gerlach, J and Hoffmann, M and Lamoreux, JF and Mittermeier, CG and Pilgrim, JD and Rodrigues, ASL},
	Date-Added = {2008-02-08 15:14:37 +0000},
	Date-Modified = {2008-02-08 15:15:50 +0000},
	Doi = {DOI 10.1126/science.1127609},
	Journal = {Science},
	Pages = {58-61},
	Timescited = {0},
	Title = {Global biodiversity conservation priorities},
	Volume = {313},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1127609},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1127609}}

@article{Faith.Walker.1996.a,
	Author = {Faith, Daniel P. and Walker, P A},
	Date-Added = {2008-02-08 11:15:15 +0000},
	Date-Modified = {2011-05-18 11:57:12 +0100},
	Journal = {Biodiversity Letters},
	Keywords = {Hotspots; environmental diversity; biodiversity; ordination; indicator groups; DIVERSITY; complementarity},
	Number = {1},
	Pages = {18-25},
	Title = {How do indicator groups provide information about the relative biodiversity of different sets of areas?: on hotspots, complementarity and pattern-based approaches},
	Volume = {3},
	Year = {1996},
	Bdsk-File-1 = { }}

@article{Paradis.2005.a,
	Abstract = {Testing whether some species traits have a significant effect on diversification rates is central in the assessment of macroevolutionary theories. However, we still lack a powerful method to tackle this objective. I present a new method for the statistical analysis of diversification with species traits. The required data are observations of the traits on recent species, the phylogenetic tree of these species, and reconstructions of ancestral values of the traits. Several traits, either continuous or discrete, and in some cases their interactions, can be analyzed simultaneously. The parameters are estimated by the method of maximum likelihood. The statistical significance of the effects in a model can be tested with likelihood ratio tests. A simulation Study showed that past random extinction events do not affect the Type I error rate of the tests, whereas statistical power is decreased, though some power is still kept if the effect of the simulated trait on speciation is strong. The use of the method is illustrated by the analysis Of published data on primates. The analysis of these data showed that the apparent overall positive relationship between body mass and species diversity is actually an artifact due to a clade-specific effect. Within each clade the effect of body mass oil speciation rate was in fact negative. The present method allows to take both effects (clade and body mass) into account simultaneously.},
	Author = {Paradis, E},
	Date-Added = {2008-02-08 11:09:09 +0000},
	Date-Modified = {2008-02-08 11:10:42 +0000},
	Journal = {Evolution},
	Keywords = {diversification; extinction; generalized linear models; maximum likelihood; phylogeny; speciation},
	Pages = {1-12},
	Timescited = {0},
	Title = {Statistical analysis of diversification with species traits},
	Volume = {59},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Paradis.1997.a,
	Abstract = {A new method to estimate the diversification rate of a lineage from a phylogeny of recent species is presented. This uses survival models to analyse the ages of the species as derived from the phylogeny. Survival models can analyse missing data where the exact date of death is unknown (censoring). This approach allows us to include missing data (species not included in a detailed phylogenetic study) in the analysis, provided a minimum age is known for these species. Three models are presented, with emphasis on temporal variation in diversification rates. The maximum likelihood method and the Akaike information criterion are used to derive estimators and tests of hypotheses. A simulation study demonstrates that the method is able to detect a temporal variation in diversification rate only when it is present, avoiding type I and type II errors. A lineage With ten species may be sufficient to detect a temporal variation in diversification rate even with 50\% of missing data. An application is presented with data from a phylogeny of birds of the genus Ramphocelus.},
	Author = {Paradis, E},
	Date-Added = {2008-02-08 11:09:09 +0000},
	Date-Modified = {2008-02-08 11:10:14 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Pages = {1141-1147},
	Timescited = {0},
	Title = {Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing},
	Volume = {264},
	Year = {1997},
	Bdsk-File-1 = { }}

@article{Paradis.2003.a,
	Abstract = {The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood-based method to combine partly resolved phylogenies with taxonomic (species-richness) data to estimate speciation and extinction rates. This method is based on fitting a birth-and-death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed.},
	Author = {Paradis, E},
	Date-Added = {2008-02-08 11:09:09 +0000},
	Date-Modified = {2008-02-08 11:09:56 +0000},
	Doi = {DOI 10.1098/rspb.2003.2513},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {diversity; estimation; extinction; maximum likelihood; phylogeny; speciation},
	Pages = {2499-2505},
	Timescited = {0},
	Title = {Analysis of diversification: combining phylogenetic and taxonomic data},
	Volume = {270},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2003.2513},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2003.2513}}

@unpublished{Paradis.2006.a,
	Author = {Paradis, Emmanuel},
	Date-Added = {2008-02-08 11:05:37 +0000},
	Date-Modified = {2008-02-08 11:06:49 +0000},
	Month = {December},
	Title = {Definition of Formats for Coding Phylogenetic Trees in R},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Barker.Cibois.ea.2004.a,
	Abstract = {The order Passeriformes ("perching birds") comprises extant species diversity comparable to that of living mammals. For over a decade, a single phylogenetic hypothesis based on DNA-DNA hybridization has provided the primary framework for numerous comparative analyses of passerine ecological and behavioral evolution and for tests of the causal factors accounting for rapid radiations within the group. We report here a strongly supported phylogenetic tree based on two single-copy nuclear gene sequences for the most complete sampling of passerine families to date. This tree is incongruent with that derived from DNA-DNA hybridization, with half of the nodes from the latter in conflict and over a third of the conflicts significant as assessed under maximum likelihood. Our historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. The revised history implied by these data will require reassessment of comparative analyses of passerine diversification and adaptation.},
	Author = {Barker, FK and Cibois, A and Schikler, P and Feinstein, J and Cracraft, J},
	Date-Added = {2008-02-07 19:31:08 +0000},
	Date-Modified = {2008-02-07 19:31:22 +0000},
	Doi = {DOI 10.1073/pnas.0401892101},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Pages = {11040-11045},
	Timescited = {0},
	Title = {Phylogeny and diversification of the largest avian radiation},
	Volume = {101},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0401892101},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0401892101}}

@article{Baker.Huynen.ea.2005.a,
	Abstract = {The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6\% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximate to 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.},
	Author = {Baker, AJ and Huynen, LJ and Haddrath, O and Millar, CD and Lambert, DM},
	Date-Added = {2008-02-07 19:30:17 +0000},
	Date-Modified = {2008-02-07 19:30:24 +0000},
	Doi = {DOI 10.1073/pnas.0409435102},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {adaptive radiation; extinct moas; environmental changes},
	Pages = {8257-8262},
	Timescited = {0},
	Title = {Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand},
	Volume = {102},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0409435102},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0409435102}}

@article{Lamoreux.Morrison.ea.2006.a,
	Abstract = {Understanding patterns of biodiversity distribution is essential to conservation strategies(1), but severe data constraints make surrogate measures necessary(2-4). For this reason, many studies have tested the performance of terrestrial vertebrates as surrogates for overall species diversity, but these tests have typically been limited to a single taxon or region(3-10). Here we show that global patterns of richness are highly correlated among amphibians, reptiles, birds and mammals, as are endemism patterns. Furthermore, we demonstrate that although the correlation between global richness and endemism is low, aggregate regions selected for high levels of endemism capture significantly more species than expected by chance. Although areas high in endemism have long been targeted for the protection of narrow-ranging species(11,12), our findings provide evidence that endemism is also a useful surrogate for the conservation of all terrestrial vertebrates.},
	Author = {Lamoreux, John F and Morrison, John C and Ricketts, Taylor H and Olson, David M and Dinerstein, Eric and McKnight, Meghan W and Shugart, Herman H},
	Date-Added = {2008-02-07 19:23:31 +0000},
	Date-Modified = {2008-03-27 15:12:36 +0000},
	Doi = {DOI 10.1038/nature04291},
	Journal = {Nature},
	Pages = {212-214},
	Timescited = {0},
	Title = {Global tests of biodiversity concordance and the importance of endemism},
	Volume = {440},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature04291},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature04291}}

@article{Rangel.Diniz-Filho.ea.2006.a,
	Abstract = {Because most macroecological and biodiversity data are spatially autocorrelated, special tools for describing spatial structures and dealing with hypothesis testing are usually required. Unfortunately, most of these methods have not been available in a single statistical package. Consequently, using these tools is still-a challenge for most ecologists and biogeographers. In this paper, we present SAM (Spatial Analysis in Macroecology), a new, easy-to-use, freeware package for spatial analysis in macroecology and biogeography. Through an intuitive, fully graphical interface, this package allows the user to describe spatial patterns in variables and provides an explicit spatial framework for standard techniques of regression and correlation. Moran's I autocorrelation coefficient can be calculated based on a range of matrices describing spatial relationships, for original variables as well as for residuals of regression models, which can also include filtering components (obtained by standard trend surface analysis or by principal coordinates of neighbour matrices). SAM also offers tools for correcting the number of degrees of freedom when calculating the significance of correlation coefficients. Explicit spatial modelling using several forms of autoregression and generalized least-squares models are also available. We believe this new tool will provide researchers with the basic statistical tools to resolve autocorrelation problems and, simultaneously, to explore spatial components in macroecological and biogeographical data. Although the program was designed primarily for the applications in macroecology and biogeography, Most of SAM'S statistical tools will be useful for all kinds of surface pattern spatial analysis. The program is freely available at www.ecoevol.ufg.br/sam (permanent URL at http://purl.oclc.org/sam/).},
	Author = {Rangel, Thiago Fernando L. V. B. and Diniz-Filho, Jos{\'e} Alexandre Felizola and Bini, Luis Mauricio},
	Date-Added = {2008-02-07 19:10:31 +0000},
	Date-Modified = {2008-02-07 19:38:56 +0000},
	Doi = {DOI 10.1111/j.1466-822x.2006.00237.x},
	Journal = {Global Ecology and Biogeography},
	Keywords = {spatial autocorrelation; spatial statistics; modelling; macroecology; biogeography; statistical package; software; SAM},
	Pages = {321-327},
	Timescited = {0},
	Title = {Towards an integrated computational tool for spatial analysis in macroecology and biogeography},
	Volume = {15},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-822x.2006.00237.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1466-822x.2006.00237.x}}

@article{Armsworth.Daily.ea.2006.a,
	Abstract = {The full or partial purchase of land has become a cornerstone of efforts to conserve biodiversity in countries with strong private property rights. Methods used to target areas for acquisition typically ignore land market dynamics. We show how conservation purchases affect land prices and generate feedbacks that can undermine conservation goals, either by displacing development toward biologically valuable areas or by accelerating its pace. The impact of these market feedbacks on the effectiveness of conservation depends on the ecological value of land outside nature reserves. Traditional, noneconomic approaches to site prioritization should perform adequately in places where land outside reserves supports little biodiversity. However, these approaches will perform poorly in locations where the countryside surrounding reserves is important for species' persistence. Conservation investments can sometimes even be counterproductive, condemning more species than they save. Conservation is most likely to be compromised in the absence of accurate information on species distributions, which provides a strong argument for improving inventories of biodiversity. Accounting for land market dynamics in conservation planning is crucial for making smart investment decisions.},
	Author = {Armsworth, PR and Daily, GC and Kareiva, P and Sanchirico, JN},
	Date-Added = {2008-02-07 17:27:49 +0000},
	Date-Modified = {2008-02-07 17:27:55 +0000},
	Doi = {DOI 10.1073/pnas.0505278103},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {conservation planning; reserve design; site selection; development pressure; habitat destruction},
	Pages = {5403-5408},
	Timescited = {0},
	Title = {Land market feedbacks can undermine biodiversity conservation},
	Volume = {103},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0505278103},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0505278103}}

@article{Ceballos.Ehrlich.ea.2005.a,
	Abstract = {We present a global conservation analysis for an entire "flagship" taxon, [and mammals. A combination of rarity, anthropogenic impacts, and political endemism has put about a quarter of terrestrial mammal species, and a larger fraction of their populations, at risk of extinction. A new global database and complementarity analysis for selecting priority areas for conservation shows that similar to 11\% of Earth's land surface should be managed for conservation to preserve at least 10\% of terrestrial mammal geographic ranges. Different approaches, from protection (or establishment) of reserves to countryside biogeographic enhancement of human-dominated landscapes, will be required to approach this minimal goal.},
	Author = {Ceballos, G and Ehrlich, PR and Soberon, J and Salazar, I and Fay, JP},
	Date-Added = {2008-02-07 17:25:25 +0000},
	Date-Modified = {2008-02-07 17:26:04 +0000},
	Doi = {DOI 10.1126/science.1114015},
	Journal = {Science},
	Pages = {603-607},
	Timescited = {0},
	Title = {Global mammal conservation: What must we manage?},
	Volume = {309},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1114015},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1114015}}

@article{Barraclough.Savolainen.2001.a,
	Abstract = {Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants tin both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity.},
	Author = {Barraclough, TG and Savolainen, V},
	Date-Added = {2008-02-07 17:21:18 +0000},
	Date-Modified = {2008-02-07 17:22:14 +0000},
	Journal = {Evolution},
	Keywords = {angiosperms; DNA; molecular evolution; speciation; species richness},
	Pages = {677-683},
	Timescited = {0},
	Title = {Evolutionary rates and species diversity in flowering plants},
	Volume = {55},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Morand.Harvey.2000.a,
	Abstract = {Basal metabolic rate (BMR) scales allometrically with body mass in mammals, but the reasons why some species have higher or lower metabolic rates than predicted from their body mass remain unclear. We tested the idea that parasite species richness may be a contributory factor by performing a comparative analysis on 23 species of mammals for which data were available on parasite species richness, BMR, body mass and two potentially confounding variables, i.e. host density and host longevity. Parasite species richness was positively correlated with BMR and negatively correlated with host longevity independent of body mass.},
	Author = {Morand, S and Harvey, PH},
	Date-Added = {2008-02-07 17:18:31 +0000},
	Date-Modified = {2008-02-07 17:20:16 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {basal metabolic rate; mammals; comparative analysis; independent contrasts method; helminths; parasite species richness},
	Pages = {1999-2003},
	Timescited = {0},
	Title = {Mammalian metabolism, longevity and parasite species richness},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Pybus.Harvey.2000.a,
	Abstract = {Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.},
	Author = {Pybus, Oliver G and Harvey, Paul H.},
	Date-Added = {2008-02-07 17:18:31 +0000},
	Date-Modified = {2008-08-21 09:35:42 +0100},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {phylogeny; speciation; extinction; primates; Dendroica; Sorex},
	Pages = {2267-2272},
	Timescited = {0},
	Title = {Testing macro-evolutionary models using incomplete molecular phylogenies},
	Volume = {267},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Purvis.Agapow.ea.2000.a,
	Abstract = {The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra Loss of mammalian evolutionary history alone would be equivalent to Losing a monotypic phylum.},
	Author = {Purvis, Andy and Agapow, Paul-Michael and Gittleman, John L. and Mace, Georgina M.},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-04-16 15:09:43 +0100},
	Journal = {Science},
	Pages = {328-330},
	Timescited = {0},
	Title = {Nonrandom extinction and the loss of evolutionary history},
	Volume = {288},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Purvis.Garland.1993.a,
	Author = {Purvis, Andy and Garland, Theodore},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-08-20 17:48:58 +0100},
	Journal = {Systematic Biology},
	Pages = {569-575},
	Timescited = {0},
	Title = {Polytomies in comparative analyses of continuous characters},
	Volume = {42},
	Year = {1993},
	Bdsk-File-1 = { }}

@article{Purvis.Gittleman.ea.1994.a,
	Author = {Purvis, Andy and Gittleman, John L. and Luh, Hang-Kwang},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-03-27 15:09:42 +0000},
	Journal = {Journal of Theoretical Biology},
	Pages = {293-300},
	Timescited = {0},
	Title = {TRUTH OR CONSEQUENCES - EFFECTS OF PHYLOGENETIC ACCURACY ON 2 COMPARATIVE METHODS},
	Volume = {167},
	Year = {1994},
	Bdsk-File-1 = { }}

@article{Purvis.Jones.ea.2000.a,
	Abstract = {In the life of any species, extinction is the final evolutionary process. It is a common one at present, as the world is entering a major extinction crisis. The pattern of extinction and threat is very non-random, with some taxa being more vulnerable than others. Explaining why some taxa are affected and some escape is a major goal of conservation biology. More ambitiously, a predictive model could, In principle, be built by integrating comparable studies of past and present extinctions, We review progress towards both explanatory and predictive frameworks, comparing correlates of extinction In different groups at different times. Progress towards explanatory models for the current crisis is promising, at least in some well-studied tare, but the development of a truly predictive model is hampered by the formidable difficulties of Integrating studies of present and past extinctions. (C) 2000 John Wiley \& Sons, Inc.},
	Author = {Purvis, A and Jones, KE and Mace, GM},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-02-07 17:13:27 +0000},
	Journal = {Bioessays},
	Pages = {1123-1133},
	Timescited = {0},
	Title = {Extinction},
	Volume = {22},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Purvis.Nee.ea.1995.a,
	Abstract = {We apply new statistical methods to a recent estimate of the phylogeny of all living primate species to test a range of models of cladogenesis. Null models in which probabilities of speciation and extinction do not differ among contemporaneous lineages are not consistent with the phylogeny. We present evidence that the net rate of cladogenesis (speciation rate minus extinction rate) increased in the lineage leading to the Cercopithecidae (Old World monkeys), and that there have been further increases in some lineages within that family. Such increases suggest the occurrence of clade selection, although we have not identified the selected trait or traits. There is no evidence that the net rate of cladogenesis is a function either of how many primate lineages are already present or of time. Intriguingly, three other major clades Strepsirhini, Platyrrhini and Hominoidea - appear to have had very similar rates of clade growth, in spite of their great biological differences.},
	Author = {Purvis, Andy and Nee, Sean and Harvey, Paul H.},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-04-16 15:08:34 +0100},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Pages = {329-333},
	Timescited = {0},
	Title = {MACROEVOLUTIONARY INFERENCES FROM PRIMATE PHYLOGENY},
	Volume = {260},
	Year = {1995},
	Bdsk-File-1 = { }}

@article{Purvis.Rambaut.1995.a,
	Abstract = {CAIC is an application for the Apple Macintosh which allows the valid analysis of comparative (multi-species) data sets that include continuous variables. Comparison among species is the most common technique for testing hypotheses of how organisms are adapted to their environments, but standard statistical tests like regression should not be used with species data. Such tests assume independence of data points, but related species often share traits by common descent rather than through independent adaptation. CAIC uses a phylogeny of the species in the data set to partition the variance among species into independent comparisons (technically, linear contrasts), each comparison being made at a different node in the phylogeny. There are two partitioning procedures-one used when all variables are continuous, the other when one variable is discrete, The resulting comparisons cart be analysed validly in standard statistical packages to test hypotheses about correlated evolution among traits, to estimate parameters such as allometric exponents, and to compare rates of evolution. Previous versions of the package have already been used widely, this version is simpler to use and works on a wider range of machines. The package and manual are freely available by anonymous ftp or front the authors.},
	Author = {Purvis, Andy and Rambaut, Andy},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-08-20 17:43:50 +0100},
	Journal = {Computer Applications In the Biosciences},
	Pages = {247-251},
	Timescited = {0},
	Title = {Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data},
	Volume = {11},
	Year = {1995},
	Bdsk-File-1 = { }}

@article{Purvis.Hector.2000.a,
	Abstract = {The term 'biodiversity' is a simple contraction of 'biological diversity', and at first sight the concept is simple too: biodiversity is the sum total of all biotic variation from the level of genes to ecosystems. The challenge comes in measuring such a broad concept in ways that are useful. We show that, although biodiversity can never be fully captured by a single number, study of particular facets has led to rapid, exciting and sometimes alarming discoveries. Phylogenetic and temporal analyses are shedding light on the ecological and evolutionary processes that have shaped current biodiversity. There is no doubt that humans are now destroying this diversity at an alarming rate. A vital question now being tackled is how badly this loss affects ecosystem functioning. Although current research efforts are impressive, they are tiny in comparison to the amount of unknown diversity and the urgency and importance of the task.},
	Author = {Purvis, Andy and Hector, Andy},
	Date-Added = {2008-02-07 17:06:11 +0000},
	Date-Modified = {2008-03-27 15:13:02 +0000},
	Journal = {Nature},
	Pages = {212-219},
	Timescited = {0},
	Title = {Getting the measure of biodiversity},
	Volume = {405},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Katzourakis.Purvis.ea.2001.a,
	Abstract = {We test a near-complete genus level phylogeny of hoverflies (Diptera: Syrphidae) for consistency with a null model of clade growth having uniform probabilities of speciation and extinction among contemporaneous species. The phylogeny is too unbalanced for this null model. Importantly, the degree of imbalance in the phylogeny depends on whether the phylogeny is analysed at the genus level or species level, suggesting that genera ought not to be used uncritically as surrogates for species in large-scale evolutionary analyses. Tests for a range of morphological, life-history and ecological correlates of diversity give equivocal results, but suggest that high species-richness may be associated with sexual selection and diet breadth. We find no correlation between species-richness and either body size or reproductive rate.},
	Author = {Katzourakis, A and Purvis, A and Azmeh, S and Rotheray, G and Gilbert, F},
	Date-Added = {2008-02-07 17:03:56 +0000},
	Date-Modified = {2008-02-07 17:04:08 +0000},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {adaptive radiation; hoverflies; imbalance; macroevolution; sister clade comparisons; species-richness},
	Pages = {219-227},
	Timescited = {0},
	Title = {Macroevolution of hoverflies (Diptera : Syrphidae): the effect of using higher-level taxa in studies of biodiversity, and correlates of species richness},
	Volume = {14},
	Year = {2001},
	Bdsk-File-1 = { }}

@article{Barraclough.Hogan.ea.1999.a,
	Abstract = {We investigate the role of ecological differentiation in cladogenesis of a monophyletic group of North American tiger beetles, the subgenus Ellipsoptera (genus: Cicindela), by reconstructing their species-level phylogeny from mitochondrial DNA sequences. Observed reconstructions of ecological characters on the phylogeny are compared to those expected under simple null models of no association with cladogenesis. We find no evidence that ecological disparity is associated with either species coexistence, speciation or long-term persistence and/or radiation of lineages. Ecomorphological traits have evolved in response to differences in habitat occupied by species, but without detectable relationship with cladogenesis.},
	Author = {Barraclough, TG and Hogan, JE and Vogler, AP},
	Date-Added = {2008-02-07 17:02:51 +0000},
	Date-Modified = {2008-02-07 17:03:01 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {species richness; cladogenesis; ecological diversity; DNA phylogeny; tiger beetles},
	Pages = {1061-1067},
	Timescited = {0},
	Title = {Testing whether ecological factors promote cladogenesis in a group of tiger beetles (Coleoptera : Cicindelidae)},
	Volume = {266},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Avise.Walker.1999.a,
	Abstract = {A literature review is conducted on the phylogenetic discontinuities in mtDNA sequences of 252 taxonomic species of vertebrates. About 140 of these species (56\%) were subdivided clearly into two or more highly distinctive matrilineal phylogroups, the vast majority of which were localized geographically. However, only a small number (two to six) of salient phylogeographic subdivisions (those that stand out against mean within-group divergences) characterized individual species. A previous literature summary showed that vertebrate sister species and other congeners also usually have pronounced phylogenetic distinctions in mtDNA sequence. These observations, taken together, suggest that current taxonomic species often agree reasonably well in number (certainly within an order-of-magnitude) and composition with biotic entities registered in mtDNA genealogies alone. In other words, mtDNA data and traditional taxonomic assignments tend to converge on what therefore may be "real" biotic units in nature. All branches in mtDNA phylogenies are nonanastomose, connected strictly via historical genealogy. Thus, patterns of historical phylogenetic connection may be at least as important as contemporary reproductive relationships per se in accounting for microevolutionary unities and discontinuities in sexually reproducing vertebrates. Findings are discussed in the context of the biological and phylogenetic species concepts.},
	Author = {Avise, JC and Walker, DE},
	Date-Added = {2008-02-07 16:55:48 +0000},
	Date-Modified = {2008-02-07 16:58:37 +0000},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {speciation; phylogeny; sister species; comparative molecular evolution; phylogeography},
	Pages = {992-995},
	Timescited = {0},
	Title = {Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome},
	Volume = {96},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Avise.Walker.ea.1998.a,
	Abstract = {An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic effects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspecific phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic differentiation among now-extant conspecific populations as well as in further sculpting pre-existing phylogeographic variety into many of today's sister species; and (iii) for herpetofauna and fishes, inferred Pleistocene biogeographic influences on present-day taxa differ depending on alternative but currently plausible mtDNA rate calibrations.},
	Author = {Avise, JC and Walker, D and Johns, GC},
	Date-Added = {2008-02-07 16:55:48 +0000},
	Date-Modified = {2008-02-07 16:57:29 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {population structure; phylogroups; sister species; molecular clocks; genetic distances; comparative molecular evolution},
	Pages = {1707-1712},
	Timescited = {0},
	Title = {Speciation durations and Pleistocene effects on vertebrate phylogeography},
	Volume = {265},
	Year = {1998},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Avise.Walker.1998.a,
	Abstract = {Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59\%) are sundered into recognizable phylogeographic units, and 28 of these separations (76\%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.},
	Author = {Avise, JC and Walker, D},
	Date-Added = {2008-02-07 16:55:48 +0000},
	Date-Modified = {2008-02-07 16:56:20 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {mtDNA; population structure; phylogeography; birds; speciation},
	Pages = {457-463},
	Timescited = {0},
	Title = {Pleistocene phylogeographic effects on avian populations and the speciation process},
	Volume = {265},
	Year = {1998},
	Bdsk-File-1 = { }}

@article{Cardillo.1999.a,
	Abstract = {Central to many explanations of latitudinal diversity gradients is the idea that rates of species diversification increase towards the equator. However, there hare been few explicit tests of whether or not this pattern exists. Using sister-group analyses to compare 48 clades of passerine birds and swallowtail butterflies from different latitudes, I found evidence that relative rates of diversification per unit time are indeed higher towards the equator. This pattern is explicable in terms of abiotic factors which vary continuously with latitude, and may be further enhanced by diversity-dependent speciation and extinction processes.},
	Author = {Cardillo, M},
	Date-Added = {2008-02-07 16:52:23 +0000},
	Date-Modified = {2008-02-07 16:52:40 +0000},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {extinction; latitudinal gradients; sister groups; speciation; species richness},
	Pages = {1221-1225},
	Timescited = {0},
	Title = {Latitude and rates of diversification in birds and butterflies},
	Volume = {266},
	Year = {1999},
	Bdsk-File-1 = { }}

@article{Barraclough.Vogler.2002.a,
	Abstract = {Species-level phylogenies derived from DNA sequence data provide a tool for estimating diversification rates and how these rates change over time, but to date there have been few empirical studies, particularly on insect groups. We use a densely sampled phylogenetic tree based on mitochondrial DNA to investigate diversification rates in the North American tiger beetles (genus Cicindela). Using node ages estimated from sequence data and calibrated by biogeographical evidence, we estimate an average per-lineage diversification rate of at least 0.22 +/- 0.08 species/Myr over the time interval since the most recent colonization that led to a radiation within the continent. In addition, we find evidence for a weak, recent increase in the net diversification rate. This is more consistent with a late Pleistocene increase in the speciation rate than with a constant rate of background extinction, but the results are sensitive to the dating method and taxon sampling. We discuss practical limitations to phylogenetic studies of diversification rates.},
	Author = {Barraclough, Timothy G. and Vogler, Alfried P.},
	Date-Added = {2008-02-07 16:01:42 +0000},
	Date-Modified = {2008-03-27 15:10:37 +0000},
	Journal = {Molecular Biology and Evolution},
	Keywords = {diversification rates; speciation; extinction; tiger beetles; Pleistocene},
	Pages = {1706-1716},
	Timescited = {0},
	Title = {Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree},
	Volume = {19},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Barraclough.Vogler.2000.a,
	Abstract = {We introduce a general approach for investigating the role of geography in speciation, based on analyzing the geography of sister clades across all nodes in a species-level phylogeny. We examine the predictions of allopatric, sympatric, and peripatric models of speciation in several animal groups, using patterns of range overlap and range size symmetry between sister clades. A simple model of cladogenesis incorporating random movements of species' ranges is used to illustrate the effects of range changes on expected patterns. We find evidence for a predominantly allopatric mode of speciation in our study groups, with sympatry arising through post-speciational range changes. In addition, we find that relatively recent speciation events are characterized by greater asymmetry in range size between sister clades than expected under our null models, providing potential support for the peripatric model of speciation. We discuss the possible confounding effects of post-speciational range changes on our conclusions.},
	Author = {Barraclough, TG and Vogler, AP},
	Date-Added = {2008-02-07 16:01:42 +0000},
	Date-Modified = {2008-02-07 16:02:37 +0000},
	Journal = {American Naturalist},
	Keywords = {speciation; diversity; null models; biogeography; modes},
	Pages = {419-434},
	Timescited = {0},
	Title = {Detecting the geographical pattern of speciation from species-level phylogenies},
	Volume = {155},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Barraclough.Nee.2001.a,
	Abstract = {Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales.},
	Author = {Barraclough, TG and Nee, S},
	Date-Added = {2008-02-07 16:01:42 +0000},
	Date-Modified = {2008-02-07 16:53:34 +0000},
	Journal = {Trends In Ecology \& Evolution},
	Pages = {391-399},
	Timescited = {0},
	Title = {Phylogenetics and speciation},
	Volume = {16},
	Year = {2001},
	Bdsk-File-1 = { }}

@book{Chapman.2005.a,
	Author = {Chapman, Arthur D.},
	Date-Added = {2008-02-07 15:52:48 +0000},
	Date-Modified = {2008-02-07 15:59:43 +0000},
	Keywords = {species richness; biodiversity},
	Publisher = {Australian Biological Resources Study},
	Read = {No},
	Title = {Numbers of Living Species in Australia and the World},
	Url = {http://www.deh.gov.au/biodiversity/abrs/publications/other/species-numbers/index.html},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://www.deh.gov.au/biodiversity/abrs/publications/other/species-numbers/index.html%20}}

@article{Best.Johst.ea.2007.a,
	Abstract = {Understanding the ability of species to shift their geographic range is of considerable importance given the current period of rapid climate change. Furthermore, a greater understanding of the spatial population dynamics underlying range shifting is required to complement the advances made in climate niche modelling. A simulation model is developed which incorporates three key features that have been largely overlooked in studies of range shifting dynamics: the form of intraspecific competition, density dependent dispersal and the transient dynamics of habitat patches. The results show that the exact shape of the response depends critically on both local and patch dynamics. Species whose intraspecific competition is contest based are more vulnerable than those whose competition is scramble based. Contesters are especially sensitive when combined with density dependent dispersal. Species living in patches whose carrying capacity grows slowly are also susceptible to rapid shifts of environmental conditions. A complementary analytic approach further highlights the importance of intraspecific competition.},
	Author = {Best, A. S. and Johst, K. and Muenkemueller, T. and Travis, J. M. J.},
	Date-Added = {2008-02-07 15:52:24 +0000},
	Date-Modified = {2008-02-07 15:52:27 +0000},
	Doi = {DOI 10.1111/j.2007.0030-1299.16047.x},
	Journal = {Oikos},
	Pages = {1531-1539},
	Timescited = {0},
	Title = {Which species will succesfully track climate change? The influence of intraspecific competition and density dependent dispersal on range shifting dynamics},
	Volume = {116},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.2007.0030-1299.16047.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.2007.0030-1299.16047.x}}

@article{Alsos.Eidesen.ea.2007.a,
	Abstract = {The ability of species to track their ecological niche after climate change is a major source of uncertainty in predicting their future distribution. By analyzing DNA fingerprinting ( amplified fragment-length polymorphism) of nine plant species, we show that long-distance colonization of a remote arctic archipelago, Svalbard, has occurred repeatedly and from several source regions. Propagules are likely carried by wind and drifting sea ice. The genetic effect of restricted colonization was strongly correlated with the temperature requirements of the species, indicating that establishment limits distribution more than dispersal. Thus, it may be appropriate to assume unlimited dispersal when predicting long-term range shifts in the Arctic.},
	Author = {Alsos, Inger Greve and Eidesen, Pernille Bronken and Ehrich, Dorothee and Skrede, Inger and Westergaard, Kristine and Jacobsen, Gro Hilde and Landvik, Jon Y. and Taberlet, Pierre and Brochmann, Christian},
	Date-Added = {2008-02-07 15:51:16 +0000},
	Date-Modified = {2008-02-07 15:51:22 +0000},
	Doi = {DOI 10.1126/science.1139178},
	Journal = {Science},
	Pages = {1606-1609},
	Timescited = {0},
	Title = {Frequent long-distance plant colonization in the changing Arctic},
	Volume = {316},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1139178},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1139178}}

@article{Salzburger.Mack.ea.2005.a,
	Abstract = {Background: The adaptive radiations of cichlid fishes in East Africa are well known for their spectacular diversity and their astonishingly fast rates of speciation. About 80\% of all 2,500 cichlid species in East Africa, and virtually all cichlid species from Lakes Victoria (similar to 500 species) and Malawi (similar to 1,000 species) are haplochromines. Here, we present the most extensive phylogenetic and phylogeographic analysis so far that includes about 100 species and is based on about 2,000 bp of the mitochondrial DNA.

Results: Our analyses revealed that all haplochromine lineages are ultimately derived from Lake Tanganyika endemics. We find that the three most ancestral lineages of the haplochromines sensu lato are relatively species poor, albeit widely distributed in Africa, whereas a fourth newly defined lineage - the 'modern haplochromines' - contains an unparalleled diversity that makes up more than 7\% of the worlds' similar to 25,000 teleost species. The modern haplochromines' ancestor, most likely a riverine generalist, repeatedly gave rise to similar ecomorphs now found in several of the species flocks. Also, the Tanganyikan Tropheini are derived from that riverine ancestor suggesting that they successfully re-colonized Lake Tanganyika and speciated in parallel to an already established cichlid adaptive radiation. In contrast to most other known examples of adaptive radiations, these generalist ancestors were derived from highly diverse and specialized endemics from Lake Tanganyika. A reconstruction of life-history traits revealed that in an ancestral lineage leading to the modern haplochromines the characteristic egg-spots on anal fins of male individuals evolved.

Conclusion: We conclude that Lake Tanganyika is the geographic and genetic cradle of all haplochromine lineages. In the ancestors of the replicate adaptive radiations of the 'modern haplochromines', behavioral (maternal mouthbrooding), morphological (egg-spots) and sexually selected (color polymorphism) key-innovations arose. These might be - together with the ecological opportunity that the habitat diversity of the large lakes provides - responsible for their evolutionary success and their propensity for explosive speciation.},
	Author = {Salzburger, Walter and Mack, Tanja and Verheyen, Erik and Meyer, Axel},
	Date-Added = {2008-02-07 15:50:13 +0000},
	Date-Modified = {2008-08-21 09:41:09 +0100},
	Doi = {ARTN 17},
	Journal = {Bmc Evolutionary Biology},
	Timescited = {0},
	Title = {Out of Tanganyika: Genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes},
	Volume = {5},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/17},
	Bdsk-Url-2 = {http://dx.doi.org/17}}

@article{Warton.Wright.ea.2006.a,
	Abstract = {Fitting a line to a bivariate dataset can be a deceptively complex problem, and there has been much debate on this issue in the literature. In this review, we describe for the practitioner the essential features of fine-fitting methods for estimating the relationship between two variables: what methods are commonly used, which method should be used when, and how to make inferences from these lines to answer common research questions.

A particularly important point for line-fitting in allometry is that usually, two sources of error are present (which we call measurement and equation error), and these have quite different implications for choice of line-fitting method. As a consequence, the approach in this review and the methods presented have subtle but important differences from previous reviews in the biology literature. Linear regression, major axis and standardised major axis are alternative methods that can be appropriate when there is no measurement error. When there is measurement error, this often needs to be estimated and used to adjust the variance terms in formulae for line-fitting. We also review fine-fitting methods for phylogenetic analyses.

Methods of inference are described for the line-fitting techniques discussed in this paper. The types of inference considered here are testing if the slope or elevation equals a given value, constructing confidence intervals for the slope or elevation, comparing several slopes or elevations, and testing for shift along the axis amongst several groups. In some cases several methods have been proposed in the literature. These are discussed and compared. In other cases there is little or no previous guidance available in the literature.

Simulations were conducted to check whether the methods of inference proposed have the intended coverage probability or Type I error. We identified the methods of inference that perform well and recommend the techniques that should be adopted in future work.},
	Author = {Warton, David I. and Wright, Ian J. and Falster, Daniel S. and Westoby, Mark},
	Date-Added = {2008-02-07 15:47:30 +0000},
	Date-Modified = {2008-02-07 16:00:27 +0000},
	Doi = {DOI 10.1017/S1464793106007007},
	Journal = {Biological Reviews},
	Keywords = {model II regression; errors-in-variables models; standardised major axis; functional and structural relationships; measurement error; method-of-moments regression; test for common slopes; analysis of covariance},
	Pages = {259-291},
	Rating = {0},
	Timescited = {0},
	Title = {Bivariate line-fitting methods for allometry},
	Volume = {81},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1017/S1464793106007007},
	Bdsk-Url-2 = {http://dx.doi.org/10.1017/S1464793106007007}}

@article{Korner.2003.a,
	Abstract = {Global change has many facets, of which land use and the change of atmospheric chemistry are unquestioned primary agents, which induce a suite of secondary effects, including climatic changes. The largest single contribution to the compositional change of the atmosphere, CO2 enrichment, has (besides its influence on climate) immediate and direct effects on plants. Quantitatively, CO2 is the plant 'food' number one, and the rate of photosynthetic CO2 uptake by leaves is not yet CO2-saturated. This abrupt change of the biosphere's diet does and will affect all aspects of life, including our food. However, the plant and ecosystem responses are more subtle than had been assumed from the results of responses of isolated, well-fertilized and well-watered plants in greenhouses during the early days Of CO2-enrichment research. In this article, I discuss potential responses of complex natural grassland and diverse forests, and address three key themes: CO2 and nutrients, CO2 and water; CO2 and plant-animal interactions. Examples from a suite of climatic regions emphasize that the most important ecosystem level responses to elevated CO2 Will be introduced by differential responses of species. Atmospheric CO2 enrichment is a biodiversity issue. Classical physiological baseline responses of leaves to elevated CO2 can be overrun by biodiversity effects to such an extent that some of the traditional predictions may even become reversed. For instance, biodiversity effects may cause humid tropical forests (those which avoid destruction) to become more dynamic and store less, rather than more, carbon as CO2 enrichment continues. The abundance of certain life forms and species and their lifespans exert major controls over the half-life of carbon stored in forest biomass, and there is evidence that elevated CO2 can affect these controls and most likely does so already. Also, long-term hydrological consequences of atmospheric CO2 enrichment will be driven by biodiversity effects, given that some, but not all, species reduce their rate of water loss when exposed to a CO2-rich atmosphere. Such insights call for much more realistic experimental conditions and larger-scale test units, which permit biotic interactions across taxa and trophic levels to occur while simulating our CO2 future. The evidence currently available suggests that ecosystem processes reflect the composition of their biological inventory and this will be affected by a shift in carbon supply.},
	Author = {Korner, C},
	Date-Added = {2008-02-07 15:45:29 +0000},
	Date-Modified = {2008-02-07 15:45:44 +0000},
	Doi = {DOI 10.1098/rsta.2003.1241},
	Journal = {Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical and Engineering Sciences},
	Keywords = {biodiversity; grassland; forest; nutrients; plant-animal interaction; water},
	Pages = {2023-2041},
	Timescited = {0},
	Title = {Ecological impacts of atmospheric CO2 enrichment on terrestrial ecosystems},
	Volume = {361},
	Year = {2003},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rsta.2003.1241},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rsta.2003.1241}}

@article{Vitt.Pianka.2005.a,
	Abstract = {Lizards and snakes putatively arose between the early Jurassic and late Triassic; they diversified worldwide and now occupy many different ecological niches, making them ideal for testing theories on the origin of ecological traits. We propose and test the "deep history hypothesis," which claims that differences in ecological traits among species arose early in evolutionary history of major clades, and that present-day assemblages are structured largely because of ancient, preexisting differences. We combine phylogenetic data with ecological data collected over nearly 40 years to reconstruct the evolution of dietary shifts in squamate reptiles. Data on diets of 184 lizard species in 12 families from 4 continents reveal significant dietary shifts at 6 major divergence points, reducing variation by 79.8\%. The most striking dietary divergence (27.6\%) occurred in the late Triassic, when Iguania and Scleroglossa split. These two clades occupy different regions of dietary niche space. Acquisition of chemical prey discrimination, jaw prehension, and wide foraging providedscleroglossans access to sedentary and hidden prey that are unavailable to iguanians. This cladogenic event may have profoundly influenced subsequent evolutionary history and diversification. We suggest the hypothesis that ancient events in squamate cladogenesis, rather than present-day competition, caused dietary shifts in major clades such that some lizard clades gained access to new resources, which in turn led to much of the biodiversity observed today.},
	Author = {Vitt, LJ and Pianka, ER},
	Date-Added = {2008-02-07 15:42:56 +0000},
	Date-Modified = {2008-02-07 15:43:07 +0000},
	Doi = {DOI 10.1073/pnas.0501104102},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {cladogenesis; community ecology; historical ecology; squamate evolution},
	Pages = {7877-7881},
	Timescited = {0},
	Title = {Deep history impacts present-day ecology and biodiversity},
	Volume = {102},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0501104102},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0501104102}}

@article{Dolphin.Belshaw.ea.2000.a,
	Abstract = {Incongruence between data sets is an important concept in molecular phylogenetics and is commonly measured by the incongruence length difference (ILD) test (J. S. Farris et al. Cladistics 10, 315-319). The ILD test has been used to infer specific evolutionary events and to determine whether to combine data sets for phylogenetic analysis. However, the interpretation in the literature of the test's results varies because authors have conflicting expectations of the effect that noise will have. Using simulations we demonstrate that noise can by itself generate highly significant results in the ILD test and demonstrate why this is the case. To clarify the interpretation of test results, we suggest an additional procedure in which the result is compared against a frequency distribution generated from completely shuffled data. As examples, we apply this approach to two previous studies that have reported incongruence. (C) 2000 Academic Press.},
	Author = {Dolphin, Konrad and Belshaw, Robert and Orme, C. David L. and Quicke, Donald L J},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-03-27 15:11:15 +0000},
	Journal = {Molecular Phylogenetics and Evolution},
	Pages = {401-406},
	Timescited = {0},
	Title = {Noise and incongruence: Interpreting results of the incongruence length difference test},
	Volume = {17},
	Year = {2000},
	Bdsk-File-1 = { }}

@article{Orme.Quicke.ea.2002.a,
	Abstract = {We present a comparative study of the relationship between body size and described taxonomic diversity in the Metazoa. We find no pattern between body size and taxonomic diversity; neither the smallest organisms nor organisms at an intermediate body size are consistently more diverse than their closest relatives. This conclusion holds for both nonphylogenetic analysis, in which phyla are treated as independent points, and analysis of independent contrasts using several recent hypotheses of metazoan phylogeny. These results appear surprising in the context of existing models of body size distributions. However, such models arc built around the prevalence of right-skewed distributions and we find no evidence for such a distribution.},
	Author = {Orme, C. David L. and Quicke, Donald L J and Cook, James M and Purvis, Andy},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-08-20 17:36:23 +0100},
	Journal = {Journal of Evolutionary Biology},
	Keywords = {independent contrasts; macroevolution; Metazoa},
	Pages = {235-247},
	Timescited = {0},
	Title = {Body size does not predict species richness among the metazoan phyla},
	Volume = {15},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { }}

@article{Orme.Isaac.ea.2002.a,
	Abstract = {The robust macro-ecological observation that there are more small-bodied species implies that small-bodied organisms have experienced elevated net rates of diversification. We investigate the role of body size in creating non-random differences in rates of cladogenesis using a set of 38 species-level phylogenies drawn from a range of animal groups. We use independent contrasts to explore the relationship between body size and species richness within individual phylogenies and across related sets of phylogenies. We also carry out a meta-analysis looking for associations between body size and species richness across the taxa. We find little evidence for increased cladogenesis among small-bodied organisms within taxa, and no evidence for any consistent differences between taxa. We explore possible explanations for the inconsistency of our findings with macro-ecological patterns.},
	Author = {Orme, C. David L. and Isaac, Nick J B and Purvis, Andy},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-08-20 17:36:46 +0100},
	Doi = {DOI 10.1098/rspb.2002.2003},
	Journal = {Proceedings of the Royal Society of London Series B-Biological Sciences},
	Keywords = {diversity; speciation; phylogeny; body size},
	Pages = {1279-1287},
	Timescited = {0},
	Title = {Are most species small? Not within species-level phylogenies},
	Volume = {269},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2002.2003},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2002.2003}}

@article{Barker.Power.ea.2004.a,
	Abstract = {A field experiment was carried out to investigate the impact of four different management treatments on the response of Callun-adominated heathland to nitrogen additions of 0 or 30 kg ha(-1) yr(-1) at a lowland heath in Surrey, England. Post-management Calluna regeneration, growth and canopy development were significantly affected by both the form of management and by nitrogen addition. The effect of nitrogen on shoot growth was lower, in absolute terms, in those plots which had undergone more intensive management treatments. Seedling establishment was higher in plots which received a simulated accidental burn treatment, reflecting the greater proportion of bare ground and the high degree of physical disturbance associated with this treatment. Invasion by Deschampsia seedlings was increased by nitrogen addition, particularly in simulated accidental burn plots. In the long term, the need to maintain a low nutrient environment to favour Calluna dominance, particularly in the face of elevated nitrogen deposition, favours the use of managements which result in the export of a significant proportion of the organic nitrogen stores. However, further study is required to ensure that initial enhancement of seedling invasion by grass and other species, associated with these more intense managements, does not outweigh the long term benefits of associated nutrient removal. (C) 2004 Elsevier Ltd. All rights reserved.},
	Author = {Barker, CG and Power, SA and Bell, JNB and Orme, CDL},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:06 +0000},
	Doi = {DOI 10.1016/j.biocon.2004.01.024},
	Journal = {Biological Conservation},
	Keywords = {Calluna vulgaris; Deschampsia flexuosa; nitrogen deposition; heathland management; seedling invasion},
	Pages = {41-52},
	Timescited = {0},
	Title = {Effects of habitat management on heathland response to atmospheric nitrogen deposition},
	Volume = {120},
	Year = {2004},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.biocon.2004.01.024},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.biocon.2004.01.024}}

@article{Orme.Davies.ea.2005.a,
	Abstract = {Biodiversity hotspots have a prominent role in conservation biology(1-9), but it remains controversial to what extent different types of hotspot are congruent(4,10-14). Previous studies were unable to provide a general answer because they used a single biodiversity index, were geographically restricted, compared areas of unequal size or did not quantitatively compare hotspot types(1-10,12-22). Here we use a new global database on the breeding distribution of all known extant bird species to test for congruence across three types of hotspot. We demonstrate that hotspots of species richness, threat and endemism do not show the same geographical distribution. Only 2.5\% of hotspot areas are common to all three aspects of diversity, with over 80\% of hotspots being idiosyncratic. More generally, there is a surprisingly low overall congruence of biodiversity indices, with any one index explaining less than 24\% of variation in the other indices. These results suggest that, even within a single taxonomic class, different mechanisms are responsible for the origin and maintenance of different aspects of diversity. Consequently, the different types of hotspots also vary greatly in their utility as conservation tools.},
	Author = {Orme, C. David L. and Davies, Richard G. and Burgess, Malcolm and Eigenbrod, Felix and Pickup, Nicola and Olson, Valerie A. and Webster, Andrea J. and Ding, Tzung-Su and Rasmussen, Pamela C. and Ridgely, Robert S. and Stattersfield, Ali J. and Bennett, Peter M. and Blackburn, Tim M. and Gaston, Kevin J. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-03-27 15:15:39 +0000},
	Doi = {DOI 10.1038/nature03850},
	Journal = {Nature},
	Pages = {1016-1019},
	Timescited = {0},
	Title = {Global hotspots of species richness are not congruent with endemism or threat},
	Volume = {436},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature03850},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature03850}}

@article{Cardillo.Mace.ea.2005.a,
	Abstract = {Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.},
	Author = {Cardillo, Marcel and Mace, Georgina M. and Jones, Kate E. and Bielby, Jon and Bininda-Emonds, Olaf R. P. and Sechrest, Wes and Orme, C. David L. and Purvis, Andy},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2009-10-21 17:46:56 +0100},
	Doi = {DOI 10.1126/science.1116030},
	Journal = {Science},
	Pages = {1239-1241},
	Timescited = {0},
	Title = {Multiple causes of high extinction risk in large mammal species},
	Volume = {309},
	Year = {2005},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1116030},
	Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1116030}}

@article{Cardillo.Orme.ea.2005.a,
	Abstract = {Study of the latitudinal diversity gradient to date has focused largely on pattern description, with relatively little work on the possible mechanisms underlying the pattern. One proximate mechanism is a latitudinal bias in the discrepancy between speciation and extinction rates, leading to higher rates of species diversification toward lower latitudes. Despite being central to many explanations for high tropical diversity, this mechanism is tested very rarely. We discuss some of the problems involved in testing for latitudinal bias in diversification rates and present an example phylogenetic analysis for endemic bird genera of the New World. The results provide evidence for higher diversification rates in clades inhabiting lower latitudes, both when genera are considered independent and when phylogeny is controlled for using independent contrasts. High rates of diversification are also associated with larger geographic area and higher net primary productivity, although these do not fully account for the latitudinal effect. The latitudinal pattern is stronger in younger clades, supporting the prediction of a simple model in. which the signal of latitudinal bias in diversification rates diminishes as clades age and become saturated with species. Our study demonstrates that a clade-based approach can help answer important questions that a geographic approach cannot, but large phylogenies and geographic databases are needed to cope with the large amount of noise inherent in this type of analysis.},
	Author = {Cardillo, Marcel and Orme, C. David L. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-03-27 15:07:44 +0000},
	Journal = {Ecology},
	Keywords = {diversification; extinction; latitudinal diversity gradient; New World birds; speciation; species richness},
	Pages = {2278-2287},
	Timescited = {0},
	Title = {Testing for latitudinal bias in diversification rates: An example using New World birds},
	Volume = {86},
	Year = {2005},
	Bdsk-File-1 = { }}

@article{Orme.Davies.ea.2006.a,
	Abstract = {Large-scale patterns of spatial variation in species geographic range size are central to many fundamental questions in macroecology and conservation biology. However, the global nature of these patterns has remained contentious, since previous studies have been geographically restricted and/or based on small taxonomic groups. Here, using a database on the breeding distributions of birds, we report the first ( to our knowledge) global maps of variation in species range sizes for an entire taxonomic class. We show that range area does not follow a simple latitudinal pattern. Instead, the smallest range areas are attained on islands, in mountainous areas, and largely in the southern hemisphere. In contrast, bird species richness peaks around the equator, and towards higher latitudes. Despite these profoundly different latitudinal patterns, spatially explicit models reveal a weak tendency for areas with high species richness to house species with significantly smaller median range area. Taken together, these results show that for birds many spatial patterns in range size described in geographically restricted analyses do not reflect global rules. It remains to be discovered whether global patterns in geographic range size are best interpreted in terms of geographical variation in species assemblage packing, or in the rates of speciation, extinction, and dispersal that ultimately underlie biodiversity.},
	Author = {Orme, C. David L. and Davies, Richard G. and Olson, Valerie A. and Thomas, Gavin H. and Ding, Tzung-Su and Rasmussen, Pamela C. and Ridgely, Robert S. and Stattersfield, Ali J. and Bennett, Peter M. and Owens, Ian P. F. and Blackburn, Tim M. and Gaston, Kevin J.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:18:26 +0000},
	Doi = {ARTN e208},
	Journal = {PLoS Biology},
	Pages = {1276-1283},
	Timescited = {0},
	Title = {Global patterns of geographic range size in birds},
	Volume = {4},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/208},
	Bdsk-Url-2 = {http://dx.doi.org/208}}

@article{Phillimore.Freckleton.ea.2006.a,
	Abstract = {One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50\% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large- scale patterns in avian diversification can be explained by variation in intrinsic biology.},
	Author = {Phillimore, Albert B. and Freckleton, Robert P. and Orme, C. David L. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:03 +0000},
	Journal = {American Naturalist},
	Keywords = {birds; diversification; phylogeny; ecology; dispersal; body size},
	Pages = {220-229},
	Timescited = {0},
	Title = {Ecology predicts large-scale patterns of phylogenetic diversification in birds},
	Volume = {168},
	Year = {2006},
	Bdsk-File-1 = { }}

@article{Davies.Orme.ea.2006.a,
	Abstract = {Understanding the global geographical distribution of extinction risk is a key challenge in conservation biology. It remains controversial, however, to what extent areas become threat hotspots simply because of high human impacts or due to predisposing ecological conditions. Limits to the taxonomic and geographical extent, resolution and quality of previously available data have precluded a full global assessment of the relative roles of these factors. Here, we use a new global database on the geographical distributions of birds on continents and continental islands to show that, after controlling for species richness, the best predictors of the global pattern of extinction risk are measures of human impact. Ecological gradients are of secondary importance at a global scale. The converse is true for individual biogeographic realms, within which variation in human impact is reduced and its influence on extinction risk globally is therefore underestimated. These results underline the importance of a global perspective on driving spatial patterns of extinction risk, and the key role of anthropogenic factors in driving the current extinction crisis.},
	Author = {Davies, Richard G. and Orme, C. David L. and Olson, Valerie and Thomas, Gavin H. and Ross, Simon G. and Ding, Tzung-Su and Rasmussen, Pamela C. and Stattersfield, Ali J. and Bennett, Peter M. and Blackburn, Tim M. and Owens, Ian P. F. and Gaston, Kevin J.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:02 +0000},
	Doi = {DOI 10.1098/rspb.2006.3551},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {extinction risk; global biodiversity; human population; species richness; threatened species},
	Pages = {2127-2133},
	Timescited = {0},
	Title = {Human impacts and the global distribution of extinction risk},
	Volume = {273},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2006.3551},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098/rspb.2006.3551}}

@article{Grenyer.Orme.ea.2006.a,
	Abstract = {Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made(1-4). The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent(5-12). Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.},
	Author = {Grenyer, Richard and Orme, C. David L. and Jackson, Sarah F. and Thomas, Gavin H. and Davies, Richard G. and Davies, T. Jonathan and Jones, Kate E. and Olson, Valerie A. and Ridgely, Robert S. and Rasmussen, Pamela C. and Ding, Tzung-Su and Bennett, Peter M. and Blackburn, Tim M. and Gaston, Kevin J. and Gittleman, John L. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:02 +0000},
	Doi = {DOI 10.1038/nature05237},
	Journal = {Nature},
	Pages = {93-96},
	Timescited = {0},
	Title = {Global distribution and conservation of rare and threatened vertebrates},
	Volume = {444},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature05237},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature05237}}

@article{Storch.Davies.ea.2006.a,
	Abstract = {Spatial patterns of species richness follow climatic and environmental variation, but could reflect random dynamics of species ranges (the mid-domain effect, MDE). Using data on the global distribution of birds, we compared predictions based on energy availability (actual evapotranspiration, AET, the best single correlate of avian richness) with those of range dynamics models. MDE operating within the global terrestrial area provides a poor prediction of richness variation, but if it operates separately within traditional biogeographic realms, it explains more global variation in richness than AET. The best predictions, however, are given by a model of global range dynamics modulated by AET, such that the probability of a range spreading into an area is proportional to its AET. This model also accurately predicts the latitudinal variation in species richness and variation of species richness both within and between realms, thus representing a compelling mechanism for the major trends in global biodiversity.},
	Author = {Storch, David and Davies, Richard G. and Zajicek, Samuel and Orme, C. David L. and Olson, Valerie and Thomas, Gavin H. and Ding, Tzung-Su and Rasmussen, Pamela C. and Ridgely, Robert S. and Bennett, Peter M. and Blackburn, Tim M. and Owens, Ian P. F. and Gaston, Kevin J.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:01 +0000},
	Doi = {DOI 10.1111/j.1461-0248.2006.00984.x},
	Journal = {Ecology Letters},
	Keywords = {biogeography; climate-richness relationship; hotspots; latitudinal gradient of diversity; mid-domain effect; more-individuals hypothesis; mountains; productivity; spatial models; species-energy relationship},
	Pages = {1308-1320},
	Timescited = {0},
	Title = {Energy, range dynamics and global species richness patterns: reconciling mid-domain effects and environmental determinants of avian diversity},
	Volume = {9},
	Year = {2006},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1461-0248.2006.00984.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2006.00984.x}}

@article{Davies.Orme.ea.2007.b,
	Abstract = {Aim Spatial patterns of phylogenetic diversity (PD) aid our ability to discern diversification rate mechanisms underlying hypotheses for the large-scale distribution of biodiversity. We develop a predictive framework for the way in which spatial patterns of PD vary with those of species richness, depending on the balance between speciation and extinction rates. Within this framework, diversification processes thought to underlie the productive energy, ambient energy, topographic variability and habitat variety hypotheses predict that gradients of increase in species richness will be associated with: (1) decreasing extinction rates where driven by productive energy, hence increasing relative PD (i.e. PD controlling for species richness, or PDrel); (2) a similar positive relationship between ambient energy and PDrel; (3) increasing speciation rates where driven by topographic variability, hence decreasing PDrel; and (4) no consistent relationship between PDrel and habitat variety when driven by the latter. We test these predictions using distributional data on parrots.

Location Neotropical, Afrotropical, Indo-Malayan and Australasian realms.

Methods Spatial models were used to test the predictions.

Results Globally, a positive association between productive energy and PDrel confirms prediction (1). However, within realms, hump-shaped relationships suggest the importance of decreasing extinction rates up to a threshold level of productive energy, and the increasing importance of speciation rates thereafter. Ambient energy is positively associated with PDrel in Australasia, Indo-Malaya, and globally, supporting prediction (2). However, this is driven by the coincidence of highest PDrel in areas of high ambient energy and intermediate productive energy (i.e. in seasonal tropical environments), which may be characterized by relatively low speciation and extinction rates. In the Neotropics, increasing topographic variability is associated with decreasing PDrel and increasing species richness, suggesting an increasing gradient of speciation, supporting prediction (3). Elsewhere, the signal of this mechanism may be obscured by collinearities with energy gradients. The lack of an overall relationship between habitat diversity and PDrel confirms prediction (4).

Main conclusions Spatial patterns of PDrel in relation to environmental gradients may be sensitive to collinearities among those gradients. Nevertheless, patterns emerge which have implications for the relative importance of speciation and extinction processes in generating latitudinal diversity gradients.},
	Author = {Davies, Richard G. and Orme, C. David L. and Webster, Andrea J. and Jones, Kate E. and Blackburn, Tim M. and Gaston, Kevin J.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:05:00 +0000},
	Doi = {DOI 10.1111/j.1466-8238.2007.00282.x},
	Journal = {Global Ecology and Biogeography},
	Keywords = {diversification rate; energy hypothesis; extinction rate; habitat heterogeneity; phylogenetic diversity; speciation rate; species richness},
	Pages = {220-233},
	Timescited = {0},
	Title = {Environmental predictors of global parrot (Aves : Psittaciformes) species richness and phylogenetic diversity},
	Volume = {16},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00282.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1466-8238.2007.00282.x}}

@article{Davies.Orme.ea.2007.a,
	Abstract = {A major goal of ecology is to determine the causes of the latitudinal gradient in global distribution of species richness. Current evidence points to either energy availability or habitat heterogeneity as the most likely environmental drivers in terrestrial systems, but their relative importance is controversial in the absence of analyses of global (rather than continental or regional) extent. Here we use data on the global distribution of extant continental and continental island bird species to test the explanatory power of energy availability and habitat heterogeneity while simultaneously addressing issues of spatial resolution, spatial autocorrelation, geometric constraints upon species' range dynamics, and the impact of human populations and historical glacial ice-cover. At the finest resolution (1 degrees), topographical variability and temperature are identified as the most important global predictors of avian species richness in multipredictor models. Topographical variability is most important in single-predictor models, followed by productive energy. Adjusting for null expectations based on geometric constraints on species richness improves overall model fit but has negligible impact on tests of environmental predictors. Conclusions concerning the relative importance of environmental predictors of species richness cannot be extrapolated from one biogeographic realm to others or the globe. Rather a global perspective confirms the primary importance of mountain ranges in high-energy areas.},
	Author = {Davies, Richard G. and Orme, C. David L. and Storch, David and Olson, Valerie A. and Thomas, Gavin H. and Ross, Simon G. and Ding, Tzung-Su and Rasmussen, Pamela C. and Bennett, Peter M. and Owens, Ian P. F. and Blackburn, Tim M. and Gaston, Kevin J.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:04:59 +0000},
	Doi = {DOI 10.1098//rspb.2006.0061},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {geometric constraints; global biodiversity; habitat heterogeneity; species richness; species-energy theory; topography},
	Pages = {1189-1197},
	Timescited = {0},
	Title = {Topography, energy and the global distribution of bird species richness},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098//rspb.2006.0061},
	Bdsk-Url-2 = {http://dx.doi.org/10.1098//rspb.2006.0061}}

@article{Phillimore.Orme.ea.2007.a,
	Abstract = {Theory predicts that biogeographic factors should play a central role in promoting population divergence and speciation. Previous empirical studies into biogeography and diversification have been relatively restricted in terms of the geographical area, phylogenetic scope, and the range of biogeographic factors considered. Here we present a global analysis of allopatric phenotypic divergence (measured as subspecies richness) across more than 9600 bird species. The main aim of this study was to examine the extent to which biogeographical factors can explain patterns of phenotypic divergence. Analysis of the taxonomic distribution of subspecies among species suggests that subspecies formation and extinction have occurred at a considerably faster rate than has species formation. However, the observed distribution departs from the expectation under a random birth-death model of diversification. Across 19 phylogenetic trees, we find no significant linear relationship between species age and subspecies richness, implying that species age is a poor predictor of subspecies richness. Both subspecies richness and subspecies diversification rate are found to exhibit low phylogenetic signal, meaning that closely related species do not tend to possess similar numbers of subspecies. As predicted by theory, high subspecies richness was associated with large breeding range size, island dwelling, inhabitation of montane regions, habitat heterogeneity, and low latitude. Of these factors, breeding range size was the variable that explained the most variation. Unravelling whether species that have invaded previously glacial areas have more or fewer subspecies than expected proves to be complicated due to a covariation between the postglacial colonization, latitude, geographic range size, and subspecies richness. However, the effect of postglacial colonization on subspecies richness appears to be small. Mapping the distribution of species' subspecies richness globally reveals geographical patterns that correspond to many of the predictions of the statistical models, but may also reflect geographical variation in taxonomic practice. Overall, we demonstrate that biogeographic models can explain about 30\% of the global variation in subspecies richness in birds.},
	Author = {Phillimore, Albert B. and Orme, C. David L. and Davies, Richard G. and Hadfield, Jarrod D. and Reed, William J. and Gaston, Kevin J. and Freckleton, Robert P. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 16:00:27 +0000},
	Doi = {DOI 10.1111/j.1558-5646.2007.00068.x},
	Journal = {Evolution},
	Keywords = {birds; divergence; extinction; islands; range size; subspecies},
	Pages = {942-957},
	Timescited = {0},
	Title = {Biogeographical basis of recent phenotypic divergence among birds: A global study of subspecies richness},
	Volume = {61},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2007.00068.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1558-5646.2007.00068.x}}

@article{Bielby.Mace.ea.2007.a,
	Abstract = {Many life-history traits co-vary across species, even when body size differences are controlled for. This phenomenon has led to the concept of a "fast-slow continuum," which has been influential in both empirical and theoretical studies of life-history evolution. We present a comparative analysis of mammalian life histories showing that, for mammals at least, there is not a single fast-slow continuum. Rather, both across and within mammalian clades, the speed of life varies along at least two largely independent axes when body size effects are removed. One axis reflects how species balance offspring size against offspring number, while the other describes the timing of reproductive bouts.},
	Author = {Bielby, J. and Mace, G. M. and Bininda-Emonds, O. R. P. and Cardillo, M. and Gittleman, J. L. and Jones, K. E. and Orme, C. D. L. and Purvis, A.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:04:57 +0000},
	Journal = {American Naturalist},
	Keywords = {life history; fast-slow continuum; comparative study; phylogeny; mammals},
	Pages = {748-757},
	Timescited = {0},
	Title = {The fast-slow continuum in mammalian life history: An empirical reevaluation},
	Volume = {169},
	Year = {2007},
	Bdsk-File-1 = { }}

@article{Gaston.Davies.ea.2007.a,
	Abstract = {Despite its wide implications for many ecological issues, the global pattern of spatial turnover in the occurrence of species has been little studied, unlike the global pattern of species richness. Here, using a database on the breeding distributions of birds, we present the first global maps of variation in spatial turnover for an entire taxonomic class, a pattern that has to date remained largely a matter of conjecture, based on theoretical expectations and extrapolation of inconsistent patterns from different biogeographic realms. We use these maps to test four predictions from niche theory as to the form that this variation should take, namely that turnover should increase with species richness, towards lower latitudes, and with the steepness of environmental gradients and that variation in turnover is determined principally by rare (restricted) species. Contrary to prediction, we show that turnover is high both in areas of extremely low and high species richness, does not increase strongly towards the tropics, and is related both to average environmental conditions and spatial variation in those conditions. These results are closely associated with a further important and novel finding, namely that global patterns of spatial turnover are driven principally by widespread species rather than the restricted ones. This complements recent demonstrations that spatial patterns of species richness are also driven principally by widespread species, and thus provides an important contribution towards a unified model of how terrestrial biodiversity varies both within and between the Earth's major land masses.},
	Author = {Gaston, Kevin J. and Davies, Richard G. and Orme, C. David L. and Olson, Valerie A. and Thomas, Gavin H. and Ding, Tzung-Su and Rasmussen, Pamela C. and Lennon, Jack J. and Bennett, Peter M. and Owens, Ian P. F. and Blackburn, Tim M.},
	Date-Added = {2008-02-07 15:04:30 +0000},
	Date-Modified = {2008-02-07 15:04:56 +0000},
	Doi = {DOI 10.1098/rspb.2007.0236},
	Journal = {Proceedings of the Royal Society B-Biological Sciences},
	Keywords = {beta diversity; environmental gradients; global avifauna; niche theory; spatial turnover},
	Pages = {1567-1574},
	Timescited = {0},
	Title = {Spatial turnover in the global avifauna},
	Volume = {274},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-File-2 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2007.0236}}

@article{Economo.Keitt.2008.a,
	Abstract = {Biologists seek an understanding of the processes underlying spatial biodiversity patterns. Neutral theory links those patterns to dispersal, speciation and community drift. Here, we advance the spatially explicit neutral model by representing the metacommunity as a network of smaller communities. Analytic theory is presented for a set of equilibrium diversity patterns in networks of communities, facilitating the exploration of parameter space not accessible by simulation. We use this theory to evaluate how the basic properties of a metacommunity - connectivity, size, and speciation rate - determine overall metacommunity gamma-diversity, and how that is partitioned into alpha- and beta-components. We find spatial structure can increase gamma-diversity relative to a well-mixed model, even when theta is held constant. The magnitude of deviations from the well-mixed model and the partitioning into alpha- and beta-diversity is related to the ratio of migration and speciation rates. gamma-diversity scales linearly with metacommunity size even as alpha- and beta-diversity scale nonlinearly with size.},
	Author = {Economo, Evan P. and Keitt, Timothy H.},
	Date-Added = {2008-02-07 11:49:21 +0000},
	Date-Modified = {2008-02-08 10:51:42 +0000},
	Doi = {DOI 10.1111/j.1461-0248.2007.01126.x},
	Journal = {Ecology Letters},
	Keywords = {beta-Diversity; biodiversity scaling; diversity partitioning; island biogeography; metacommunities; neutral theory; patch networks; biodiversity},
	Pages = {52-62},
	Timescited = {0},
	Title = {Species diversity in neutral metacommunities: a network approach},
	Volume = {11},
	Year = {2008},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1461-0248.2007.01126.x},
	Bdsk-Url-2 = {http://dx.doi.org/10.1111/j.1461-0248.2007.01126.x}}

@article{Grenyer.Orme.ea.2007.a,
	Author = {Grenyer, Richard and Orme, C. David L. and Davies, T. Jonathan and Jackson, Sarah F. and Davies, Richard G. and Olson, Valerie A. and Jones, Kate E. and Gaston, Kevin J. and Blackburn, Tim M. and Thomas, Gavin H. and Bennett, Peter M. and Rasmussen, Pamela C. and Ding, Tzung-Su and Gittleman, John L. and Owens, Ian P. F.},
	Date-Added = {2008-02-07 11:35:15 +0000},
	Date-Modified = {2008-02-07 16:00:27 +0000},
	Doi = {DOI 10.1038/nature06375},
	Journal = {Nature},
	Keywords = {species richness},
	Pages = {E20-E20},
	Timescited = {0},
	Title = {Effective global conservation strategies - Reply},
	Volume = {450},
	Year = {2007},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature06375},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/nature06375}}

@article{Fusco.Cronk.1995.a,
	Abstract = {The symmetry of branching of evolutionary trees is considered to be informative of the evolutionary process. Most recent methods for measuring this symmetry (''imbalance'') measure only one aspect of tree shape. The method we present here provides an almost complete description of tree shape and allows calculation of imbalance parameters for very large phylogenies. The method can detect different patterns of radiation, both among nodes within a tree and among trees. Preliminary tests of the method suggest that bird and angiosperm cladograms have similar tree balance if only the resolved topology of the tree is considered, but very different balance if the dimensions of terminal taxa, measured as number of species, are also included. (C) 1995 Academic Press Limited},
	Author = {Fusco, Guiseppe and Cronk, Quentin C B},
	Date-Added = {2008-02-06 18:00:45 +0000},
	Date-Modified = {2008-03-27 15:10:13 +0000},
	Journal = {Journal of Theoretical Biology},
	Keywords = {imbalance},
	Pages = {235-243},
	Timescited = {0},
	Title = {A NEW METHOD FOR EVALUATING THE SHAPE OF LARGE PHYLOGENIES},
	Volume = {175},
	Year = {1995},
	Bdsk-File-1 = { }}

@article{Purvis.Katzourakis.ea.2002.a,
	Abstract = {Measurement of the degree of asymmetry in phylogenetic trees is important because a tree's shape reflects the process by which it has grown. For example, highly asymmetric trees are evidence that species have had different potential for diversification. Of the tree shape measures in the literature, that proposed by Fusco \& Cronk (J. theor. Biol. 175, 235-243) appears to be particularly useful, because it does not require fully-resolved trees whose terminals are of equal taxonomic rank. The value of the asymmetry or imbalance at a node is intended to be independent of the number of species ultimately descended from the node. In this paper, however, we point out that the value does depend upon species number. We propose two modifications that remove the dependency and so increase the measure's usefulness. We illustrate the use of the modified measures, which are implemented in a freely-available program, MESA. (C) 2002 Academic Press.},
	Author = {Purvis, Andy and Katzourakis, Aris and Agapow, Paul-Michael},
	Date-Added = {2008-02-06 17:02:35 +0000},
	Date-Modified = {2008-08-21 09:35:18 +0100},
	Doi = {DOI 10.1006/jtbi.2001.2443},
	Journal = {Journal of Theoretical Biology},
	Keywords = {imbalance signatures; imbalance},
	Pages = {99-103},
	Timescited = {0},
	Title = {Evaluating phylogenetic tree shape: Two modifications to Fusco \& Cronk's method},
	Volume = {214},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1006/jtbi.2001.2443},
	Bdsk-Url-2 = {http://dx.doi.org/10.1006/jtbi.2001.2443}}

@article{Agapow.Isaac.2002.a,
	Abstract = {Studies of species richness have been hampered by the use of methods that fail to account for phylogenetic non-independence of character states. MacroCAIC is a computer program that extends the method of phylogenetically independent contrasts to encompass species-richness data. It examines user-selected characters for correlation with species richness, thus allowing clearer identification of the factors driving large-scale patterns of diversity.},
	Author = {Agapow, Paul-Michael and Isaac, Nick J B},
	Date-Added = {2008-02-06 17:02:35 +0000},
	Date-Modified = {2008-08-21 09:43:39 +0100},
	Journal = {Diversity and Distributions},
	Keywords = {species richness; phylogeny; comparative analysis; independent contrasts; macroevolution},
	Pages = {41-43},
	Timescited = {0},
	Title = {MacroCAIC: revealing correlates of species richness by comparative analysis},
	Volume = {8},
	Year = {2002},
	Bdsk-File-1 = { }}

@article{Agapow.Purvis.2002.a,
	Abstract = {We used simulations to compare the relative power of eight statistical tests to detect imbalance in phylogenies that is too great to be ascribed to an equal-rates Markov null model. Three of these tests have never had their power assessed before. Our simulations are the first to assess performance under scenarios in which the speciation rates of various lineages can evolve independently. In one of the scenarios explored, rates depend upon the value of an evolving trait, whereas in the other the probability that a species will speciate declines with the time since it last did so. The results indicate that the relative performance of the methods depends upon how the imbalance is generated. Different types of processes lead to different imbalance signatures, i.e., different patterns of imbalance at different depths in the phylogeny, and the measures of tree shape differ in the depth of phylogeny at which they are most sensitive. Relative performance is also affected by tree size but does not appear to depend greatly upon the degree of speciation rate variation among lineages. Two of the indices (Colless's index I-c and Shao and Sokal's (N) over bar) show reasonable performance throughout, but another (Shao and Sokal's B-2) is never indicated to be a preferred method. Two tests that do not require completely resolved phylogenies, mean I' and mean I-10', have reasonable power.},
	Author = {Agapow, Paul-Michael and Purvis, Andy},
	Date-Added = {2008-02-06 17:02:35 +0000},
	Date-Modified = {2008-08-21 09:56:29 +0100},
	Doi = {DOI 10.1080/10635150290155845},
	Journal = {Systematic Biology},
	Keywords = {imbalance; imbalance signatures; macroevolution; simulation; phylogeny; power; simulation},
	Pages = {866-872},
	Timescited = {0},
	Title = {Power of eight tree shape statistics to detect nonrandom diversification: A comparison by simulation of two models of cladogenesis},
	Volume = {51},
	Year = {2002},
	Bdsk-File-1 = { },
	Bdsk-Url-1 = {http://dx.doi.org/10.1080/10635150290155845},
	Bdsk-Url-2 = {http://dx.doi.org/10.1080/10635150290155845}}

@article{Garland.Harvey.ea.1992.a,
	Abstract = {We discuss and clarify several aspects of applying Felsenstein's (1985, Am. Nat. 125: 
1-15) procedures to test for correlated evolution of continuous traits. This is one of several 
available comparative methods that maps data for phenotypic traits onto an existing phylogenetic 
tree (derived from independent information). Application of Felsenstein's method does not 
require an entirely dichotomous topology. It also does not require an assumption of gradual, 
clocklike character evolution, as might be modeled by Brownian motion. Almost any available 
information can be used to estimate branch lengths (e.g., genetic distances, divergence times 
estimated from the fossil record or from molecular clocks, numbers of character changes from 
a cladistic analysis). However, the adequacy for statistical purposes of any proposed branch 
lengths must be verified empirically for each phylogeny and for each character. We suggest a 
simple way of doing this, based on graphical analysis of plots of standardized independent 
contrasts versus their standard deviations (i.e., the square roots of the sums of their branch 
lengths). In some cases, the branch lengths and/or the values of traits being studied will require 
transformation. An example involving the scaling of mammalian home range area is presented. 
Once adequately standardized, sets of independent contrasts can be analyzed using either linear 
or nonlinear (multiple) regression. In all cases, however, regressions (or correlations) must be 
computed through the origin. We also discuss ways of correcting for body size effects and how 
this relates to making graphical representations of relationships of standardized independent 
contrasts. We close with a consideration of the types of traits that can be analyzed with inde- 
pendent contrasts procedures and conclude that any (continuous) trait that is inherited from 
ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic 
or cultural). },
	Author = {Garland, Theodore and Harvey, Paul H. and Ives, Anthony R.},
	Date = {MAR},
	Date-Added = {2008-02-06 16:40:30 +0000},
	Date-Modified = {2008-04-16 13:59:26 +0100},
	Isi = {ISI:A1992JL28900003},
	Issn = {1063-5157},
	Journal = {Systematic Biology},
	Keywords = {phylogeny; independent contrasts; Allometry; body size; branch lengths; comparative method; evolutionary rates; functional morphology; home range; statistics},
	Month = {Mar},
	Number = {1},
	Pages = {18--32},
	Publication-Type = {J},
	Rating = {0},
	Read = {No},
	Title = {PROCEDURES FOR THE ANALYSIS OF COMPARATIVE DATA USING PHYLOGENETICALLY INDEPENDENT CONTRASTS},
	Volume = {41},
	Year = {1992},
	Bdsk-File-1 = { }}

@comment{BibDesk Static Groups{
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<array>
	<dict>
		<key>group name</key>
		<string>! To Read</string>
		<key>keys</key>
		<string></string>
	</dict>
	<dict>
		<key>group name</key>
		<string>2008 - Avian Bergmann</string>
		<key>keys</key>
		<string>Ramirez.Diniz-Filho.ea.2008.b,Cardillo.2002.a,ISLSCP.2004.a,Ashton.2001.a,YOMTOV.NIX.1986.a,Meiri.Thomas.2007.a,Clegg.Owens.2002.a,COUSINS.1989.a,James.1970.a,Bergmann.1847.a,Greve.Gaston.ea.2008.a,Calder.1974.a,Littell.Wolfinger.1996.a,Lindsey.1966.a,Rosenzweig.1968.a,Rahbek.Graves.2000.a,Meiri.Dayan.2003.a,New.Lister.ea.2002.a,Brown.Nicoletto.1991.a,Clifford.Richardson.ea.1989.a,Boyce.1978.a,Graves.1991.a,McNab.1971.a,Orme.Davies.ea.2006.a,Del-Hoyo.Sargatal.1992.a,Cressie.1991.a,Orme.Davies.ea.2005.a,McKechnie.Lovegrove.2002.a,Marsh.1989.a,Zeveloff.Boyce.1988.a,Burnham.Anderson.2002.a,Newton.Dale.1996.a,USGS.2003.b,Cartron.Kelly.ea.2000.a,Sibley.Monroe.1990.a,Diniz.2001.a,Boyce.1979.a,Hedges.Olkin.1985.a,Cassey.Blackburn.ea.2005.a,GEIST.1987.a,Blackburn.Gaston.1996.a,USGS.2003.a,Steadman.2006.a,Quinn.Keough.2002.a,Hamilton.1961.a</string>
	</dict>
	<dict>
		<key>group name</key>
		<string>2008 - Family PSAR</string>
		<key>keys</key>
		<string>Jablonski.2001.a,Rosenzweig.1995.a,Gaston.Blackburn.2000.a,Brown.1995.a,Simberloff.1974.a,Coyne.Orr.2004.a,GUYER.SLOWINSKI.1993.a,Harvey.LeighBrown.ea.1996.a,Schluter.2000.a,Losos.Schluter.2000.a,MacArthur.Wilson.1967.a,Barraclough.Harvey.ea.1995.a,Davies.Savolainen.ea.2005.a,McPeek.Brown.2007.a,Triantis.Mylonas.ea.2003.a,Valentine.1980.a,Ricklefs.Lovette.1999.a,Foote.2000.a,Mittelbach.Schemske.ea.2007.a,Shmida.Wilson.1985.a,Purvis.1996.a,Slowinski.Guyer.1993.a,Gaston.Blackburn.1997.a,Willis.1922.a,Ricklefs.Losos.ea.2007.a,Revell.Harrison.2008.a,Owens.Bennett.ea.1999.a,Price.Wagner.2004.a,Scotland.Sanderson.2004.a</string>
	</dict>
	<dict>
		<key>group name</key>
		<string>2008 - Nick Isaac</string>
		<key>keys</key>
		<string>Kunin.Hartley.ea.2000.a,Kalmar.Currie.2007.a,Blackburn.Gaston.2006.a,Hartley.Kunin.ea.2004.a,Harte.Conlisk.ea.2005.a,Petrik.Bruelheide.2006.a,Naidoo.Balmford.ea.2008.a,Burgess.Balmford.ea.2007.a,Storch.Sizling.ea.2008.a,Hickling.Roy.ea.2006.a,Pocock.Hartley.ea.2006.a,Hickling.Roy.ea.2005.a,Ricketts.Regetz.ea.2008.a,Kerr.Kharouba.ea.2007.a,Naidoo.Ricketts.2006.a,Green.Harte.ea.2003.a,Tilman.2004.a,Wilson.Thomas.ea.2004.a,Prendergast.Quinn.ea.1993.a,Thomas.Telfer.ea.2004.a,Conlisk.Bloxham.ea.2007.a,Halley.Hartley.ea.2004.a,Hui.McGeoch.2007.a,Lennon.Kunin.ea.2002.a,Schroter.Cramer.ea.2005.a,Lennon.Kunin.ea.2002.b</string>
	</dict>
	<dict>
		<key>group name</key>
		<string>caper package</string>
		<key>keys</key>
		<string>Burt.1989.a,Freckleton.Harvey.ea.2002.a,Harvey.Clutton-Brock.1985.a,Pagel.1994.a,Faith.1992.a,Jones.Bielby.ea.2009.a,Purvis.Rambaut.1995.a,Diaz-Uriarte.Garland.ea.2010.a,Lislevand.Thomas.2006.a,Fusco.Cronk.1995.a,Purvis.Katzourakis.ea.2002.a,Martins.2004.a,Pagel.1992.a,Felsenstein.1989.a,Price.1997.a,Isaac.Agapow.ea.2003.a,Felsenstein.1985.a,Purvis.Rambaut.1995.b,Agapow.Isaac.2002.a,Pagel.Meade.2011.a,Clutton-Brock.Harvey.1977.a,Isaac.Turvey.ea.2007.a,Jones.Purvis.1997.a,Garland.Harvey.ea.1992.a,Fritz.Purvis.2010.a,R-Development-Core-Team.2011.a,Pagel.Harvey.1989.a,R-Hackathon.Bolker.ea.2011.a,Webb.Ackerly.ea.2002.a,Katzourakis.Purvis.ea.2001.a,Isaac.Jones.ea.2005.a,Paradis.Claude.ea.2004.a,Pagel.1999.a,Thomas.2008.a,Grafen.1989.a</string>
	</dict>
	<dict>
		<key>group name</key>
		<string>Software Manuals</string>
		<key>keys</key>
		<string>Dominus.2005.a,Martins.2004.a,Pilgrim.2004.a,McCoy.2004.a,Tucker.2004.a</string>
	</dict>
	<dict>
		<key>group name</key>
		<string>tcclim MS</string>
		<key>keys</key>
		<string>Mitchell.Carter.ea..a,Mitchell.Jones.2005.a,Hijmans.Cameron.ea.2005.a,Tarroso.Rebelo.2010.a</string>
	</dict>
</array>
</plist>
}}

@comment{BibDesk Smart Groups{
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<array>
	<dict>
		<key>conditions</key>
		<array>
			<dict>
				<key>comparison</key>
				<integer>0</integer>
				<key>key</key>
				<string>Local File</string>
				<key>value</key>
				<string>0</string>
				<key>version</key>
				<string>1</string>
			</dict>
			<dict>
				<key>comparison</key>
				<integer>4</integer>
				<key>key</key>
				<string>BibTeX Type</string>
				<key>value</key>
				<string>article</string>
				<key>version</key>
				<string>1</string>
			</dict>
		</array>
		<key>conjunction</key>
		<integer>0</integer>
		<key>group name</key>
		<string>Papers with no pdf</string>
	</dict>
</array>
</plist>
}}
