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Using the *** website to obtain robust phylogenies for avian comparative studies： A primer

Current Zoology 2015年第6期61卷 959-965页

作者： Diego RUBOLINI Andras LIKER Laszlo Z. GARAMSZEGI Anders P. MOLLEIR Nicola SAINO Dipartimento di Bioscienze Universita degli Studi di Milano via Celoria 26 1-20133 Milano Italy Department of Limnology University of Pannonia Pf. 158 H-8201 Veszpr6m Hungary Department of Evolutionary Ecology Estaci6n Biol6gica de Dofiana-CSIC c/Americo Vespucio s/n E-41092 Seville Spain Laboratoire Ecologie Systematique et Evolution UMR 8079 CNRS Universit6 Paris-Sud XI-AgroParisTech Batiment 362 Universit6 Paris-Sud XI F-91405 Orsay Cedex France

Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by includ- ing phylogenetic hypotheses into statistical analyses of species＇ traits, for which birds often serve as excellent models. The online publication of the most complete molecular phylogeny of extant bird species （***, birdtree hereafter） now allows evolutionary biologists to rapidly obtain sets of equally plausible phylogenetic trees for any set of species to be incorporated as a phylogenetic hypothesis in comparative analyses. We discuss methods to use birdtree tree sets for comparative studies, either by building a consensus tree that can be incorporated into standard comparative analyses, or by using tree sets to account for the ef- fect of phylogenetie uncertainty. Methods accounting for phylogenetic uncertainty should be preferred whenever possible because they should provide more reliable parameter estimates and realistic confidence intervals around them. Based on a real compara- tive dataset, we ran simulations to investigate the effect of variation in the size of the random tree sets downloaded from birdtree on the variability of parameter estimates from a bivariate relationship between mass-specific productivity and body mass. Irre- spective of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small （〈 0.15%） co- efficients of variation. We argue that birdtree, due to the ease of use and the major advantages over previous ＇traditional＇ meth- ods to obtain phylogenetic hypotheses of bird species （e.g. supertrees or manual coding of published phylogenies）, will become the standard reference in avian comparative studies for years to come.

关键词： Birds birdtree Comparative method PGLM PGLS Phylogenetic uncertainty

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