Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by including
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 (www.birdtree.org, 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 effect
of phylogenetic 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 comparative
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. Irrespective
of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small (< 0.15%) coefficients
of variation. We argue that BirdTree, due to the ease of use and the major advantages over previous ‘traditional’ methods
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 comePeer reviewe
