Rubolini Diego, Liker András, Garamszegi László Z, Møller Anders P, Saino Nicola
Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133 Milano, Italy.
Department of Limnology, University of Pannonia, Pf. 158, H-8201 Veszprém, Hungary.
Curr Zool. 2015 Dec;61(6):959-965. doi: 10.1093/czoolo/61.6.959. Epub 2015 Dec 1.
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 come.
性状进化的比较研究需要考虑共同的进化历史。这通过将系统发育假说纳入物种性状的统计分析来实现，鸟类常常是这类分析的优秀模型。现存鸟类物种最完整分子系统发育树的在线发布（www.birdtree.org，以下简称BirdTree），现在使进化生物学家能够快速获取任何一组物种的同等合理的系统发育树集，以便在比较分析中作为系统发育假说纳入。我们讨论了将BirdTree树集用于比较研究的方法，要么构建一个可纳入标准比较分析的共识树，要么使用树集来考虑系统发育不确定性的影响。只要有可能，应优先选择考虑系统发育不确定性的方法，因为它们应能提供更可靠的参数估计以及围绕这些估计的现实置信区间。基于一个真实的比较数据集，我们进行了模拟，以研究从BirdTree下载的随机树集大小变化对特定质量生产力与体重之间二元关系参数估计变异性的影响。无论采用何种分析方法，使用至少1000棵树能够获得变异系数非常小（<0.15%）的参数估计。我们认为，由于使用便捷且相较于以往获取鸟类物种系统发育假说的“传统”方法（例如超级树或对已发表系统发育树的手动编码）具有主要优势，BirdTree在未来几年将成为鸟类比较研究的标准参考。
