Data from: Phylogenetic uncertainty revisited: implications for ecological analyses

Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximizes the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade-wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.

生态学家与生物地理学家通常依赖单棵系统发育树（phylogenetic tree）来研究影响宏观生态格局的演化过程。该方法忽略了一个核心事实：每一棵系统发育树都仅是某一支系类群（clade）演化历史的假说，且无法在自然界中被直接观测到。此外，系统发育树往往会遗漏大量现存物种，或是由于缺乏类群间亲缘关系的相关信息，将缺失物种以多歧支（polytomies）的形式纳入树中。尽管如此，研究者们通常并未量化系统发育不确定性在生态分析中产生的影响。本文提出一种全新的分析策略，可最大化利用不完备的系统发育信息，同时兼顾可能扭曲演化过程统计推断的多类系统发育不确定性来源。我们以蜂鸟类群的全支系分析为例演示该方法，评估不同不确定性来源对性状演化与生物地理格局的多项系统发育比较分析产生的影响。尽管尚无任何统计近似方法能够完全替代完整且稳健的系统发育树，但我们所阐述并演示的方法可帮助研究者拓展可开展演化关系导向研究的支系类群数量，同时允许对系统发育不确定性所引发的统计误差进行估计与控制。本文还提供了用于执行所需计算的软件工具。