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 trai...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。该研究范式忽略了一项核心事实：每一棵系统发育树都仅是针对某一演化支（clade）演化历史提出的假说，且无法在自然状态下被直接观测。此外，系统发育树往往会遗漏大量现存物种，或是因分类单元（taxon，复数taxa）间亲缘关系信息匮乏，将缺失物种以多歧支（polytomy）的形式纳入树中。尽管如此，研究者通常并未量化生态分析中系统发育不确定性（phylogenetic uncertainty）所带来的影响。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对该方法进行演示，评估不同不确定性来源对多项性状系统发育比较分析的影响……