Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada.
Syst Biol. 2009 Dec;58(6):595-611. doi: 10.1093/sysbio/syp067. Epub 2009 Oct 15.
Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies.
物种特征可能会影响物种形成和灭绝的速度，从而影响谱系之间多样化的模式和物种之间特征的分布。现有的检测分化多样化的可能性方法需要完整的系统发育；也就是说，每个现存的物种都必须存在于一个分辨率良好的系统发育中。我们开发了 2 种可能性方法，可以在没有完整系统发育信息的情况下推断特征对物种形成和灭绝的影响，从而推广了最近的二元状态物种形成和灭绝方法。我们的方法可以用于假设系统发育可以合理地视为现存物种的随机样本，或者所有现存物种都包括在内，但有些物种只被分配到未解决的末端分支中。我们使用模拟系统发育在贝叶斯框架内探索了系统发育分辨率降低对我们方法检测分化多样化能力的影响。由于物种形成率的不对称性引起的分化多样化，即使只有 50%的现存物种在系统发育上得到解决，也几乎可以与完整的系统发育知识一样得到很好的检测。我们使用涉禽（Charadriiformes）的性二态性和多样化分析来演示我们的未解决分支方法。我们的方法允许使用未解决的系统发育直接估计特征对物种形成和灭绝率的影响。
