Data from: Estimating speciation and extinction rates for phylogenies of higher taxa

Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time xcut, and fully unresolved thereafter, so that for all subclades, stem age > xcut > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.物种形成与灭绝速率可通过分子系统发育（molecular phylogenies）进行估算。近期已有多项方法问世，表明即便系统发育存在不完全性——即未囊括所有现存物种时，此类速率仍可被估算。我们的研究表明，此类方法的准确性高度依赖于对采样过程所遵循规则的正确假设。 我们聚焦于因部分亚支（subclades，如属与科）均以单一支系形式呈现而导致不完全的系统发育。此前的方法默认，此类亚支的定义方式为：从完整的物种种系发育树中随机（或极端确定性地）选取界定亚支的分支。我们证明，若高级分类单元的定义方式与此不同，则此类方法将产生有偏结果。 我们引入严格高阶系统发育（strict higher level phylogenies）的概念：此类系统发育中，亚支的定义需满足整个发育树从起源至时间截点x_cut处完全解析，此后则完全未解；即对于所有亚支而言，其茎龄（stem age）均大于x_cut，而x_cut又大于其冠龄（crown age）。 我们基于应用了该亚支定义规则的鸟类系统发育数据，估算了物种形成与灭绝速率。然而，文献中绝大多数高阶系统发育的高级分类单元定义方式尚不明确，但这类系统发育通常可被便捷地转换为严格高阶系统发育——我们通过对近乎完整但仅部分解析的哺乳类物种级系统发育进行物种形成与灭绝速率估算，对此进行了演示。最后，我们通过模拟实验验证了所提方法的准确性。