Data from: Challenges in the estimation of extinction from molecular phylogenies: a response to Beaulieu and O'Meara

Time-calibrated phylogenies that contain only living species have been widely used to study the dynamics of speciation and extinction. Concerns about the reliability of phylogenetic extinction estimates were raised by Rabosky (2010), where I suggested that unaccommodated heterogeneity in speciation rate could lead to positively biased extinction estimates. In a recent article, Beaulieu and O'Meara (2015) correctly point out several technical errors in the execution of my 2010 study and concluded that phylogenetic extinction estimates are robust to speciation rate heterogeneity under a range of model parameters. I demonstrate that Beaulieu and O'Meara underestimated the magnitude of speciation rate variation in real phylogenies and consequently did not incorporate biologically meaningful levels of rate heterogeneity into their simulations. Using parameter values drawn from the recent literature, I find that modest levels of heterogeneity in speciation rate result in a consistent, positive bias in extinction estimates that are exacerbated by phylogenetic tree size. This bias, combined with the inherent lack of information about extinction in molecular phylogenies, suggests that extinction rate estimates from phylogenies of extant taxa only should be treated with caution.

仅包含现生物种的时间校准系统发育树（time-calibrated phylogenies）已被广泛应用于物种形成与灭绝动态的相关研究。Rabosky（2010）曾针对系统发育灭绝估计（phylogenetic extinction estimates）的可靠性提出质疑，其研究指出，未被模型纳入的物种形成率异质性（speciation rate heterogeneity），可能会使灭绝估计值产生正向偏差。在近期发表的一篇论文中，Beaulieu与O'Meara（2015）准确指出了本文作者2010年研究中存在的多项技术瑕疵，并得出结论：在一系列模型参数设定下，系统发育灭绝估计对物种形成率异质性具备稳健性。本文证明，Beaulieu与O'Meara低估了真实系统发育树中物种形成率变异的幅度，因此未在其模拟实验中纳入具备生物学意义的异质性水平。通过采用近期文献中的参数值开展分析，本文发现，适度的物种形成率异质性会使灭绝估计值持续出现正向偏差，且该偏差会随系统发育树规模的扩大而加剧。结合分子系统发育树中本就缺乏灭绝相关信息这一局限，上述偏差表明，仅基于现生类群（extant taxa）的系统发育树所得到的灭绝率估计值，应当审慎对待。