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.仅包含现存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的动态过程研究。2010年，拉博斯基（Rabosky, 2010）首次对系统发育灭绝估计的可靠性提出质疑，其研究指出，未被校正的物种形成速率异质性，会导致灭绝速率估计值产生正偏倚。近期，博利厄与奥米拉（Beaulieu and O'Meara, 2015）在一篇学术文章中，准确指出了我2010年研究中存在的多项技术疏漏，并得出结论：在多组模型参数范围内，系统发育灭绝估计对物种形成速率异质性具备稳健性。本文证明，博利厄与奥米拉低估了真实系统发育树中物种形成速率变异的幅度，因此其模拟实验未纳入具备生物学意义的速率异质性水平。通过采用近期学术文献中的参数取值，本文发现，适度的物种形成速率异质性会使灭绝估计值持续呈现正偏倚，且该偏倚会随系统发育树的规模增大而加剧。结合分子系统发育树中固有的灭绝信息缺失问题，这种偏倚表明：仅基于现存类群系统发育树得到的灭绝速率估计值，应当被谨慎对待。