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, positiv...仅包含现生物种的时间校准系统发育树（time-calibrated phylogenies）已被广泛用于探究物种形成与灭绝的动态演化规律。拉博斯基（Rabosky，2010）曾在其研究中对系统发育灭绝估计的可靠性提出质疑，并指出未被纳入考量的物种形成速率异质性可能会导致灭绝估计值出现正向偏倚。在近期的一篇学术论文中，博利厄与奥米拉（Beaulieu和O'Meara，2015）准确指出了我2010年研究中存在的若干技术错误，并得出结论：在一系列模型参数设定下，系统发育灭绝估计结果对物种形成速率异质性具有稳健性。本文证明，博利厄与奥米拉低估了真实系统发育中物种形成速率变异的幅度，因此未在其模拟实验中纳入具备生物学意义的速率异质性水平。基于从近期学术文献中提取的参数值，本文发现，当物种形成速率仅存在中等程度的异质性时，便会产生一致的正向……