Extinction can be estimated from moderately sized molecular phylogenies

Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. While it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree estimates of the extinction fraction (i.e., extinction rate/speciation rate) will appear strongly bimodal, with a peak suggesting no extinction and a peak implying speciation and extinction rates are approaching equality. On the basis of these results, and the realistic nature of this form of rate variation, it is now generally assumed by many practitioners that extinction cannot be understood from molecular phylogenies alone. Here we reevaluated and extended the analyses of Rabosky (2010) and come to the opposite conclusion – namely, that it is possible to estimate extinction from molecular phylogenies, even with model violations due to heritable variati...

已有数百项研究致力于从现生物种的系统发育树（phylogeny）中估算物种形成速率与灭绝速率。长期以来学界已知，仅依靠现生类群的系统发育树估算灭绝率往往存在较大不确定性，但Rabosky（2010）发表的一篇颇具影响力的论文提出：当物种形成速率在系统发育树上连续变化时，灭绝比例（即灭绝速率与物种形成速率的比值）的估算结果会呈现显著的双峰分布，其中一个峰值对应无灭绝的情景，另一个峰值则暗示物种形成速率与灭绝速率趋近相等。基于这一研究结果以及这种速率变异模式的现实合理性，当前许多研究者普遍认为，仅依靠分子系统发育树无法推断灭绝事件。本文重新评估并拓展了Rabosky（2010）的分析，得出了截然相反的结论——即即便存在由遗传变异引发的模型偏差，依然可以通过分子系统发育树估算灭绝速率。