A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record.
Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magni...

古生物化石记录记载了多起大规模灭绝事件（mass extinction），这些事件曾严重削减生命之树的物种多样性。长期以来，生物学家一直致力于评估此类大灭绝事件对特定生物类群的影响程度。本研究提出了一种全新方法，可用于检测大灭绝事件对分子系统发育树（molecular phylogenies）的影响，即便存在全树范围的多样化速率变异，且缺乏化石记录提供的额外辅助信息时依然适用。

我们的方法基于幕式随机分支过程模型，该模型假设事件发生间隔内的物种形成速率与灭绝速率均保持恒定。我们将三类事件纳入建模范畴：(i) 物种形成速率的瞬时全树范围调整；(ii) 灭绝速率的瞬时全树范围调整；以及(iii) 瞬时全树范围的大规模灭绝事件。每一类事件均被建模为独立的复合泊松过程（compound Poisson process, CPP），事件间的等待时间服从指数分布，且各事件类型拥有专属的速率参数。The magni...