Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach.
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach.
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DOI：
10.1093/sysbio/syaa048
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发表时间：
2021-02-10
影响因子：
6.5
通讯作者：
Etienne RS
中科院分区：
文献类型：
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作者：
Laudanno G;Haegeman B;Rabosky DL;Etienne RS
一般认为，分子生物学的分支模式包含了潜在的物种形成和灭绝过程的信息。简单的出生-死亡模型与常数，随时间变化，或多样性依赖的利率已被调用来解释这些模式。他们有一个共同的假设：在给定的时间点上，所有的谱系都有相同的多样化率。然而，系统发育树中各个亚支的多样化率似乎可能存在差异。这激发了模型的构建，允许跨多个利率制度，这些制度之间的瞬时转换。存在几种方法来计算的可能性下一个特定的映射多样化制度和执行推理的最有可能的多样化的历史，产生了一个特定的系统发育树的一个同源性。在这里，我们表明，这些方法的似然计算是不正确的。我们提供了一个新的框架来正确计算的可能性，并显示，与模拟的一个单一的转变，正确的可能性确实导致参数估计，平均更好地与生成参数比不正确的可能性。此外，我们表明，我们的校正后的似然可以扩展到多个利率变化的时间依赖和多样性依赖的模型。我们认为，确定多样化率的变化是一个不平凡的模型选择练习，人们必须选择是否考虑到现在灭绝的血统的变化。因此，我们的框架也解决了最近关于这种未观察到的变化的争论。[多样化;宏观进化;物种发生;物种形成]
The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth–death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation]