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. 15 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 non-trivial 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.

中文翻译：

---

检测多样化中特定于谱系的转变：一种适当的似然方法

通常假设分子系统发育的分支模式包含有关潜在物种形成和灭绝过程速率的信息。已经调用了具有恒定、时变或多样性相关速率的简单生死模型来解释这些模式。他们有一个共同的假设：所有谱系在给定的时间点都具有相同的多样化率。然而，系统发育树中的子分支之间的多样化率似乎存在差异。这激发了模型的构建，该模型允许跨系统发育的多个速率机制，并在这些机制之间进行瞬时转换。存在几种方法来计算特定的多样化制度映射下的系统发育的可能性，以及对产生特定系统发育树的最可能的多样化历史进行推断。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似然性，并通过模拟单班次表明，正确的似然性确实导致参数估计与生成参数的平均一致性比不正确的似然性好得多。15 此外，我们表明我们的校正似然可以扩展到时间相关和多样性相关模型中的多个速率变化。我们认为，识别多样化率的变化是一项重要的模型选择练习，必须选择是否考虑现已灭绝的谱系的变化。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。