Abstract

A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.

Highlights

  • Perhaps the most general feature of biological diversity on Earth is the extent to which it varies - either through space, through time, or among different kinds of organisms

  • Paleontological evidence indicates that species richness has undergone dramatic changes during the past 550 million years [1,2]

  • The causes of phylogenetic, temporal, and spatial variation in species richness are thought to reside in the evolutionary processes of speciation and extinction

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Summary

Introduction

Perhaps the most general feature of biological diversity on Earth is the extent to which it varies - either through space, through time, or among different kinds of organisms. Within vertebrates, lineages such as tetrapods (22000+ species), therian mammals (5000+ species), and teleosts (30000+ species) are several orders of magnitude more diverse than their respective sister clades (lungfishes, 6 species; monotremes, 5 species; holosteian fishes, ,10 species). This phylogenetic variation in species richness is mirrored by analogous variation in diversity through time. There has been great interest in studying historical patterns of species diversification through time, towards understanding how and why speciation and extinction rates might vary through time, through space, and among clades [5,6,7,8,9]

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