A GENERAL MULTIPROCESS DIVERSIFICATION MODEL FOR PALEONTOLOGICAL AND MOLECULAR PHYLOGENETIC DATA

Time-calibrated phylogenies of living species only have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification — extinction rates in particular — can be misleading in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of living and extinct species. Our model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The model we describe is a more general version of the birth-death process as typically applied to phylogenies of extant species only, and the framework can thus be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both living and extinct taxa.