TOTAL-EVIDENCE BAYESIAN INFERENCE OF PAST DIVERSITY: THE OCCURRENCE BIRTH-DEATH PROCESS

Phylodynamic methods in macroevolution generally aim at jointly inferring phylogenetic relationships, model parameters (e.g. speciation and extinction rate), and more recently the past number of species (diversity) through time for clades of interest. In recent years, these methods have seen the rise of a total evidence trend, aiming at combining molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even fossils lacking morphological data and characterized only by their sampling time, which we call occurrences, provide invaluable information to reconstruct past population sizes

Here, we build on recent methodological developments around the Fossilized Birth-Death Process enabling us to (i) efficiently incorporate occurrence data while remaining computationally tractable and scalable; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct past population sizes, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.

We finally illustrate the method on an empirical case study of cetaceans, inferring the diversity trajectory using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. Our results highlight the benefit of using a model-based phylodynamic framework to jointly integrate all available data and explicitly take into account key features of clades' macroevolutionary history.