Understanding the Tripartite Approach to Bayesian Divergence Time Estimation Elements of Paleontology Series

Placing evolutionary events in the context of geological time is a fundamental goal in paleobiology and macroevolution. In this Element we describe the tripartite model used for Bayesian estimation of time calibrated phylogenetic trees. The model can be readily separated into its component models: the substitution model, the clock model and the tree model. We provide an overview of the most widely used models for each component and highlight the advantages of implementing the tripartite model within a Bayesian framework.

1. Introduction; 2. A brief introduction to Bayesian inference in phylogenetics; 3. A tripartite model for divergence time estimation; 4. Substitution models; 5. Clock models; 6. Tree models for time-calibrated tree inference; 7. Expanding the potential of the tripartite model within the Bayesian framework; 8. Conclusions.