A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics

by Albert C. Soewongsono & Michael J. Landis

Read the paper

Although diffusion approximations are widely used in population genetics, they remain underused for modelling phylogenetic diversification dynamics. We bridge this gap by establishing a general diffusion-based framework to study a wide and highly influential class of phylogenetics birth-death models, known as cladogenetic state-dependent-speciation-extinction (ClaSSE) models. We validate our diffusion-based framework is reliable under a variety of diversification scenarios. We also derive relationships between model rates and their stationary state frequencies. In summary, our work helps to formalize relationships between evolutionary state patterns, process rates, and mixing times for ClaSSE-type models.

(Upper panel) Relationships between different evolutionary scenarios with species richness at present; (Lower panel) Illustration of an event-based phylogenetic tree viewed as a diffusion-based frequency simulation.