Reading tree leaves: inferring speciation anfd extinction processes using phylogenies

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

The birth–death process (BDP) is widely used in evolutionary biology as a model for generating phylogenetic trees of species. generalized (GBDP) allows rate variation over time, with speciation and extinction rates to be arbitrary functions time. Here we review the probability theory underpinning GBDP cladogenesis recent findings concerning its identifiability. continuous has been shown non-identifiable from lineage-through-time data: even species phylogenies infinite size parameters cannot estimated. However, restricted class BDPs piecewise-constant identifiable. We illustrate these results using simple examples discuss their implications biologists interested inferring past tempo mode evolution reconstructed trees. This article part theme issue ‘“A mathematical evolution”: models dating back 100 years’.

Language: Английский

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

Bulletin of Mathematical Biology, Journal Year: 2024, Volume and Issue: 86(8)

Published: July 6, 2024

Language: Английский