The ClaDS rate‑heterogeneous birth–death prior for full phylogenetic inference in BEAST2

Abstract

Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process that gives rise to the phylogeny. Existing birth–death diversification models include a wide range of features, for instance, lineage‑specific variations in speciation and extinction (SSE) rates. While across‑lineage variation in SSE rates is widespread in empirical datasets, few heterogeneous rate models have been implemented as tree priors for Bayesian phylogenetic infer‑ ence. As a consequence, rate heterogeneity is typically ignored when reconstructing phylogenies, and rate heterogeneity is usually investigated on fixed trees. In this paper, we present a new BEAST2 package implementing the cladogenetic diversification rate shift (ClaDS) model as a tree prior. ClaDS is a birth–death diversification model designed to capture small progressive variations in birth and death rates along a phylogeny. Unlike previous implementations of ClaDS, which were designed to be used with fixed, user‑chosen phylogenies, our package is implemented in the BEAST2 framework and thus allows full phylogenetic inference, where the phylogeny and model parameters are co‑estimated from a molecular alignment. Our package provides all necessary components of the inference, including a new tree object and operators to propose moves to the Monte‑Carlo Markov chain. It also includes a graphical interface through BEAUti. We validate our implementation of the package by comparing the produced distributions to simulated data and show an empirical exam‑ ple of the full inference, using a dataset of cetaceans.