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Article Dans Une Revue Systematic Biology Année : 2023

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

Hélène Morlon

Résumé

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 inference. 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 example of the full inference, using a dataset of cetaceans.
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Origine : Publication financée par une institution
Licence : CC BY - Paternité

Dates et versions

hal-04378658 , version 1 (08-01-2024)

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Paternité

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Joëlle Barido-Sottani, Hélène Morlon. The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2. Systematic Biology, 2023, 72 (5), pp.1180-1187. ⟨10.1093/sysbio/syad027⟩. ⟨hal-04378658⟩
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