Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent.

ABSTRACT: The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes-Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating sp

SUBMITTER: Flouri T 

PROVIDER: S-EPMC9366188 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature