Phylogenetic inference under recombination using Bayesian stochastic topology selection.

ABSTRACT:

Motivation

Conventional phylogenetic analysis for characterizing the relatedness between taxa typically assumes that a single relationship exists between species at every site along the genome. This assumption fails to take into account recombination which is a fundamental process for generating diversity and can lead to spurious results. Recombination induces a localized phylogenetic structure which may vary along the genome. Here, we generalize a hidden Markov model (HMM) to infer changes in phylogeny along multiple sequence alignments while accounting for rate heterogeneity; the hidden states refer to the unobserved phylogenic topology underlying the relatedness at a genomic location. The dimensionality of the number of hidden states (topologies) and their structure are random (

SUBMITTER: Webb A 

PROVIDER: S-EPMC2639012 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature