Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.

ABSTRACT: Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework that offers great modeling flexibility in drawing inference about any discrete data type characterized as a continuous-time Markov chain, including phylogeographic trait

SUBMITTER: Bielejec F 

PROVIDER: S-EPMC4055869 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature