Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated.

ABSTRACT:

Motivation

As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates.

SUBMITTER: Barba-Montoya J 

PROVIDER: S-EPMC7773479 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature