Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data.

ABSTRACT: Estimation of natural selection on protein-coding sequences is a key comparative genomics approach for de novo prediction of lineage-specific adaptations. Selective pressure is measured on a per-gene basis by comparing the rate of nonsynonymous substitutions to the rate of synonymous substitutions. All published codon substitution models have been time-reversible and thus assume that sequence composition does not change over time. We previously demonstrated that if time-reversible DNA substitution models are applied in the presence of changing sequence composition, the number of substitutions is systematically biased towards overestimation. We extend these findings to the case of codon substitution models and further demonstrate that the ratio of nonsynonymous to synonymous rates of substi

SUBMITTER: Kaehler BD 

PROVIDER: S-EPMC5381540 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature