Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.

ABSTRACT: There are numerous sources of variation in the rate of synonymous substitutions inside genes, such as direct selection on the nucleotide sequence, or mutation rate variation. Yet scans for positive selection rely on codon models which incorporate an assumption of effectively neutral synonymous substitution rate, constant between sites of each gene. Here we perform a large-scale comparison of approaches which incorporate codon substitution rate variation and propose our own simple yet effective modification of existing models. We find strong effects of substitution rate variation on positive selection inference. More than 70% of the genes detected by the classical branch-site model are presumably false positives caused by the incorrect assumption of uniform synonymous substitution rate. We

SUBMITTER: Davydov II 

PROVIDER: S-EPMC6526913 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature