The effectiveness of selection in a species affects the direction of amino acid frequency evolution.

ABSTRACT: Nearly neutral theory predicts that species with higher effective population size Ne are better at purging slightly deleterious mutations. We compare evolution in high- Ne vs. low- Ne vertebrates to reveal subtle selective preferences among amino acids. We take three complementary approaches. First, we fit non-stationary substitution models using maximum likelihood, comparing the high- Ne clade of rodents and lagomorphs to its low- Ne sister clade of primates and colugos. Second, we compared evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and Ne . Third, we dissected which amino acids substitutions occurred in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enabled comparison to a historical paper. All methods

SUBMITTER: McShea H 

PROVIDER: S-EPMC11212923 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature