Phylogenetic inference of changes in amino acid propensities with single-position resolution.

ABSTRACT: Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a pr

SUBMITTER: Klink GV 

PROVIDER: S-EPMC9106220 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature