Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.

ABSTRACT: We present a new phylogenetic approach, selection on amino acids and codons (SelAC), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models that assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein-coding DNA under the assumption of consistent, stabilizing selection using a cost-benefit approach. This cost-benefit approach allows us to generate a set of 20 optimal amino acid-specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate. Using a yeast data set of 100 orthologs for 6 taxa, we find SelAC fits the data much better than popular models

SUBMITTER: Beaulieu JM 

PROVIDER: S-EPMC6445302 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature