Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.

摘要: The nonsynonymous (amino acid–altering) to synonymous (silent) substitution rate ratio (ω= d N/d S) provides a measure of natural selection at the protein level, with ω= 1,> 1, and< 1, indicating neutral evolution, purifying selection, and positive selection, respectively. Previous studies that used this measure to detect positive selection have often taken an approach of pairwise comparison, estimating substitution rates by averaging over all sites in the protein. As most amino acids in a functional protein are under structural and functional …