amino acid sequences indicators of evolution

A significant excess of nonsynonymous over synonymous substitution has been used as evidence for adaptive evolution (for a review, see Y ang and B ielawski 2000). If a nonsynonymous change makes the protein more or less fit on average then ω will be greater or less than 1, respectively. If a nonsynonymous mutation does not affect the fitness of a protein, it would become fixed within the population at the same rate as a synonymous mutation, giving a nonsynonymous/synonymous rate ratio (ω) of 1. Synonymous mutations do not change the encoded protein and so are often assumed to be selectively neutral. In particular, the ratio of the rates of nonsynonymous and synonymous fixation has been used to measure the level of selective pressure on proteins ( M cD onald and K reitman 1991, for example). We also show that the SLR method performs well even under circumstances where the results from some previous methods can be misleading.ĪNALYZING the instantaneous rate of nonsynonymous (amino acid-changing) and synonymous (silent) nucleotide substitutions in protein-coding molecular sequences can give important clues to understanding how they evolved. The increase in power is achieved while relaxing assumptions about how the strength of selection varies over sites and without elevated rates of false-positive results that have been reported with some other methods. We show that the SLR method can be more powerful than currently published methods for detecting the location of positive selection, especially in difficult cases where the strength of selection is low. This article describes the “sitewise likelihood-ratio” (SLR) method for detecting nonneutral evolution, a statistical test that can identify sites that are unusually conserved as well as those that are unusually variable. Several methods exist to detect the presence, and sometimes location, of positively selected sites in alignments of protein-coding sequences. An excess of nonsynonymous over synonymous substitution at individual amino acid sites is an important indicator that positive selection has affected the evolution of a protein between the extant sequences under study and their most recent common ancestor.

Amino acid sequences indicators of evolution