Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence.
BACKGROUND
Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (d(N)) to synonymous nucleotide divergence (d(S)). That is, the more a mutation changes protein function, the more likely it is to be either selected against or selectively favored, and because the d(N)/d(S) ratio is a measure of natural selection, this ratio can be used to predict the degree of functional divergence (d(F)). However, these hypotheses have rarely been experimentally tested.


RESULTS
I present a novel method to address this issue, and demonstrate that divergence in bacteria-killing activity among animal antimicrobial peptides is positively correlated with the log of the d(N)/d(S) ratio. The primary cause of this pattern appears to be that positively selected substitutions change protein function more than neutral substitutions do. Thus, the d(N)/d(S) ratio is an accurate estimator of adaptive functional divergence.


BACKGROUND
tennessj@science.oregonstate.edu


BACKGROUND
Supplementary data, including GenBank Accession numbers, are available at Bioinformatics online.
Tennessen
Jacob A
JA
Department of Zoology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA. tennessj@science.oregonstate.edu
D000595:Amino Acid Sequence; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry* / Q000235:genetics*; D001483:Base Sequence; D003198:Computer Simulation; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D012641:Selection, Genetic; D013223:Statistics as Topic
D023181:Antimicrobial Cationic Peptides