Consistent with this expectation, estimates of fitness from comparative genomics suggest that synonymous sites are under weak purifying selection13,14,15, although a recent study suggests that up to 22% of synonymous sites in the Drosophila melanogaster genome may be under strong purifying selection16.
In addition to positive selection, 158 sites were identified to be under strong purifying or negative selection (Figure 2B).
One out of the three investigated protein coding genes psbA appeared to be under strong purifying selection in Schiedea, showing no non-synonymous and only eight synonymous substitutions (Table 2).
Since many amino sites might be under strong purifying selection due to functional constraint (dN/dS≈zero) and positive selection often operates episodically on a few amino acid sites [47], it seems likely that this is a more conservative test and amino acid sites under positive selection cannot be detected.
More than 85% of the genes were found to be under strong purifying selection, six genes to have a neutral evolution, while the 11 genes with the highest Ka/Ks values seemed to be evolving under positive selection or relaxed selective constraint.
Specifically, Mytilus spp. COX1 residues were all found to be under strong purifying selection whereas of the 165 amino acid positions in the F-ORF-VD1 alignment portion, 125 residues (76%) were found under purifying selection, 5 (3%) were under neutral selection and 35 (21%) were found to possess a Ka/Ks>1, indicating positive selection.
Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions.
American subtype B viruses also appear to be under stronger purifying selection (ω = 0.43 0.58) than the Thai subtype B viruses (0.78).
This indicates that among vertebrates, genes with HCP are likely to be under stronger purifying selection pressure than genes with LCP.
Nonsynonymous mutations are expected to be under stronger purifying selection than changes at synonymous or noncoding sites because they alter the encoded protein and may be deleterious.
