A2, Gossypium arboreum; AT, Allotetraploid Gossypium A-genome; contig, Contiguous DNA fragment; D5, Gossypium raimondii; dN, Nonsynonymous mutation rate; dS, Synonymous mutation rate DT, allotetraploid Gossypium D-genome; EST, Expressed sequence tag; NRHR, Nonreciprocal homoeologous recombination; SNP, Single nucleotide polymorphism.
Because processes operating at the DNA level, such as local mutation rate variation [9], should affect both dS and dN [10: p. 65] while natural selection on the protein should affects dN but not dS, and because protein-level selection is expected to vary across amino acid sites or protein domains, we expect dN to be more variable than dS [see also 3].
Because the average dS for extracellular (0.24) and intracellular (0.21) proteins differ by only 13.5% (fig. 1 B ), elevated mutation rate does not fully explain the difference in dN.
c The average rate (dN) of nonsynonymous substitutions (nucleotide mutations that alter the amino acid sequence) for all orthologous genes within a give COG role category is displayed, followed by the standard error that is represented in parentheses.
In contrast, the small subunit ribosomal protein genes had only an elevated dN, strongly suggesting a change in selective regime, and not underlying mutation rate has led to the elevated dN/dS ratio in these genes.
Surprisingly, the dN rate in Gaur is higher than Mithan, suggesting a faster mutation rate in this species.
Relative to other genes, ycf1 and ycf2 exhibit both an elevated dN and dS, though the increase in dN was greater than dS (2.5× and 1.5× higher respectively), suggesting that the underlying mutation rate, as well as potentially the selective regime, has been altered in the these genes.
Comparing dN, dS, and ω (dN/dS) to species-richness of clades allows us to separate the effect of mutation rate on net diversification from the effect of selection and effective population size.
Our data show a non-synonymous mutation rate of 0.00095496 and a synonymous mutation rate of 0.00024 resulting in a Dn/Ds ratio of 3.979, indicating strong positive selection for structural evolution of the adhesin gene yqi within the sequence type 95 complex.
