When both pairwise divergence and the proportion divergent TFBS/miRNA target sites are taken into account, we find that regions that exhibit statistically significant divergence are not necessarily those regions that exhibit greater pairwise sequence divergence.
Thus, if adaptation is mutation limited, rates of adaptation are expected to be higher in species with larger N e, and given the higher efficacy of selection against mildly deleterious mutations, so is the proportion of divergence attributable to positive selection relative to mildly deleterious or neutral mutations.
These analyses revealed that dominant morphs are associated with highly divergent haplotypes of this gene in P. dardanus, with a large proportion of the divergence occurring at non-synonymous sites, but not in other species.
Therefore, we investigated why KB(m) did not increase in proportion to the divergence time of alleles (m).
Third, the proportion of nucleotide divergence attributable to the presence of an indel decreases over time, indicating that indels cause a short burst of nucleotide diversity but only transiently (McDonald et al. 2011).
Given the general observation that a substantial proportion of protein divergence is adaptive in Drosophila (Smith and Eyre-Walker 2002; Fay et al. 2002; Begun et al. 2007; Langley et al. 2012), one interpretation of increased dN/ dS ratio on the X is more adaptive protein evolution on the X chromosome.
In each region we compare the proportion of divergent TFBS/miRNA target sites with the amount expected given the over-all sequence divergence of the opsin BACs and introns (a measure of neutral evolutionary divergence [ 42, 43]).
Furthermore, the proportion of total expression divergence between parents explained by trans-effects (% trans) increased with the magnitude of divergence (fig. 3 B).
Lastly, we assigned each orthologous pair to one of three categories based on its level of divergence (or proportion amino acids that differ): High (≥0.138), Intermediate (<0.138 and >0.058) and Low (≤0.058) divergence, with bin cutoffs empirically determined so that one-third of transcripts fall into each category.
In summary, an increased overlapping proportion causes a higher divergence between the SS and NSS libraries.
