The intraspecific and intra-population stability of rRNA locus on one hand and relatively fast evolution of ITS1 and ITS2, which are under lower selective pressure, made the ITS one of the most popular marker in phylogenetic studies [17], [19] [21].
Nucleotides that are under lower selective constraint might be expected to have higher substitution rates, and thus may be expected to have more alleles across populations.
Highly expressed proteins are well known to be under stronger selective pressures than proteins expressed at lower levels and therefore to be significantly less variable across species (Drummond et al. 2005; Larracuente et al. 2008).
Comparisons of Bsu- ebrA and Bsu- ebrB together or with other chromosomal ebrA/ ebrB homologues demonstrated that both sequences are maintained under slightly lower selective pressures (dS/dN values of 1.0 4.1), but not when compared to integron encoded Qac homologues (dS/dN values of 4.5 5.6) (Additional file 2).
The proportion of polymorphic sites (Table 1, last column) is similar among protein coding genes and lower for RNA coding genes, which are under more selective constraint.
This idea is also corroborated by the fact that highly expressed miRNAs are under intense selective pressure to maintain sequence uniformity while lowly expressed miRNAs tend to have much lower selection pressure being more prone to evolve rapidly [ 44].
(c) Genes that remain GCO have on average significantly lower Ka/Ks ratio than the nGCO ones, indicating that they are under higher selective pressure (Fig. 2).
That is, compared to the genome-wide levels of selective pressure, genes that were identified as involved in cold response based on functional studies (i.e., CRG genes) displayed significantly lower levels of selective pressure, while cold responsive (CGO) genes were under more selective constraints.
Interestingly, the significantly lower short intron GC content in nonrecombining compared with RA genes suggests that short introns in recombining regions are under some selective constraints, contrary to what is often assumed (Halligan and Keightley 2006; Parsch et al. 2010).
