The similar genetic distance reported in this study suggests that H. armigera and H. zea are more closely related to each other than the case with the Busseola fusca species, possibly due to a more rapid divergence rate.
In a comparison with the sequences from coelacanth, a species with both NPDC1L and NPDC1 (to control for lineage-specific differences in divergence rate), the dogfish sequence was clearly more similar to NPDC1L than to NPDC1, indicating that its clustering with NPDC1L in the consensus trees was not simply due to more rapid divergence from an ancestral NPDC1-like sequence.
If stronger discrimination were favoured by selection, the prediction based on this finding is more rapid future divergence than if the genes were spread evenly across chromosomes.
Thus, the second mini-clade underwent a more rapid evolutionary divergence process compared to the first one.
Gene tatA has a paralog tatE (bd2196 in HD100), [ 23] likely allowing more rapid sequence divergence of tatA as evidenced by the high omega score.
Just as genes involved in different biological pathways have been observed to evolve at the sequence level at different rates (Aris-Brosou 2005; Wolf et al. 2006), certain classes of genes may show more rapid functional divergence.
This result is consistent with the finding that the intergenic DNA flanking centromeres shows more rapid evolutionary divergence than other intergenic regions in S. paradoxus [ 5], and the observation that centromere flanking DNA also fails to align between Saccharomyces species (see Additional file 1, Figures S1 and S2).
By contrast, if higher net diversification was an outcome of elevated mutation rates causing more rapid reproductive isolation and divergence, then we would expect to observe positive relationships between all measures of substitution rate and clade size, but not necessarily a relationship between ω and clade size [ 5].
The rate of evolution of genes expressed in testis and accessory gland tissue should be greater compared with those expressed in body tissue because sexual selection is expected to act more strongly on, and cause rapid divergence in, gene products expressed in the context of mating, for example, proteins produced in the accessory glands (Walters and Harrison 2008, 2010; Wolfner 2002).
More generally, we should note that rapid divergence of many components of the CRISPR-Cas systems including most of the RAMPs certainly is their salient and important feature.
Although it operates in the same molecular pathways as the other USPs, the rapid divergence of the more recently generated USP11 enzyme precludes its functional interchangeability with USP4 and USP15.
