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This might not be so surprising being most probably the reflection of the evolutionary rates of change in the DNAs of each lineage (seen, for instance, as branch lengths in phylogenetic analysis).
Therefore, on its own, this phylogenetic reconstruction cannot be taken as a reliable reflection of the evolutionary history of these genes and it was not possible to analyze the concordance/congruence between the larger groups described above for the EI topology and their HPr counterparts.
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Some more reflection on the evolutionary processes, patterns and theoretical consequences would be useful for this question.
Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity.
This is probably a reflection of the increased evolutionary rate of the sponge, Amphimedon queenslandica, the parasitic nematodes; Clonorchis sinensis and Schistosoma mansoni (Tsai et al. 2013), and the tunicate Oikopleura dioica (Denoeud et al. 2010).
Therefore, it is probable that the expression of the DUB/USP17 genes is tightly controlled and their existence within a highly polymorphic sequence is not so much a reflection of the selective evolutionary pressures on these genes, but a consequence of the unstable and copy number variable region of the genome in which they have evolved.
The recent proven ability of A. crassus to exploit new, phylogenetically well-separated hosts may be a reflection of this evolutionary propensity for switching.
This perhaps is a reflection of the ecological or evolutionary pressures exerted on planktonic cyanobacteria.
Why repeats are enriched in certain intergenic regions and whether they are related to developmental variations of caecilians or just a reflection of the relaxation of evolutionary constraints remains unknown.
Indeed, the high degree of conservancy found between the salivary transcripts of P. perniciosus from Spain and Italy may be a reflection of little evolutionary pressure from the host immune response on the analyzed salivary proteins in contrast with previous observations of maxadilan.
We therefore hypothesize that genotype-specific clinical response rates to interferon-based therapies are a reflection of HCV evolutionary adaptations to the immune system.
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