The phenomenon examined here has probably been formed by long-term evolutionary selection, which introduced functional divergence among the AMP families and even within their paralogs, and established the broad antimicrobial spectrum of the immune system.
This indicates that gene expression levels of this biological system have been modulated by long-term evolutionary forces.
Synonymous substitution rates within the hominid malaria clade were similar across all levels of conservation but non-synonymous substitution rates were strongly influenced by long-term evolutionary context.
The region of the genome containing the mating-type locus in M. lychnidis-dioicae has likely been shaped by long-term evolutionary processes, in contrast to fungi suggested to serve as models for the early evolution of sex chromosomes of plants and animals (Fraser and Heitman 2004; Menkis et al. 2008).
Angiosperms, for example, are similar to diatoms in both taxonomic diversity and geologic age, but with just a few noteworthy exceptions (Cai et al. 2008; Sloan et al. 2012), their plastid genomes are characterized by long-term evolutionary stasis (Jansen and Ruhlman 2012).
We propose that the drift to an AT-rich genome might be induced as a long term evolutionary adaptation to this over-stabilization by magnesium and can be balanced by lowering the GC content of the genome.
By thus affecting the selective challenges faced by the organism, the evolutionary feedback loop can turn short-term hereditary effects, that would not survive many generations, into long term evolutionary change.
Thus, the phylogeny may be less accurate for long term evolutionary events due to a past history of extensive recombination, but nevertheless, it appears to recapitulate the short term evolution detected by goeBURST.
It is thus a key issue for interpreting short and long term evolutionary patterns to identify whether main directions of phenotypic variance indeed constitute direction of facilitated evolution, and whether this is favored by developmental processes preferably generating certain phenotypes.
