Synonymous mutation, the basis of the evolution of codon usage, are clearly the kind of "nearly neutral" mutations that likely play a large role in molecular evolution [ 57].
Nevertheless, the recent evolution of codon usage in the Drosophila saltans complex shows that major evolution of codon usage could occur (Rodriguez-Trelles et al. 1999; Singh et al. 2006).
While the phylogenetic relationships of selenoprotein families and the evolution of selenocysteine usage are well documented, the evolutionary history of SECIS binding proteins has not been explored.
The patterns appear to be lineage-specific and evolutionarily labile (i.e., strong preferences for a particular control region are widely dispersed on the tree), which may indicate rapid evolution of the strength of the replication-associated substitution gradient (as suggested in primates [ 3]) or rapid evolution of differential usage of the two control regions.
There is no evidence that the codon usage bias drives the evolution of tRNA anticodons or the tRNA anticodon bias drives the evolution of codon usage in marine bivalve mitogenomes.
Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments.
As host choice is hypothesized to drive the evolution of specialization (Whitlock 1996; Kawecki 1998), the genetics of host preference is particularly relevant to the evolution of host usage in Nasonia.
A bias favoring G and T is also visible in the third codon positions of protein-coding genes and the wobble sites of anticodons, rejecting that codon usage bias drives the wobble sites of tRNA anticodons or tRNA anticodon bias drives the evolution of codon usage.
Currently, few data are available about the genomic traits and evolution of N. tetrasperma and N. discreta, including the evolution of codon usage in gene coding DNA.
The evolution of codon usage bias has been studied extensively in many organisms, notably prokaryotes (Shah and Gilchrist 2010; Supek et al. 2010) and Drosophila (Akashi 1994, 1995, 1996; Heger and Ponting 2007).
