Third, the duplication may represent a precursor enhancing the likelihood of the substitution of a beneficial mutation through an increase in the mutational target and in local mutation rates.
However, it remains unclear whether this high recurrence reflects positive selection, because any factors not included in our background model of the mutational process, such as local mutation hotspots, could also explain a mild excess of mutations at a given nucleotide.
The λ- μ individuals that do not undergo recombination are then mutated, according to the local mutation operator m: I → I. Mutation is performed according to a non-isotropic self-adaptive mutation rule, in the sense that each individual i has associated with it a step size for mutation (a mutation rate) for each parameter j, denoted as.
Moreover, emerging concepts such as multi-parent crossover and local mutation are employed.
These observations excluded a higher local mutation rate as a major cause of greater diversity in human populations.
Thus we applied the NS to S ratio test to each gene, in cascade after that for the local mutation frequency (pAA) described above.
Hypothetically, several mutations affecting Wolbachia action in the host could also arise subsequently within one population (be it through occasional migrational influx or through actual local mutation).
For example, genetic change could be driven by local mutation, small-scale deletion or insertion of a particular sequence, or via major chromosomal changes, including whole-arm transposition and chromosome losses or duplications.
To determine if the greater nucleotide diversity was due to an increase in the local mutation rate, we evaluated the nucleotide differences in the 28.5 kb sequenced region by comparing one human sequence with one chimpanzee sequence retrieved from the UCSC genome browser.
Because processes operating at the DNA level, such as local mutation rate variation [9], should affect both dS and dN [10: p. 65] while natural selection on the protein should affects dN but not dS, and because protein-level selection is expected to vary across amino acid sites or protein domains, we expect dN to be more variable than dS [see also 3].
Consequently, the shortness of highly expressed genes could not be ascribed to local mutation bias.
