We reasoned that these functional classes of V2R would likely be under divergent selective pressures within and between species/subspecies of mouse.
For these analyses, we compared 1) clade model D to sites model M3, which allows a class of sites to be under divergent selective pressure between foreground branches and the rest of the tree, and 2) modified Model A, which includes an extra class of sites under positive selection with ω > 1 in the foreground branches, to the null model A, in which the last site class has ω = 1.
We describe complex patterns of non-random sequence variation that indicate these receptors are under divergent selective pressures that correlate with proposed ligand, phylogeny, chromosomal clustering, and protein domain.
Clade model C showed 79%and62%2% of sites are under divergent selection in OBPs and CSPs, respectively.
In the absence of population structure, these correlations suggested that the alleles are under divergent selection.
Thus, different patterns of diversity, divergence, and phylogenetic clustering may be evident when comparing regions under divergent selective forces.
Using this model, which we call the 'CmC αβMVR & ββ' model, it was estimated that approximately 21% of the data set evolved under divergent selective constraint, with a ω ratio less than one along the outgroup branches (ω2 = 0.50), slightly above one along the αβMVR branches (ω3 = 1.09), and substantially higher along the βT branches (ω4 = 2.61) (Table 2).
Using this model, which we call the 'CmC α & β' model, it was estimated that approximately 21% of the data set evolved under divergent selective constraint across the three partitions, with a ω ratio less than one along the outgroup branches (ω2 = 0.50), slightly above one along the RH2aα branches (ω3 = 1.13), and somewhat higher still along the RH2aβ branches (ω4 = 1.54) (Table 2).
Finally, the clade model (Table 3) is a combination of branch and site models and allows investigating specifically the presence of sites evolving under divergent selective pressures between the paralogous genes and quantify its proportion.
CG can be an adaptive response by which organisms buffer environmental variability (Ali et al. 2003), and it may have co-evolved with a suite of phenotypic traits under divergent selective regimes (Fraser et al. 2007).
These results revealed, for each pair, the presence of sites evolving under divergent selective pressures between the paralogous gene clades.
