Third, we fitted a branch-site model to test for the presence of codons showing purifying selection on within-class branches (dN/dS ratio < 1) but evolving either neutrally or by positive selection on between-class branches (dN/dS ratio ≥ 1) [ 46].
We hypothesize that large FST estimates for MHC SNPs One_MHC2-1900 FST = 0.434; One_MHC2-251 FST = 0.387) in comparison with putatively neutral loci are consistent with signatures of diversifying selection; such force is expected to drive adaptive mutations and tightly linked sites to fixation by positive selection, hence increasing differentiation between populations [ 33].
Approximately 20% amino acid changes between chicken and zebra finch have been fixed by positive selection [ 8], so by comparing coding sequences (CDS) between these birds, chicken genes with signals suggestive of adaptation can be identified.
Since both methods depends heavily on the fraction of the genome that has been affected by positive selection, we allowed this fraction to vary between 0 and 0.1, reporting the corresponding range of values for power, false positive rates, and false discovery rates.
Similarly, studies of the sperm receptor lysin and its egg ligand VERL in Haliotis revealed a strong excess of nonsynonymous to synonymous divergence (d N /d S ) between species driven by positive selection and concerted evolution [ 22, 23], making it one of the fastest evolving metazoan proteins known.
This would imply that differences between populations should be driven by positive selection to new environmental conditions.
Thus, roughly half of the protein divergence between D. miranda and D. pseudoobscura is driven by positive selection.
This analysis emphasizes that divergence between cystatin copies from the same wasp species occurred by positive selection.
We found that both core and accessory genes are subject to evolution by positive selection, most likely in the form of diversifying selection resulting from the antagonistic interaction between host and parasite.
