2.11 Detection of positive selective genes
Based on the phylogenetic tree, we estimated the rate ratio (ω) of
non synonymous(Ka ) to synonymous(Ks ) nucleotide
substitutions using the PAML (v4.9e) package (Yang, 2007) to examine the
selective constraints on candidate 678 single-copy orthologous genes.
After the high-quality alignments of related sequences were obtained as
described above, we compared a series of evolutionary models in the
likelihood framework using the species trees. A branch site model was
used to detect the average ω across the tree (ω0), ω of the appointed
branch to test (ω2), and ω of all of the other branches (ω1).