2.13 Positive selection genes
Proteins from 14 species were subjected to all paired alignment using Blastp (e value <= 1e-5), and orthologous genes were inferred from the aligned results. Positive selection occurs when the number of non-synonymous substitutions divided by the number of synonymous substitutions for each site (ꞷ) is greater than 1. Positive selection is common in amino acid-level changes to determine functional constraints on proteins (Fay & Wu 2003). To identify the positive selection genes of C. undulatus , the average ꞷ among orthologous genes was calculated using Codeml in the PAML package (Yang 1997) with the branch-site model. A likelihood ratio test was conducted on each model pair to determine whether there were significant positive selection genes.