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.