Positive selection
All sequences of these single-copy genes were aligned using MUSCLE
software (Edgar 2004a,
b) with default parameters. To estimate
the lineage-specific evolutionary rate of each branch, the free model
(“model = 1, NSsites = 0”) in codeml was used. After we obtained a
general evolutionary pattern of selective pressure along the lineages,
the branch-site model was used. We used the likelihood ratio test and
Chi-square test to calculate the P-value , and any positively
selected genes with P-values less than 0.05 were retained.