2.10 Gene family expansion and contraction analysis
Based on the identified gene families and the constructed phylogenetic
tree with the predicted divergence time of those fish, we used CAFE (Han
et al., 2013) to analyze gene family expansion and contraction. In CAFE,
a random birth and death model was proposed to study gene gain or loss
in gene families across a specified phylogenetic tree. Then, a
conditional p-value was calculated for each gene family, and a family
with a conditional p-value less than 0.05 was considered to have an
accelerated rate for gene gain or loss. These expanded and contracted
gene families in R. canadum (p-value ≤ 0.05) were mapped to KEGG
pathways for functional enrichment analysis, which was conducted using
the enrichment methods. This method implemented hypergeometric test
algorithms and the Q-value (FDR, False Discovery Rate) was calculated to
adjust the p-value using the R package
(https://github.com/StoreyLab/qvalue).