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).