2.12 Expansion and contraction of gene families
According to the orthologs obtained by gene family clustering and the phylogenetic tree constructed based on single-copy orthologous genes, the gene families that expanded or contracted in 14 species were analyzed using CAFÉ (De Bie et al. 2006). A random birth and death model was used to predict gene family variations along each lineage of the phylogenetic tree. The P -values were used to determine the significance of each gene family by comparing conditional likelihoods derived from a probabilistic graphical model. Significantly expanded gene families (P values < 0.05) were performed using a GO term enrichment analysis with EnrichPipeline32 (Beissbarth & Speed 2004; Huang da et al. 2009).