Expansion and contraction of gene family
The expansion and contraction of gene family were determined by CAFE (-p
0.01, -r 1000, -s; v3.1) (De Bie et
al. 2006) using the random birth-and-death (λ) model, and the
probability of each gene family with observed sizes was calculated using
10,000 Monte Carlo simulations. Three results, including the
phylogenetic relationships, divergence time, and fossil records, were
used in this analysis. Both expanded gene families in B. l.
tsinlingensis and the salmonid lineage were calculated, and these genes
were used in Gene Ontology (GO)/ KEGG enrichment analysis
(Beissbarth & Speed 2004;
Huang da et al. 2009).