Phylogenetic inference
Reciprocal BLAST (Altschul et al.1990) and OrthoMCL software (Li& L.
2003) were used to determine the homology relationships among the
protein sequences of 11 species (B. l. tsinlingensis , D.
rerio , O. mykiss , O. tshawytscha , S. trutta ,O. kisutch , O. nerka , S. salar , O. keta ,E. lucius , and L. oculatus ). After the orthologous genes
were obtained, all of these genes in these species were connected into
one super sequences in each species. MUSCLE (v3.8.31)
(Edgar 2004a,
b) was then used to align these
sequences. Lastly, RAxML (v8.2.9)
(Stamatakis& A. 2014) was used to
reconstruct the phylogenetic relationships using different models
(Protgammaauto/Gtrgamma) with 100 bootstrap replicates; L.
oculatus was used as the outgroup species.