2.4 Phylogenetic analysis
Before adaptive evolution analysis, we need a phylogenetic tree to measure the relationship among these species. Protein sequences of eight species were aligned using MUSCLE (Edgar, 2004). After multiple sequence alignments and trimming by the program Gblocks, all one-to-one orthologous genes were concatenated to one sequence for each species and used to construct a phylogenetic tree. PhyML (Guindon et al., 2010) was applied to build a maximum likelihood (ML) phylogeny with 1,000 bootstrap replicates, and we used FigTree version 1.4.2 (http://tree.bio.ed.ad.uk/software/figtree/) to visualize the topology.