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.