Phylogenomic analysis

Phylogenomic analysis was performed using Bayesian inferences (BI) and maximum likelihood (ML) methods. The wild ass (Equus asinus) was used as the outgroup [11, 12]. We chose the best-fit model of nucleotide substitutions with the standard Modeltest PAUP block in PAUP 4.0b10 [33] and Akaike’s information criterion (AIC) in Modeltest 3.7 [32]; GTR+I+G was selected as the best fitting evolutionary model. BI analysis was carried out using MrBayes 3.2.5 [36] with the following parameters: nst, 6; rates, gamma; code, vertmt; number of generation, 30,000,000; sample frequency, 500; number of chains, 1; burn-in generation, 25% of the number of generations. Bayesian posterior probability (BPP) values shown on respective internal nodes indicated confidence of the phylogenomic analysis.

In addition to the BI approach, ML analysis was conducted in PHYML 3.0 [37] under the following options: model of nucleotide substitution, GTR; initial tree, BIONJ; nonparametric bootstrap analysis, yes, 500 pseudoreplicates; proportion of invariable sites, estimated; number of substitution rate categories, 6; gamma shape parameter, estimated by program; optimize tree topology, yes.