Maximum-likelihood tree (left) and Median-joining networks (right) based on exon haplotype of Leymus and its affinitive species. Maximum-likelihood tree (-Lnlikelihood = 5903.3227, base frequencies A: 0.2630, C: 0.1880, G: 0.2688, T: 0.2802, shape = 0.9988, pinvar = 0.4451) was generated under TIM + G + I model. Numbers with bold above nodes are Bayesian posterior probability values ≥ 90%; numbers below nodes are bootstrap values ≥50%. Haplotypes in network are represented by circles. Numbers along network branches indicate the position of mutation between nodes. Abbreviations of species names are listed in table 1. The numbers after species names refer to the distinct homoeologous of Acc1 gene. The letter a and b represent two different accessions of Agropyron cristatum. This figure shows the middle quartile, for the full image please see Additional file 6.