(I). A neighbor-joining (NJ) tree of 87 haplotypes in all yaks constructed by MEGA. The highly divergent mtDNA clades found in domestic yaks were marked with A-G and haplotypes found only in the wild yaks were indicated by circles. (II). Phylogenetic tree of all domesticated (unlabeled) and wild (circles) yak haplotypes constructed by maximum likelihood analysis (-lnL = 1803.55) with the best-fit model (K81uf + I + G), rooted by one sequence of Bison bison. The solid circles indicate haplotypes found among the eight wild yaks sampled from a single population in Quinghai and the grey circle indicates the only haplotype found both in the wild population and at high frequency in the domesticated yaks. Numbers below the branches represent support values from maximum parsimony bootstrap and Bayesian inference obtained with the MrBayes program, and numbers above the branches represent the bootstrap values from a fast stepwise-addition search of the maximum-likelihood genetic values obtained with PAUP.