**4.6. Phylogenetic analysis of the Tibetan sheep populations**

Phylogenetic analyses of complete mitogenomes showed a high resolution among wild sheep as well as among the major lineages of domestic sheep [62]. The complete mitogenomes of *O. orientalis* and *O. musimon* formed a monophyletic group that was incorporated within lineage B of domestic sheep. However, the analysis of full control region and D-loop fragments showed that *O. orientalis* is also closely related to other lineages of *O. aries*. This difference could be ascribed to the small number of *O. musimon* and *O. orientalis* complete mitogenomes available in this study.

Full control region from the complete mitogenomes produced similar phylogenies with fully resolved phylogenetic relationships of wild sheep, but they failed to define the phylogenetic relationships among the major lineages of domestic sheep. Our results suggest that partial fragments of the complete mitogenomes would be problematic when making phylogenetic inferences about domestic sheep. This problem arises due to diagnostic substitutions located elsewhere in the mitogenome [62]. Thus, the diagnostic substitutions for species and lineages presented [62] here can serve as an important resource for maternal genetic differentiation between domestic and wild sheep as well as between the lineages within domestic sheep. Also, they might be helpful for addressing certain conflicts described above in future.
