**Acknowledgements**

**4.5. Population expansion of Tibetan sheep populations**

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

cantly large negative Tajima's D value and *FS*

146 Mitochondrial DNA - New Insights

available in this study.

**5. Conclusion**

The mismatch distribution analysis of the complete dataset, maternal lineages A, B, C, D, and 15 Tibetan sheep populations of the mtDNA D-loop, is presented [29]. Neutrality tests (Ewens-Watterson test, Chakraborty's test, Tajima's D test, Fu's FS test) were used to detect population expansion [29]. The complete dataset of all Tibetan sheep populations had a signifi-

expansions, consistent with a demographic model, as inferred from the mismatch distribution. The mismatch distribution of the complete dataset suggested that there were two major peaks with maximum values at 4 and 27 pairwise differences and two smaller peaks at 45 and 51 differences. Based on the results, it could be implied that there are at least two expansion events occurred in the population demographic history of the Tibetan sheep, which live on the Qinghai-Tibetan Plateau. The mismatch distribution analysis revealed a unimodal bell-shaped distribution of the pairwise sequence differences in maternal lineages A, B and C. However, the distribution of maternal lineage D was a sambong function, duo to the geographic distribution patterns of species diversity. Mismatch analysis of maternal lineages A, B, and C suggested that it happened in the demographic history of Tibetan sheep populations that single population expansion events occurred before. Similar results were found in previous reports [42, 43].

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

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.

High mtDNA genetic diversity in the sheep from the Qinghai-Tibetan Plateau areas is a rich resource for China. The evidences indicate the high diversity of four maternal lineages by doing the large-scale mtDNA D-loop sequences analysis of 15 Tibetan sheep populations. Although the maternal lineage D was only found in a single LZ, phylogenetic analysis

value. This result shows two large and sudden

The authors appreciated constructive comments from the editor Hervé Seligmann. This work was supported by the special fund from the Major International (Regional) Joint Research Project (NSFC-CGIAR 31461143020), and Gansu Provincial Agricultural biotechnology research and application projects (GNSW-2014-21, GNSW-2016-13), and the Central Level, Scientific Research Institutes for Basic R & D Special Fund Business (1610322016016).
