**4. Discussion**

**3.6. Phylogenetic relationships**

142 Mitochondrial DNA - New Insights

To extend our knowledge of the phylogenetic relationship of the 15 Tibetan sheep populations, a phylogenetic tree was constructed using ME based on the complete mtDNA D-loop sequences of 642 individuals and 350 haplotypes from 15 Tibetan sheep populations and six reference breeds [29]. We determined four distinct cluster haplogroups: A, B, C and D. Of the 350 haplotypes, there was no common haplotype identified in all of the Tibetan sheep populations; 98 haplotypes were shared, and 252 haplotypes were singletons, which including 38 in GB, 33 in GJ, 28 in TJ, and 24 in QH. The leading haplotype (Hap 39) was found in 39 individuals. The next most common haplotype was Hap 42, composed of 19 individuals, and the remaining nine haplotypes were composed of 7–10 individuals. Haplotype 42 was composed of JZ, MX, QL and TJ. Haplotype 4 was composed of 14 of the Tibetan sheep populations, but excluding LKZ, indicating close clustering. The majorities of the 490 individuals were grouped in haplogroup A, followed by haplogroups B and C; however, only one animal from the LZ belonged to haplogroup D. The DM was composed of two haplogroups, the AW was composed of one haplogroup and the remaining 13 Tibetan sheep populations were composed of three haplogroups [29]. Moreover, the maximum composite likelihood method was used to analyze the genetic distance between populations, which were in the units of the number of base substitutions per site. More specifically, the neighbor-joining phylogenetic tree of the 642 sequences of the mtDNA D-loop, based on units of the number of base substitutions per site divided the 15 Tibetan sheep populations and six reference breeds into four groups effectively. *O. ammon* and *O. vignei* were genetically distinct and separated initially. The 15 Tibetan sheep populations and four reference breeds were then divided into three sub-clusters. The first cluster included JZ, QL, QH, GN, QK, MX and GD. The second cluster included *OasiaA*, AW, TJ, GJ, LKZ, DM, GB, HB and LZ. The third cluster included *Omexic*, *Oeuro*reB and *Omusimon*. The AMOVA was conducted, and the results are shown in Liu et al. [29]. The AMOVA revealed a variation of 4.46% among the populations and of 95.54% within

**Figure 2.** Genetic differentiation and absolute difference between altitudes for population GD.
