**3. Results**

#### **3.1. Polymorphic site and sequencing analysis of the complete control region**

Based on the reference sequences from GenBank accession numbers (AY091487, AY091490, AJ238300, AF039578, AF039577, AY582801), all of the sequences were aligned with 1274 comparative sites, and 350 haplotypes were obtained from the 642 sequenced individuals. The length of the sequences obtained from the 636 individuals varied considerably, between 1031 and 1259 bp, although the majority were between 1180 and 1183 bp [29]. A total of 196 variable sites were obtained from the sequences, including 63 singleton variable sites and 133 parsimony-informative variable sites. There were 158 transitions and 38 transversions within the 196 variable sites, among which 15 sites had both transitions and transversions. Transition mutations were caused by observed substitutions. The variability of the number of 75 bp tandem repeat motifs [38] caused the observed variation in the length of the mtDNA D-loop sequences of the Tibetan sheep, with the exception of the insertion or deletion of several nucleotide sites.

Whole haplotypes' nucleotide composition was 32.96% A, 29.71% T, 22.89% C, 14.44% G, 62.67% A+T, and 37.33% G+C, and the A+T were more common than the G+C haplotype substantially, showing an AT bias [29]. The largest haplogroup A consisted of 490 individuals and 259 haplotypes; the next largest haplogroup B and haplogroup C consisted of 145 individuals and 43 haplotypes. The smallest haplogroup D consisted of 1 individual and 1 haplotype. The number of haplotypes, individuals, and frequency detected in each Tibetan sheep population of haplotype group varied from 1 to 49, from 0 to 62, and from 0 to 0.88, respectively. The haplotype diversity and nucleotide diversity were calculated separately for each Tibetan sheep population and were estimated to be 0.99 ± 0.01 and 0.02 ± 0.00, respectively. The values of haplotype diversity and nucleotide diversity ranged from 0.90 ± 0.16 to 1.00 ± 0.05 and from 0.01 ± 0.00 to 0.03 ± 0.00, respectively, thus demonstrating the high level of genetic diversity in the 15 Tibetan sheep populations. The nucleotide diversity value of the LZ and JZ populations was higher than that of the remaining 13 Tibetan sheep populations, indicating a relatively high level of diversity. Similarly, the haplotype diversity values were highest in LKZ and LZ populations and the lowest in the AW population.

## **3.2. Genetic distance and average number of nucleotide differences**

The study presents the genetic distance and average number of nucleotide differences between and within the 15 Tibetan sheep populations. The genetic distance values ranged from 0.01 to 0.04 within the population diagonals, and the genetic distance values ranged from 0.01 to 0.04 among populations in Liu et al. [29]. Among the Tibetan sheep populations, the genetic distance within populations reached a maximum value in LZ and a minimum value in AW. Similarly, the genetic distance between the populations had a maximum value for LZ and JZ and a minimum value for AW and TJ. The average number of nucleotide differences values ranged from 10.00 to 29.81 within populations along the digital diagonal, and the average number of nucleotide difference values ranged from 10.73 to 30.99 between the populations below the diagonals. Among the Tibetan sheep populations, the average number of nucleotide differences within the populations reached its value maximum in LZ and its minimum value in AW. Similarly, the average number of nucleotide differences between populations reached a value maximum in LZ and JZ and a minimum value in AW and TJ populations [29].
