3.4 | Genetic variation and genetic diversity of complete D-loop region
The mtDNA D-loop sequences had a total of 23 variable sites and 11 haplotypes (named sequentially from H1 to H11, GenBank accession no. OP095367~OP095377.) (Table 4). The A + T content of D-loop region was 52%, with a positive AT-skew (+0.1692) and negative GC-skew (–0.4542), which was found betweentrnP and trnF . The haplotype and nucleotide diversity values were 0.87000 ± 0.00046 and 0.02115 ± 0.01180, respectively. There were two single polymorphic sites and 21 parsimony-informative polymorphic sites. All polymorphisms were A/G and T/C transitions. We observed several variable sites in Clade Ⅱ (66 A/G, 72 C/T, 85 C/T, 151 A/G, 162 A/G, 180 T/C, 226 A/G, 234 T/C, 224 A/G, 280 T/C, 352 T/C, 383 T/C, 388 T/C, 402 T/C, and 404 A/G) and only two polymorphic sites in Clade Ⅰ(181 A/G and 403 A/G). The calculated number of polymorphic sites and haplotypic diversity of Huaibei grey donkey are shown in Table 4.