Maternal Phylogeny and Genetic Structure of Wild Sheep/Argali (Bovidae, Ruminantia) Populations in China

Argali, also known as wild sheep (Ovis ammon), is a prominent alpine mammal found in Central Asia. It is of conservation concern globally and domestically in China. Our study aims to unveil the genetic diversity and phylogenetic relationships among argali populations in China using the mitochondrial cytochrome b (Cytb) and control region (CR) sequences. We noninvasively collected a total of 77 fecal or tissue samples from various locations within Xinjiang, covering most of its range. Consequently, we identified 22 distinct haplotypic sequences for Cytb (1140 bp) and 36 for CR (1107–1260 bp). In our phylogenetic analyses, all sequences from China and abroad were grouped into 10 different clades, labeled as clade A through clade J. The network clustering pattern was consistent with the phylogenetic topology. The genetic distance and genetic divergence between clades ranged from 1.21% to 9.25% and from 0.30 to 0.94, respectively. Our analysis of molecular variation (AMOVA) analysis also revealed that more than 70% of the variation was accounted for among the clades. The genetic differentiation between populations was positively corelated with geography distances (r = 0.472, p < 0.01). We observed significant differences in genetic diversity among the various populations. The mismatch distribution analysis showed a multimodal distribution for all clades. Fu’s Fs and Tajima’s D values were not statistically significant. In conclusion, we genetically identified 10 matrilineal populations, which may represent subspecies of argali population, eight of which were in China. The demographic history analyses suggest that the population size of all argali evolutionary populations remained relatively stable. Nonetheless, some populations need special attention due to their low level of genetic diversity.