Genome-Wide Insights into Intraspecific Taxonomy and Genetic Diversity of Argali (Ovis ammon)

Argali (Ovis ammon), the largest species among all wild sheep, is native to mountainous regions of Central and East Asia, spreading mainly throughout such countries as Tajikistan, Kyrgyzstan, Kazakhstan, Afghanistan, Mongolia, Russia and China. Intraspecific taxonomy of argali remains unclear, and currently, most researchers recognize up to nine subspecies. The aim of our work was to investigate the phylogenetic relationship between populations of O. ammon based on genomewide SNP analysis. Five subspecies, Altai (O. a. ammon) (n = 6), Gobi (O. a. darwini) (n = 5), Pamir (O. a. polii) (n = 12), Tian Shan (O.a. karelini) (n = 15) and Kyzylkum (O. a. severtzovi) (n = 4), were genotyped using Illumina OvineHD BeadChip. In addition, complete mitogenome sequences from 30 of those samples were obtained. After quality control procedures, 65,158 SNPs were selected for the subsequent analyses. Neighbor-Net dendrogram and principal component analysis (PCA) revealed that the five subspecies could be grouped into four clusters. It was shown that a population from Altai formed a cluster with Gobi subspecies. The highest pairwise F-ST genetic distance was between O. a. ammon and O. a. severtzovi (0.421) and the lowest were between O. a. polii and O.a. karelini (0.083) and between O. a. ammon and O. a. darwini (0.040) subspecies. Genetic diversity was higher in Central Asian argali as compared to East Asian populations. O. a. severtzovi had an admixed origin and consisted of two genetic components-73.5 +/- 0.2% of O. a. polli and 26.5 +/- 0.2% of urial (O. vignei). TreeMix analysis revealed a migration event from urial to O. a. severtzovi argali. The analysis of complete mitogenomes supported the results based on whole-genome genotyping. Considering that all the mtDNA sequences of O. a severtzovi belonged to O. ammon and not to O. vignei, we concluded that gene flow in this group was associated with urial males. As this is only the first work on intraspecific taxonomy and genetic diversity of argali based on genome-wide SNP genotyping and the analysis of complete mitogenomes, we suggest that more genetic studies are needed to clarify the status of Gobi and Tian Shan argali.