Fine-Scale Population Structure and Relatedness of Argali (Ovis ammon) in Kyrgyzstan Revealed by High-Density SNP Data

Argali (Ovis ammon), the largest wild sheep in Asia, are of high conservation concern and remain taxonomically and genetically debated across parts of their range. We investigated population structure, relatedness, and inbreeding within Argali sampled in Kyrgyzstan using the Illumina Ovine High-Density SNP array, with an emphasis on dense within-population sampling rather than range-wide comparisons. After quality control, 72 individuals and 135,242 markers were retained for analysis. Principal component analysis revealed subtle genetic variation within the sampled population, but no clustering consistent with discrete subspecies. In particular, we found no genomic support for separating O. a. polii and O. a. karelini within Kyrgyzstan, suggesting that they represent a single genetic unit in this region. Estimates of identity by descent indicated a high average relatedness (0.35), consistent with harem-based breeding systems typical of wild sheep, while individual inbreeding coefficients averaged near zero, with some evidence of moderate inbreeding in a subset of animals. Together, these results characterize fine-scale genetic structure and kinship within Tian Shan Argali and provide a regional genomic baseline for conservation planning in Kyrgyzstan. Our findings highlight the importance of maintaining connectivity within and among managed populations while acknowledging that broader inference will require sampling across the core Pamir range and other parts of the species’ distribution.