Adaptive introgression shaping genomic adaptation and ancestral mosaicism of Changthangi sheep for high-altitude survival and pashmina excellence

Conservation of genetic diversity is fundamental to safeguarding the adaptive potential of any species. Sheep (Ovis aries), domesticated approximately 10,000 years ago in the Fertile Crescent, have developed extensive genetic diversity, particularly in Asia, which hosts over 40% of global sheep breeds. This study focuses on the Changthangi sheep, indigenous to the high-altitude regions of Ladakh, India, and examines their genomic structure, diversity, and locus-specific ancestry in comparison with Tibetan and Deccani sheep breeds. Genome-wide diversity analyses, including Heterozygosity, Effective population size (Ne), Linkage Disequilibrium (LD) decay, Haplotype block analysis, Runs of Homozygosity (ROH), and Allelic Richness (AR), revealed high genetic diversity in Changthangi and Tibetan breeds, attributed to their adaptation to extreme Himalayan environments, while Deccani exhibited lower diversity. Population structure analyses, including Principal Component Analysis (PCA) and Admixture, confirmed Changthangi’s admixed ancestry, with 11.9% Tibetan and 13.91% Deccani contributions, validated by f3 statistics. Admixture timing, inferred using Alder, estimated Deccani introgression approximately 52–68 years ago and Tibetan introgression 35–44 years ago, reflecting historical gene flow. Locus-specific ancestry analysis using Local Ancestry in adMixed populations (LAMP) software, identified adaptive admixture signals, with Deccani ancestry enriched on Ovis aries chromosome (OAR) 7, 8, 15, 17, 19, 20, 22, and 23, and Tibetan ancestry on OAR 3, 5, 9, 12, 14, 18, 21, 25, and 26. Functional annotation of these regions revealed genes associated with high-altitude adaptation, immune response, wool, and meat production, highlighting the adaptive significance of these introgressions. These findings highlight Changthangi’s genetic architecture, shaped by adaptive introgression, and emphasize the importance of conserving this breed for its superior Pashmina fiber and resilience to extreme environments, offering critical insights for breeding and conservation strategies.