Genomics Insights into the Demographic History and Introgression of Tibetan Pigs

Tibetan pigs are an important indigenous genetic resource on the Qinghai-Tibetan Plateau, but their population history remains unclear. Here, we analyzed whole-genome resequencing data from 29 Tibetan pigs and 69 wild boars from different regions to investigate their genetic structure and origin. Population structure analyses showed that Tibetan pigs formed a distinct genetic cluster, but clear substructure was present among the four Tibetan pig groups. Demographic analyses indicated that all Tibetan pigs shared a similar deep ancestral background, whereas the Tibetan population from Tibet (TT) showed a distinct recent demographic trajectory relative to the other Tibetan pig groups. Model inference based on multidimensional site frequency spectra further supported a mixed origin of TT from northern and southern Asian wild boar-related ancestral components. In contrast, the other three Tibetan pig groups were best explained as lineages derived from TT after its formation. We also detected a persistent western Eurasian-related excess-sharing signal in TT, consistent with potential introgression. Selection scans identified candidate genes and pathways potentially related to hypoxia adaptation, cardiovascular function, and lung development.