Pre-divergence hybridization and adaptive introgression shaped the genetic architecture of East Asian domestic pigs

Understanding how biodiversity arises and how organisms adapt to different environments is fundamental to evolutionary biology. Hybridization may play an essential role in generating genetic diversity and promoting adaptation. In this work, we analyzed the population structure, demographic history, and selective landscapes of East Asian domestic pigs using a whole-genome resequencing dataset of 1,092 samples from 43 breeds. Our results indicate that North and South pigs form two deeply divergent lineages that split approximately 17,797 years ago, with no extant wild boar population identified as the direct ancestor of South pigs. In contrast, Central and Southwest pigs originated from a North ancestral background (∼9,012 years ago) with introgression from South pigs before their divergence (∼6,284 years ago), which was likely driven by bidirectional migrations between ancient northern and southern human populations in China. The North ancestry under selection contributed to increased body weight, while the South ancestry enhanced environmental adaptation through pathways involved in UV-B response, stress tolerance, and extracellular matrix remodeling. This South-derived ancestry facilitated the geographic expansion of North pigs into broader ecological zones, which led to the establishment of the Central and Southwest pigs. Specifically, we demonstrate that North-South hybridization increases genetic diversity and produces a mosaic inheritance pattern. Moreover, hybridization and adaptive introgression contribute to novel phenotypic variation in domesticated animals, offering valuable insights for genetic improvement and selective breeding.