Tracing the maternal lineage of Sus scrofa in Northern India and its correlation with ancient human migration patterns

We aimed to explore the distribution and variation of porcine mitochondrial DNA (mtDNA) lineages in northern India. The mtDNA control region (417 bp) was sequenced from 83 domestic pigs from three North Indian states. The 18 haplotypes that were obtained were compared with 1518 published mtDNA control region sequences of Sus scrofa from various regions across the world. The analysis revealed complex clustering patterns of porcine haplotypes with distinct phylogeographic signals. The study unveiled diverse maternal lineages among the domestic pig populations in northern Indian states situated in the foothills of the majestic Himalayas. Additionally, the study identified the presence of two distinct subspecies of wild boar in India (W1 and W2), demonstrating their migration routes and offering a strong phylogeographic signal. Evidence for a separate domestication center in the Himalayan foothills and Indian sub-continent was found within Mixed Clade 5 (MC5). A novel clade (MC4) with a localized distribution in the Chotanagpur plateau was detected, suggesting a unique population of wild boar in this region. Diverse maternal lineages among domestic pigs were observed, which may reflect human-mediated dispersal of pigs within and into the region; hence, a hypothesis linking ancient human migration with the presence of these maternal lineage clades has been proposed. Overall, the porcine haplotypes discovered in the Indian subcontinent highlight its unique and significant contribution to genetic resources.