Phylogeography and genetic structure of domestic pigs in Uttarakhand and Jharkhand: a mitochondrial DNA perspective

We aimed to explore the distribution and variation of porcine mitochondrial DNA (mtDNA) lineages in northern India, expanding on previous local-scale research by incorporating a broader, global context. A total of 82 domestic pigs samples from Uttarakhand and Jharkhand were sequenced for the mtDNA control region (417 bp) and compared to 1517 published sequences of Sus scrofa from various regions worldwide. The Uttarakhand sequences, previously analyzed in a local context by our research group, were incorporated into this study for a broader global comparative analysis. The analysis revealed complex clustering patterns of 18 haplotypes with distinct phylogeographic signals, reflecting diverse maternal lineages within the domestic pig populations in these two states of India. Two distinct subspecies of wild boar (W1 and W2) were identified, providing strong phylogeographic evidence for their distribution in India. A novel cluster (MC-I), localized to the Chotanagpur plateau, was detected, offering insights into its connection with the D5 cluster. Significantly, the study found evidence for a separate domestication center in the Himalayan foothills, supported by the presence of most Uttarakhand samples in Cluster D3, linking it to ancient human migration and subsequent pig dispersal across the region. The diverse maternal lineages in Uttarakhand may be linked to ancient human migration, suggesting human-mediated dispersal of pigs in the region. These findings contribute to the understanding of Sus scrofa's evolutionary history and global migration patterns, emphasizing the genetic uniqueness of pigs in the Indian subcontinent and its significance in the broader context of porcine genetic resources.