Ancient mitogenomes from Neolithic, megalithic and medieval burials suggest complex genetic history of Kashmir valley, India

South Asia is rich in cultural and genetic diversity; however, it is hardly represented in the blooming field of archaeogenetics. The Neolithic site of Burzahom is of high cultural value and archaeological importance and is one of the earliest human settlements in the Kashmir Valley with numerous evidence of migration and cultural assimilation. In our current study, we have reconstructed for the first time the complete mitogenomes of Neolithic, megalithic and medieval individuals from the Burzahom archaeological site in Kashmir. Our findings suggest that Neolithic and Megalithic periods were characterized by predominantly local genetic influence on the maternal gene pool, with some evidence of genetic contact with the Iron Age Swat Valley. While medieval populations showed clear signs of genetic contacts with Swat Valley historical and Central Asian Bronze age populations. Interestingly, Bayesian evolutionary analysis suggests an affinity of one of the medieval samples with a medieval sample from Roopkund Lake; the finding will be more conclusive with more sample evidence. In summary, we propose that the genetics of Neolithic, megalithic and medieval Kashmir agree well with the archaeological evidence of cultural contacts with the Swat Valley and Central Asia.