A 3,300-Year-Old Hunter-Gatherer Genome from Nagaland, India, Sheds Light on the Population Histories of Tibeto-Burman Speakers in South Asia

Maanasa Raghavan1*, Esha Bandyopadhyay2, Jose Urban Aragon1, Juhyeon Lee3, Nagarjuna Pasupuleti4, David Witonsky1, Constanza de la Fuente Castro5, Natividad Lupiáñez Corpas1, David Tetso6, Mepusangba7, Yabangri Changkiri7, Ruokounou Yhome8, Tiatoshi Jamir7, Choongwon Jeong3, and Niraj Rai4

The Himalayan arc and Northeast India represent the most linguistically diverse region within the Sino-Tibetan language family - the second-largest language family globally - with populations in this region speaking predominantly non-Sinitic branches of this family. Despite this remarkable diversity, the past population dynamics underlying the dispersal of these non-Sinitic Sino-Tibetan languages into South Asia remain poorly understood. To address these questions, we performed shotgun sequencing on five mid-Holocene hunter-gatherer (~3,300 cal BP) and 20 present-day individuals from the Northeast Indian state of Nagaland. We found that both the ancient and present-day individuals from Nagaland cluster consistently with East Asian groups, sharing greater genetic affinity with ancient Yellow River farmers and Tibetan individuals, as well as with present-day populations from Northeast India, the Himalayan region, Tibet, and broader East Asia - groups that are primarily Tibeto-Burman speakers. These patterns were further corroborated through formal admixture modelling, which suggests deep genetic connections among Tibeto-Burman-speaking populations across South Asia. Collectively, our findings contribute critical evidence toward resolving long-standing questions about the genetics origins and dispersal of Sino-Tibetan languages in this understudied region.