SRINAGAR: A study of ancient DNA from burials at Kashmir’s Burzahom archaeological site has found evidence of deep maternal genetic continuity in the Valley while also establishing genetic links with the Swat Valley and Central Asia stretching from the Neolithic period to the Middle Ages.
The researchers say the findings broadly validate archaeological evidence of long-standing cultural contacts between Kashmir, Swat and Central Asia. A medieval sample also shows an intriguing genetic affinity with a medieval individual from Roopkund Lake. The researchers caution, however, that the Roopkund connection remains inconclusive because of the limited number of ancient samples available.
The research, published in Scientific Reports in 2025, is the first study to reconstruct complete mitochondrial genomes from Neolithic, megalithic and medieval individuals recovered from Burzahom.
The paper, titled Ancient mitogenomes from Neolithic, megalithic and medieval burials suggest complex genetic history of Kashmir valley, India, was authored by Aparna Dwivedi, Lomous Kumar, Snigdha Konar, Nagarjuna Pasupuleti, Sanjay Kumar Singh Gahlaud, Richa Rajpal, Mohammad Ajmal Shah, Mumtaz A Yatoo, Sachin Kumar, Shiv Kumar Patel, Ningombam Somorjit Singh and Niraj Rai. Dwivedi and Kumar contributed equally to the study, while Rai is the corresponding author.
The research involved scientists and researchers from the DST-Birbal Sahni Institute of Palaeosciences in Lucknow, the Academy of Scientific and Innovative Research, CSIR-Centre for Cellular and Molecular Biology in Hyderabad, the Anthropological Survey of India and the Centre of Central Asian Studies at the University of Kashmir.
The researchers analysed 12 human skeletal samples spanning the Neolithic, early historic and medieval periods. Although DNA was successfully extracted from all 12, complete mitochondrial genomes could be reconstructed from only four: one Neolithic, one Megalithic and two medieval individuals. The authors describe the work as a first step towards filling a major gap in South Asian archaeo-genetics, noting that the region remains poorly represented in ancient-genomic research.
The Neolithic sample, dated to 2009-2002 cal BCE, belonged to mitochondrial haplogroup M65. The researchers found that this lineage is also present in the modern Kashmiri mitochondrial gene pool, which they interpret as evidence of maternal genetic continuity in the region “over the millennia”. Phylogenetic analysis showed a close relationship with local populations, particularly the Brokpa tribe, while the estimated divergence of the Burzahom lineage was placed at roughly 6,000-7,000 years ago.
The Megalithic sample, dated to 547-580 CE, carried the U2b2 maternal lineage. The researchers found that this lineage is distributed across Kashmir, Tajikistan and Pakistan and that the Burzahom sample showed genetic relationships with Iron Age individuals from the Swat Valley, as well as North Indian Brahmins and a Uyghur individual. Yet its deep evolutionary position led the researchers to describe the lineage as having a largely local origin and a deep-rooted history in Kashmir.
Together, the Neolithic and Megalithic results strengthen the archaeological case for interaction between Kashmir and the Swat Valley. Burzahom and Swat have long been linked through similarities in pottery, tools, burial practices and other material culture. The genetic evidence now provides an additional line of evidence for those contacts. The authors say the evolutionary clustering of Burzahom samples with Iron Age Swat Valley samples “further validates the archaeological evidences of cultural similarity with SPGT (Swat valley Iron age).”
The picture changes significantly in the medieval period. One medieval Burzahom individual, designated Med1 and carrying mitochondrial haplogroup M30, showed links not only with Kashmir and the Swat Valley but also with Central Asian and Middle Eastern populations. In Bayesian analysis, the sample formed a clade with a medieval individual from Roopkund. The researchers estimate the common node at approximately 3,493 years ago, although they stress that the available evidence is insufficient to establish a direct migration from Kashmir to Roopkund or vice versa.
The second medieval individual, Med2, produced an even more striking result. It carried the W4 mitochondrial lineage, a lineage found predominantly in parts of Europe but also in Pakistan and, at lower frequency, in Kashmir.
Phylogenetic analysis placed the sample close to ancient populations associated with the Bactria-Margiana Archaeological Complex (BMAC) and other Bronze Age Central Asian sites. The researchers therefore argue that this particular lineage is more likely to reflect an ancient Central Asian connection than a European one.
The authors interpret the medieval evidence as pointing towards substantial demographic change in Kashmir. While the Neolithic and Megalithic samples largely point towards deep local maternal lineages with connections to neighbouring populations, the medieval samples show clearer evidence of wider contacts with Swat and Central Asia. The paper says these findings suggest “large scale demographic shifts in the region”.
The study is significant because Burzahom has long provided archaeological evidence of Kashmir’s interaction with neighbouring regions, but genetic evidence from ancient inhabitants has been scarce. The researchers note that Burzahom, which records human habitation from around 2900 BCE to the fifth century CE, is among South Asia’s important Neolithic sites and contains evidence of cultural connections extending towards Swat, the wider Indus region, Tibet, Central Asia and other parts of Eurasia.
The ancient DNA work was conducted under stringent laboratory conditions at the Birbal Sahni Institute of Palaeosciences. The researchers processed the skeletal material in a dedicated ancient-DNA laboratory, used contamination controls and sequenced the recovered material on an Illumina NovaSeq 6000 platform at CSIR-CCMB, Hyderabad. They subsequently used mitochondrial haplogroup analysis, maximum-likelihood and Bayesian phylogenetic methods, haplotype networks and radiocarbon dating to reconstruct the genetic relationships of the ancient individuals.
The researchers nevertheless emphasise the limitations of the findings. Only four of the 12 samples yielded complete mitogenomes, and the number of medieval samples is particularly small. The paper specifically says that the possible relationship between the medieval Kashmir individual and Roopkund migrants remains unresolved and that “more medieval samples from Kashmir will be conclusive evidence.”
In its conclusion, the study says the ancient DNA evidence establishes genetic continuity in Kashmir alongside connections with Pakistan and Central Asia through deeply rooted mitochondrial lineages including M65, U2b and M30. It also concludes that the genetic evidence supports archaeological evidence of “close tie of Kashmir with Swat valley from Neolithic to medieval periods”. The W4 lineage, meanwhile, may represent migration from Central Asia, potentially through trade routes or other movements into the region.
The study was published by Scientific Reports journal Springer Nature in 2025.
The researchers describe the work as the first attempt to investigate maternal genetic continuity in South Asia across such a long chronological span using ancient DNA and mitogenomes. Rather than pointing to a single source population for Kashmir’s ancient inhabitants, the findings present the Valley as a region of both deep local genetic continuity and repeated interaction with populations to its west and north, a pattern that the authors say is broadly consistent with Kashmir’s archaeological position at the crossroads of Eurasia.
