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50,000 years of evolutionary history of India: Impact on health and disease variation

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Kerdoncuff, Elise, Skov, Laurits, Patterson, Nick, Banerjee, Joyita, Khobragade, Pranali, Chakrabarti, Sankha S., Chakrawarty, Avinash, Chatterjee, Prasun +24 more·2025·Cell
DOI 10.1016/j.cell.2025.04.027PMC PMC12376946
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Abstract

India has been underrepresented in genomic surveys. We generated whole-genome sequences from 2,762 individuals in India, capturing the genetic diversity across most geographic regions, linguistic groups, and historically underrepresented communities. We find most Indians harbor ancestry primarily from three ancestral groups: South Asian hunter-gatherers, Eurasian Steppe pastoralists, and Neolithic farmers related to Iranian and Central Asian cultures. The extensive homozygosity and identity-by-descent sharing among individuals reflects strong founder events due to a recent shift toward endogamy. We uncover that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, followed by 1%-2% gene flow from Neanderthals and Denisovans. Notably, Indians exhibit the largest variation and possess the highest amount of population-specific Neanderthal ancestry segments among worldwide groups. Finally, we discuss how this complex evolutionary history has shaped the functional and disease variation on the subcontinent.

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  • There is evidence for superarchaic gene flow into Denisovans, into Neanderthal-Denisovan ancestors, and into Africans.

    “There is evidence for superarchaic gene flow into Denisovans 13,21,22 , into Neanderthal-Denisovan ancestors 27 , and into Africans 4 .”

    From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [13]

    The Results section (‘Gene flow from archaic hominins in India’; page unavailable) discusses Neanderthal and Denisovan ancestry in Indians, not superarchaic gene flow into Denisovans, Neanderthal-Denisovan ancestors, or Africans. Searches for superarchaic ancestry and Neanderthal-Denisovan ancestors found no passage addressing those proposed gene-flow events. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Authors
Kerdoncuff, E., Skov, L., Patterson, N., Banerjee, J., Khobragade, P., Chakrabarti, S. S., Chakrawarty, A., Chatterjee, P., Dhar, M., Gupta, M., John, J. P., Koul, P. A., Lehl, S. S., Mohanty, R. R., Padmaja, M., Perianayagam, A., Rajguru, C., Sankhe, L., Talukdar, A., Varghese, M., Yadati, S. R., Zhao, W., Leung, Y. Y., Schellenberg, G. D., Wang, Y. Z., Smith, J. A., Dey, S., Ganna, A., Dey, A. B., Kardia, S. L. R., Lee, J., & Moorjani, P.
Affiliations
  • University of California, Berkeley (US)
  • Harvard University (US)
  • All India Institute of Medical Sciences (IN)
  • University of Southern California (US)
  • Institute of Medical Sciences (IN)
  • All India Institute of Medical Sciences Rishikesh (IN)
  • Government Medical College and Hospital (IN)
  • National Institute of Mental Health and Neurosciences (IN)
  • Sher-i-Kashmir Institute of Medical Sciences (IN)
  • All India Institute of Medical Sciences Bhubaneswar (IN)
  • Nizam's Institute of Medical Sciences (IN)
  • Qatar University (QA)
  • Grant Medical College and Sir Jamshedjee Jeejeebhoy Group of Hospitals (IN)
  • Medical College and Hospital, Kolkata (IN)
  • University of Michigan (US)
  • University of Pennsylvania (US)
  • Institute for Molecular Medicine Finland (FI)
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2025-06
Volume
188
Issue
13
Pages
3389-3404.e6
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2025.04.027
PMC
PMC12376946
OpenAlex
W4411690487
Cited by
36
References
13
Citations by year
2026: 25 · 2025: 11
FWCI
21.16
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Qatar University QSpace (Qatar University) (submittedVersion, cc-by-nc-nd)
Funders
  • Burroughs Wellcome Fund
  • National Institute on Aging (R01AG051125, U01AG065958, RF1AG055273)
  • Foundation for the National Institutes of Health (R35GM142978)
  • National Institutes of Health (R35GM142978)
  • Novo Nordisk A/S (NNF23OC0081723)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
hunter-gatherers, Neolithic farmers, founder effect, endogamy, homozygosity, Neanderthal ancestry, out-of-Africa migration, functional genetic variation, population structure
MeSH terms
South Asian People, Animals, Biological Evolution, Genetics, Population, Humans, India, Genetic Variation, Genome, Human, Asian People, Gene Flow, Neanderthals, Human Migration

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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