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Reconstructing Indian population history

Author

Listed:
  • David Reich

    (Harvard Medical School, Boston, Massachusetts 02115, USA
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA)

  • Kumarasamy Thangaraj

    (Centre for Cellular and Molecular Biology)

  • Nick Patterson

    (Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA)

  • Alkes L. Price

    (Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Harvard School of Public Health, Boston, Massachusetts 02115, USA)

  • Lalji Singh

    (Centre for Cellular and Molecular Biology)

Abstract

India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.

Suggested Citation

  • David Reich & Kumarasamy Thangaraj & Nick Patterson & Alkes L. Price & Lalji Singh, 2009. "Reconstructing Indian population history," Nature, Nature, vol. 461(7263), pages 489-494, September.
    • Handle: RePEc:nat:nature:v:461:y:2009:i:7263:d:10.1038_nature08365
    DOI: 10.1038/nature08365
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    Cited by:

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    11. Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler, 2012. "Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-13, July.
    12. Kay Young McChesney, 2015. "Teaching Diversity," SAGE Open, , vol. 5(4), pages 21582440156, October.
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    15. Barbara E Engelhardt & Matthew Stephens, 2010. "Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis," PLOS Genetics, Public Library of Science, vol. 6(9), pages 1-12, September.
    16. Timothy R Braun & Latonya F Been & Akhil Singhal & Jacob Worsham & Sarju Ralhan & Gurpreet S Wander & John C Chambers & Jaspal S Kooner & Christopher E Aston & Dharambir K Sanghera, 2012. "A Replication Study of GWAS-Derived Lipid Genes in Asian Indians: The Chromosomal Region 11q23.3 Harbors Loci Contributing to Triglycerides," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-12, May.
    17. Yedael Y Waldman & Arjun Biddanda & Natalie R Davidson & Paul Billing-Ross & Maya Dubrovsky & Christopher L Campbell & Carole Oddoux & Eitan Friedman & Gil Atzmon & Eran Halperin & Harry Ostrer & Alon, 2016. "The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-28, March.
    18. Priya Moorjani & Nick Patterson & Po-Ru Loh & Mark Lipson & Péter Kisfali & Bela I Melegh & Michael Bonin & Ľudevít Kádaši & Olaf Rieß & Bonnie Berger & David Reich & Béla Melegh, 2013. "Reconstructing Roma History from Genome-Wide Data," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-11, March.
    19. Buzbas, Erkan Ozge & Verdu, Paul, 2018. "Inference on admixture fractions in a mechanistic model of recurrent admixture," Theoretical Population Biology, Elsevier, vol. 122(C), pages 149-157.
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    23. David Gordon & Shailen Nandy, 2016. "The Extent, Nature and Distribution of Child Poverty in India," Indian Journal of Human Development, , vol. 10(1), pages 64-84, April.
    24. Rozaimi Mohamad Razali & Juan Rodriguez-Flores & Mohammadmersad Ghorbani & Haroon Naeem & Waleed Aamer & Elbay Aliyev & Ali Jubran & Andrew G. Clark & Khalid A. Fakhro & Younes Mokrab, 2021. "Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
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