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Reconstructing Indian population history

Naturevolume 461, pages489–494 (2009)Cite this article

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.

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Figure 1:Map of India.
Figure 2:Linkage disequilibrium based evidence for founder events in India.
Figure 3:PCA of 22 groups from the Indian subcontinent.
Figure 4:A model relating the history of Indian and non-Indian groups.

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Acknowledgements

We thank the volunteers from throughout India who donated DNA; A. G. Reddy, A. Shah and R. Tamang for generating the Y chromosome and mtDNA data; J. Neubauer for sample preparation; and A. Tandon for data curation. We thank B. N. Sarkar and A. G. Roy for helping with group census size estimates, and D. Falush, J. Novembre, A. Ruiz-Linares and S. Watkins for comments on the manuscript. D.R., N.P. and A.L.P. were supported by NIH grant HG004168, and D.R. was supported by a Burroughs Wellcome Career Development Award in the Biomedical Sciences. K.T. and L.S. were supported by grants from the Council of Scientific and Industrial Research of the Government of India, and K.T. was supported by a UKIERI Major Award (RG-4772).

Author Contributions K.T. and L.S. collected the DNA samples, D.R., K.T. and L.S. collected the genetic data, N.P. developed the mathematical theory forf-statistics, and D.R., K.T., N.P. and A.L.P. analysed the data. D.R. wrote the manuscript andSupplementary Information with input from all authors.

Author information

Author notes

  1. David Reich, Kumarasamy Thangaraj, Nick Patterson and Alkes L. Price: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,

    David Reich

  2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA ,

    David Reich, Nick Patterson & Alkes L. Price

  3. Centre for Cellular and Molecular Biology, Hyderabad 500 007, India

    Kumarasamy Thangaraj & Lalji Singh

  4. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA,

    Alkes L. Price

Authors
  1. David Reich

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  2. Kumarasamy Thangaraj

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  3. Nick Patterson

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  5. Lalji Singh

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Corresponding authors

Correspondence toDavid Reich orLalji Singh.

Supplementary information

Supplementary Information

This file contains Supplementary Tables S1-S6, Supplementary Figures S1-S7, Supplementary Notes S1-S5 and Supplementary References. (PDF 1777 kb)

Supplementary Appendix

This file contains Supplementary Data, Supplementary Statistics and Supplementary References. (PDF 162 kb)

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Reich, D., Thangaraj, K., Patterson, N.et al. Reconstructing Indian population history.Nature461, 489–494 (2009). https://doi.org/10.1038/nature08365

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Editorial Summary

Meet the ancestors: Indian population history from gene screening

Analysis of genetic variation in 132 individuals from 25 diverse groups in India reveals that two ancient, genetically divergent populations are ancestral to most Indians today. One lineage, termed Ancestral North Indian, is genetically close to Middle Easterners, Central Asians and Europeans. The other, Ancestral South Indian, is not close to any group outside the subcontinent. The answers to several long-standing questions emerge from this work. It seems that 'caste' has been a powerful force shaping marriage in India for thousands of years — some anthropologists argued that its current strength was a product of British colonialism. And the enigmatic 'Negritos' of the Andaman Islands are identified as an ancient isolate from the Ancestral South Indian population. Allele frequency differences between population groups are high, in part due to the custom of within-group marriages, so it is likely that there is an excess of recessive diseases in India that can be screened for and mapped genetically.

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