Reconstructing Indian population history

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 for f-statistics, and D.R., K.T., N.P. and A.L.P. analysed the data. D.R. wrote the manuscript and Supplementary Information with input from all authors.

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Correspondence to David Reich or Lalji Singh.

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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. Nature 461, 489–494 (2009). https://doi.org/10.1038/nature08365

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