1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
3. Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
4. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
5. These authors contributed equally to this work.

Correspondence to: David Reich^1,2,5Lalji Singh³ Correspondence and requests for materials should be addressed to D.R. (Email: reich@genetics.med.harvard.edu) or L.S. (Email: lalji@ccmb.res.in).

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.

1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
3. Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
4. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
5. These authors contributed equally to this work.

Correspondence to: David Reich^1,2,5Lalji Singh³ Correspondence and requests for materials should be addressed to D.R. (Email: reich@genetics.med.harvard.edu) or L.S. (Email: lalji@ccmb.res.in).

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