Article
Nature 461, 489-494 (24 September 2009) | doi:10.1038/nature08365; Received 21 April 2009; Accepted 5 August 2009
Reconstructing Indian population history
David Reich1,2,5, Kumarasamy Thangaraj3,5, Nick Patterson2,5, Alkes L. Price2,4,5 & Lalji Singh3
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 Reich1,2,5Lalji Singh3 Correspondence and requests for materials should be addressed to D.R. (Email:
reich@...) or L.S. (Email:
lalji@...).
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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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