David Reich1,2*, Kumarasamy Thangaraj3*, Nick Patterson2*, Alkes L. Price2,4* & Lalji Singh3
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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