Reconstructing Indian population history - PubMed (original) (raw)

Reconstructing Indian population history

David Reich et al. Nature. 2009.

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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Figures

Figure 1

Figure 1

Map of India with the state of origin of the 25 groups that we studied.

Figure 2

Figure 2

Linkage disequilibrium based evidence for founder events in India. For each pair of samples, we calculate the autocorrelation of the number of shared alleles as a function of distance, recognizing that SNP genotypes should differ by at most one allele in regions of identity by descent. To correct for background allele sharing, we subtract the same quantity comparing across groups. Allele sharing in the Vysya decreases with an exponential decay of 0.461 cM as shown here, suggesting a founder event roughly 100/(2*0.461) = 108 generations ago. We present similar analyses for all Indian groups in Figure S2.

Figure 3

Figure 3

Principal components analysis (PCA) of 22 groups from the Indian subcontinent. Analysis of these groups along with Europeans (CEU) and Chinese (CHB) reveals a gradient of relatedness to CEU that runs through the majority of Indo-European and Dravidian groups, with the Kashmiri Pandit most related to CEU. Both the Austro-Asiatic speaking groups (Kharia and Santhal) and the tribal Sahariya are off-cline, while the two Tibeto-Burman speaking groups cluster with CHB. (Data from the outlying Siddi, Onge and Great Andamanese are not shown.)

Figure 4

Figure 4

A model relating the history of Indian and non-Indian groups. Modeling the Pathan, Vaish, Meghawal and Bhil as mixtures of ANI and ASI, and relating them to non-Indians by the phylogenetic tree (YRI,(CEU,ANI),(ASI, Onge))), provides an excellent fit to the data. While the model is precise about tree topology and ordering of splits, it provides no information about population size changes or the timings of events. We estimate genetic drift on each lineage in the sense of variance in allele frequencies, which we rescale to be comparable to FST (standard errors are typically ±0.001 but are not shown).

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