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      Reconstructing Indian Population History

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          Abstract

          India has been underrepresented in genome-wide surveys of human variation. We analyze 25 diverse groups 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, while 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 India, 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 Andamanese are an ASI-related group without ANI ancestry, showing that the peopling of the islands must have occurred before ANI-ASI gene flow on the mainland. 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 due to endogamy. We therefore predict that there will be an excess of recessive diseases in India, different in each group, which should be possible to screen and map genetically.

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          Genotype, haplotype and copy-number variation in worldwide human populations.

          Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected--including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas--the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.
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            The Jackknife and the Bootstrap for General Stationary Observations

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              Estimation of fixation indices and gene diversities.

              Considering the multinomial sampling of genotypes, unbiased estimators of various gene diversity measures in subdivided populations are presented. Using these quantities, formulae for estimating Wright's fixation indices (FIS, FIT, and FST) from a finite sample are developed.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                0028-0836
                1476-4687
                10 August 2009
                24 September 2009
                24 March 2010
                : 461
                : 7263
                : 489-494
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [2 ]Broad Institute Inc., Cambridge, MA 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, MA 02115, USA
                Author notes
                Correspondence should be addressed to: David Reich ( reich@ 123456genetics.med.harvard.edu ) or Lalji Singh ( lalji@ 123456ccmb.res.in )
                [*]

                These authors contributed equally

                Article
                nihpa137159
                10.1038/nature08365
                2842210
                19779445
                2f59376e-025f-4659-bcab-63183413b67c
                History
                Funding
                Funded by: National Human Genome Research Institute : NHGRI
                Award ID: U01 HG004168-03 ||HG
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