Reconstructing Indian population history
Open accessAbstract
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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Standard errors for all allele-frequency-based statistics were computed using a block bootstrap with 100 replicates and a block size of 1000 markers.
“Standard errors for all allele frequency based statistics were computed using the block-bootstrap using 100 replicates and a block size of 1000 markers86.”
From Paths and timings of the peopling of Polynesia inferred from genomic networks (2021) · cites this paper as [86]
The Methods Summary (page not available in our copy) says standard errors were computed using a Block Jackknife, not a block bootstrap. It does not give the claimed 100 replicates or 1,000-marker block size. (LLM, conf=0.89)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe demographic impact of steppe related populations on South Asia was substantial: the Mala are inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans.
“The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry34,35 is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans7.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [34]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredDarkly pigmented skin, or the potential for facultative dark pigmentation through tanning, evolved secondarily under positive selection in populations moving from low- to high-UVR environments.
“Evidence is mounting that darkly pigmented skin, or the potential for facultative development of dark pigmentation through tanning, evolved secondarily under positive selection in populations moving from low-to high-UVR environments.”
From Human skin pigmentation as an adaptation to UV radiation (2010) · cites this paper as [44]
The Discussion addresses ancestry and population structure in India, while Medical implications addresses genetic differentiation and disease risk. Searches for skin pigmentation, tanning, UVR, and selection found no passage in our copy addressing the claimed evolution of dark pigmentation in populations moving to high-UVR environments. (LLM, conf=0.76)
Experimental — accuracy not yet measuredIt is impossible to model the Ancestral North Indians (ANI) as being derived from any single ancient population in the dataset.
“We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [34]
The ‘Relationship of Indians to non-Indians’ section reports that ANI and CEU form a clade, but does not test whether ANI could derive from any single ancient population in a dataset. The Discussion says that the history of ANI before mixture remains a priority for future work. Searches for the claimed single-population modelling result found no passage addressing it. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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Percentages, sums and reported differences re-computed from the paper’s own numbers.
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- Authors
- Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Centre for Cellular and Molecular Biology (IN)
- Corresponding author
- Reich, David
- Singh, Lalji
- Venue
- Nature
- Published
- 2009-09
- Volume
- 461
- Issue
- 7263
- Pages
- 489-494
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2842210
- OpenAlex
- W2119228812
- Cited by
- 1,674
- References
- 53
- Citations by year
- 2026: 67 · 2025: 122 · 2024: 104 · 2023: 70 · 2022: 116 · 2021: 147 · 2020: 119 · 2019: 108 · 2018: 112 · 2017: 103 · 2016: 102 · 2015: 101 · 2014: 88 · 2013: 93 · 2012: 61
- FWCI
- 42.70
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- UK-India Education and Research Initiative
- Council of Scientific and Industrial Research, India
- National Institutes of Health
- National Human Genome Research Institute (R01HG006399, U01HG004168, HG004168)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- population structure, ancestry estimation, endogamy, founder effect, allele frequency differences, genetic admixture
- MeSH terms
- Asia, DNA, Mitochondrial, Ethnicity, Europe, Female, Gene Frequency, Genes, Recessive, Genetics, Medical, Genetics, Population, Genotype, Geography, Humans, India, Language, Male, Middle East, Phylogeny, Genetic Variation, Linkage Disequilibrium, Genome, Human, Founder Effect, Polymorphism, Single Nucleotide, Genomics, Principal Component Analysis, Chromosomes, Human, Y, Racial Groups
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