doi: 10.1016/j.ajhg.2013.07.006. Epub 2013 Aug 8.
Genetic evidence for recent population mixture in India
Affiliations
- PMID:23932107
- PMCID: PMC3769933
- DOI: 10.1016/j.ajhg.2013.07.006
Item in Clipboard
Genetic evidence for recent population mixture in India
Priya Moorjani et al. Am J Hum Genet..
Display options
Format
Display options
Format
Abstract
Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.
Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Figures
Principal Component Analysis (A) Map showing the sampling locations for Indian groups in our study (except central_mix1_nihali7). (B) Principal component analysis (PCA) of 70 of 73 groups with non-Indians (European Americans [CEU], Georgian, Iranian, Basque, and Han Chinese [CHB]) highlights the “Indian cline,” a gradient of West Eurasian relatedness. Great Andamanese and Siddi are not included because of their evidence of relatively recent admixture with non-Indian groups, and central_mix1_nihali is not included because it includes multiple ethno-linguistic groups under one label. To aid visualization, we represent each group by the average PCA coordinates of all the individuals in it. Footnote a indicates groups from Metspalu et al. and footnote b indicates groups from HGDP.
Dates of Mixture We pool samples based on linguistic affiliation (Indo-Europeans [n = 175] and Dravidians [n = 144]) and run rolloff (with the merged Illumina-Affymetrix data set of 86,213 SNPs) to measure the LD resulting from mixture between ANI and ASI. To obtain weights proportional to the allele frequency differences between ANI and ASI at each SNP (needed to run rolloff), we use SNP loadings obtained from a PCA of Basque and a pool of groups from the linguistic cluster whose admixture is not being dated (e.g., we run PCA with Indo-European and Basque when we are dating Dravidian admixture). The output of rolloff is represented as points and the line shows the exponential fit used for estimating the time in generations (n) since mixture. The nonzero constantc allows for variability in the mixture proportion among the groups we pooled andd is the genetic distance in Morgans. Standard errors are computed via a weighted block jackknife (see Material and Methods).
Similar articles
- Reconstructing Indian population history.Reich D, Thangaraj K, Patterson N, Price AL, Singh L.Reich D, et al.Nature. 2009 Sep 24;461(7263):489-94. doi: 10.1038/nature08365.Nature. 2009.PMID:19779445Free PMC article.
- Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.Chaubey G, Karmin M, Metspalu E, Metspalu M, Selvi-Rani D, Singh VK, Parik J, Solnik A, Naidu BP, Kumar A, Adarsh N, Mallick CB, Trivedi B, Prakash S, Reddy R, Shukla P, Bhagat S, Verma S, Vasnik S, Khan I, Barwa A, Sahoo D, Sharma A, Rashid M, Chandra V, Reddy AG, Torroni A, Foley RA, Thangaraj K, Singh L, Kivisild T, Villems R.Chaubey G, et al.BMC Evol Biol. 2008 Aug 4;8:227. doi: 10.1186/1471-2148-8-227.BMC Evol Biol. 2008.PMID:18680585Free PMC article.
- A novel gene THSD7A is associated with obesity.Nizamuddin S, Govindaraj P, Saxena S, Kashyap M, Mishra A, Singh S, Rotti H, Raval R, Nayak J, Bhat BK, Prasanna BV, Dhumal VR, Bhale S, Joshi KS, Dedge AP, Bharadwaj R, Gangadharan GG, Nair S, Gopinath PM, Patwardhan B, Kondaiah P, Satyamoorthy K, Valiathan MS, Thangaraj K.Nizamuddin S, et al.Int J Obes (Lond). 2015 Nov;39(11):1662-5. doi: 10.1038/ijo.2015.144. Epub 2015 Aug 4.Int J Obes (Lond). 2015.PMID:26238973
- The human genetic history of South Asia.Majumder PP.Majumder PP.Curr Biol. 2010 Feb 23;20(4):R184-7. doi: 10.1016/j.cub.2009.11.053.Curr Biol. 2010.PMID:20178765Review.
- The genetic makings of South Asia.Metspalu M, Mondal M, Chaubey G.Metspalu M, et al.Curr Opin Genet Dev. 2018 Dec;53:128-133. doi: 10.1016/j.gde.2018.09.003. Epub 2018 Oct 1.Curr Opin Genet Dev. 2018.PMID:30286387Review.
Cited by
- Genetic ancestry in population pharmacogenomics unravels distinct geographical patterns related to drug toxicity.Karamperis K, Katz S, Melograna F, Ganau FP, Van Steen K, Patrinos GP, Lao O.Karamperis K, et al.iScience. 2024 Sep 10;27(10):110916. doi: 10.1016/j.isci.2024.110916. eCollection 2024 Oct 18.iScience. 2024.PMID:39391720Free PMC article.
- Association Between Episodic Memory and Genetic Risk Factors for Alzheimer's Disease in South Asians from the Longitudinal Aging Study in India-Diagnostic Assessment of Dementia (LASI-DAD).Smith JA, Zhao W, Yu M, Rumfelt KE, Moorjani P, Ganna A, Dey AB, Lee J, Kardia SLR.Smith JA, et al.J Am Geriatr Soc. 2020 Aug;68 Suppl 3(Suppl 3):S45-S53. doi: 10.1111/jgs.16735.J Am Geriatr Soc. 2020.PMID:32815605Free PMC article.
- A comprehensive meta-analysis and a case-control study give insights into genetic susceptibility of lung cancer and subgroups.Sengupta D, Banerjee S, Mukhopadhyay P, Mitra R, Chaudhuri T, Sarkar A, Bhattacharjee G, Nath S, Roychoudhury S, Bhattacharjee S, Sengupta M.Sengupta D, et al.Sci Rep. 2021 Jul 16;11(1):14572. doi: 10.1038/s41598-021-92275-z.Sci Rep. 2021.PMID:34272429Free PMC article.
- Genetic affinities of the Jewish populations of India.Chaubey G, Singh M, Rai N, Kariappa M, Singh K, Singh A, Pratap Singh D, Tamang R, Selvi Rani D, Reddy AG, Kumar Singh V, Singh L, Thangaraj K.Chaubey G, et al.Sci Rep. 2016 Jan 13;6:19166. doi: 10.1038/srep19166.Sci Rep. 2016.PMID:26759184Free PMC article.
- Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.Hsieh P, et al.Genome Res. 2016 Mar;26(3):291-300. doi: 10.1101/gr.196634.115. Epub 2016 Feb 17.Genome Res. 2016.PMID:26888264Free PMC article.
References
- Sahoo S., Kashyap V.K. Phylogeography of mitochondrial DNA and Y-chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India. Am. J. Phys. Anthropol. 2006;131:84–97. - PubMed
- Kivisild T., Bamshad M.J., Kaldma K., Metspalu M., Metspalu E., Reidla M., Laos S., Parik J., Watkins W.S., Dixon M.E. Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages. Curr. Biol. 1999;9:1331–1334. - PubMed
- Metspalu M., Kivisild T., Metspalu E., Parik J., Hudjashov G., Kaldma K., Serk P., Karmin M., Behar D.M., Gilbert M.T.P. Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet. 2004;5:26. - PMC - PubMed
Publication types
MeSH terms
Related information
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources