{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T19:45:52Z","timestamp":1792611952280,"version":"4.5.0"},"reference-count":71,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,7]],"date-time":"2024-02-07T00:00:00Z","timestamp":1707264000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p><jats:bold>Introduction:<\/jats:bold> The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis.<\/jats:p><jats:p><jats:bold>Methods and Results:<\/jats:bold> Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, O\u1e47\u1e6di and Ku\u1e47\u1e6du. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (\u223c38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum.<\/jats:p><jats:p><jats:bold>Discussion:<\/jats:bold> Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.<\/jats:p>","DOI":"10.3389\/fgene.2023.1303628","type":"journal-article","created":{"date-parts":[[2024,2,7]],"date-time":"2024-02-07T14:06:16Z","timestamp":1707314776000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity"],"prefix":"10.3389","volume":"14","author":[{"given":"Jaison Jeevan","family":"Sequeira","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kadengodlu","family":"Vinuthalakshmi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranajit","family":"Das","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"van Driem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed S.","family":"Mustak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,2,7]]},"reference":[{"key":"B1","volume-title":"Genomic diversity in people of India: focus on mtDNA and Y-chromosome polymorphism","year":""},{"key":"B2","first-page":"11","article-title":"Mitochondrial DNA phylogeny of M haplogroup in Indian population","volume-title":"Genomic diversity in people of India","year":""},{"key":"B3","first-page":"145","article-title":"Y-chromosome phylogeny in Indian population","volume-title":"Genomic diversity in people of India","year":""},{"key":"B4","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1101\/gr.gr-1733rr","article-title":"Genetic evidence on the origins of Indian caste populations","volume":"11","author":"Bamshad","year":"2001","journal-title":"Genome Res."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1594","DOI":"10.1073\/pnas.1513197113","article-title":"Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure","volume":"113","author":"Basu","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B6","volume-title":"The Koraga Language","author":"Bhat","year":"1971"},{"key":"B7","doi-asserted-by":"publisher","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PLOS Comput. Biol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1093\/molbev\/msx267","article-title":"The paleo-Indian entry into South America according to mitogenomes","volume":"35","author":"Brandini","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B9","volume-title":"A Comparative Grammar of the Dravidian or South-Indian Family of Languages","author":"Caldwell","year":"1856"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.1016\/j.cell.2021.02.040","article-title":"Archaeogenomic distinctiveness of the Isthmo-Colombian area","volume":"184","author":"Capodiferro","year":"2021","journal-title":"Cell"},{"key":"B11","doi-asserted-by":"publisher","first-page":"e7447","DOI":"10.1371\/journal.pone.0007447","article-title":"Updating phylogeny of mitochondrial DNA macrohaplogroup M in India: dispersal of modern human in South asian corridor","volume":"4","author":"Chandrasekar","year":"2009","journal-title":"PLoS One"},{"key":"B12","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1080\/03014460701556262","article-title":"YAP insertion signature in South Asia","volume":"34","author":"Chandrasekar","year":"2007","journal-title":"Ann. Hum. Biol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1093\/molbev\/msq288","article-title":"Population genetic structure in indian austroasiatic speakers: the role of landscape barriers and sex-specific admixture","volume":"28","author":"Chaubey","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"6827","DOI":"10.1038\/s41598-022-10530-3","article-title":"Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population","volume":"12","author":"Connell","year":"2022","journal-title":"Sci. Rep."},{"key":"B15","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.cub.2004.01.024","article-title":"Independent origins of Indian caste and tribal paternal lineages","volume":"14","author":"Cordaux","year":"2004","journal-title":"Curr. Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1038\/sj.ejhg.5200949","article-title":"Mitochondrial DNA analysis reveals diverse histories of tribal populations from India","volume":"11","author":"Cordaux","year":"2003","journal-title":"Eur. J. Hum. Genet."},{"key":"B17","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1038\/jhg.2011.98","article-title":"Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India","volume":"56","author":"Debnath","year":"2011","journal-title":"J. Hum. Genet."},{"key":"B18","doi-asserted-by":"publisher","first-page":"D29","DOI":"10.1093\/nar\/gky843","article-title":"AmtDB: a database of ancient human mitochondrial genomes","volume":"47","author":"Ehler","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B19","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","article-title":"Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows","volume":"10","author":"Excoffier","year":"2010","journal-title":"Mol. Ecol. Resour."},{"key":"B20","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.202400499","article-title":"Natural radioactivity and human mitochondrial DNA mutations","volume":"99","author":"Forster","year":"2002","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1093\/jhered\/89.5.415","article-title":"Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation","volume":"89","author":"Grant","year":"1998","journal-title":"J. Hered."},{"key":"B22","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1186\/1471-2164-13-440","article-title":"Sequencing and analysis of a South Asian-Indian personal genome","volume":"13","author":"Gupta","year":"2012","journal-title":"BMC Genomics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"34288","DOI":"10.1371\/journal.pone.0034288","article-title":"Afghanistan\u2019s ethnic groups share a Y-chromosomal heritage structured by historical events","volume":"7","author":"Haber","year":"2012","journal-title":"PLoS One"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1101\/gr.686603","article-title":"Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines","volume":"13","author":"Ingman","year":"2003","journal-title":"Genome Res."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1016\/S0960-9822(00)80057-3","article-title":"Deep common ancestry of Indian and Western-Eurasian mitochondrial DNA lineages","volume":"9","author":"Kivisild","year":"1999","journal-title":"Curr. Biol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1086\/346068","article-title":"The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations","volume":"72","author":"Kivisild","year":"2003","journal-title":"Am. J. Hum. Genet."},{"key":"B27","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511486876","volume-title":"The Dravidian Languages","author":"Krishnamurti","year":"2003"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1038\/ejhg.2012.59","article-title":"Afghanistan from a Y-chromosome perspective","volume":"20","author":"Lacau","year":"2012","journal-title":"Eur. J. Hum. Genet."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"POPART: full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"B30","doi-asserted-by":"crossref","DOI":"10.2307\/1006352","article-title":"Proto Elamo Dravidian: The evidence and its implications","volume-title":"Transactions of the American Philosophical Society","author":"McAlpin","year":"1981"},{"key":"B31","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1471-2156-5-20","article-title":"A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family","volume":"5","author":"Metspalu","year":"2004","journal-title":"BMC Genet."},{"key":"B32","doi-asserted-by":"publisher","first-page":"6968","DOI":"10.1038\/s41598-019-43384-3","article-title":"The peopling of Lakshadweep archipelago","volume":"9","author":"Mustak","year":"2019","journal-title":"Sci. Rep."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1126\/science.1135566","article-title":"The mtDNA legacy of the levantine early Upper Palaeolithic in Africa","volume":"314","author":"Olivieri","year":"2006","journal-title":"Science"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1093\/molbev\/msx082","article-title":"Mitogenome diversity in Sardinians: a genetic window onto an island\u2019s past","volume":"34","author":"Olivieri","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"B35","first-page":"267","article-title":"An ethnolinguistic and genetic perspective on the origins of the Dravidian-speaking Brahui in Pakistan","volume":"97","author":"Pagani","year":"2017","journal-title":"Man In India"},{"key":"B36","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1007\/s00439-015-1547-4","article-title":"West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system","volume":"134","author":"Palanichamy","year":"2015","journal-title":"Hum. Genet."},{"key":"B37","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1086\/425871","article-title":"Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia","volume":"75","author":"Palanichamy","year":"2004","journal-title":"Am. J. Hum. Genet."},{"key":"B38","first-page":"185","article-title":"Languages and genes: modes of transmission observed through the analysis of male-specific and female-specific genes","volume-title":"Proceedings: evolution of language, 3rd international conference 3-6 april","author":"Poloni","year":"2000"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1086\/301602","article-title":"Human genetic affinities for Y-chromosome P49a,f\/TaqI haplotypes show strong correspondence with linguistics (cf. The erratum published in 1998 in the American journal of human genetics, 62: 1267","volume":"61","author":"Poloni","year":"1997","journal-title":"Am. J. Hum. Genet."},{"key":"B40","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/ng.3559","article-title":"Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences","volume":"48","author":"Poznik","year":"2016","journal-title":"Nat. Genet."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1086\/339929","article-title":"Y-chromosomal DNA variation in Pakistan","volume":"70","author":"Qamar","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"B42","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1086\/318200","article-title":"Y-chromosome lineages trace diffusion of people and languages in southwestern Asia","volume":"68","author":"Quintana-Murci","year":"2001","journal-title":"Am. J. Hum. Genet."},{"key":"B43","article-title":"C-16 population by mother tongue\u201d, Census of India","year":"2011"},{"key":"B44","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1038\/nature08365","article-title":"Reconstructing Indian population history","volume":"461","author":"Reich","year":"2009","journal-title":"Nature"},{"key":"B45","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/s004390100577","article-title":"Genomic structures and population histories of linguistically distinct tribal groups of India","volume":"109","author":"Roychoudhury","year":"2001","journal-title":"Hum. Genet."},{"key":"B46","doi-asserted-by":"publisher","first-page":"W263","DOI":"10.1093\/nar\/gkad284","article-title":"Haplogrep 3 - an interactive haplogroup classification and analysis platform","volume":"51","author":"Sch\u00f6nherr","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B47","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.ajhg.2011.05.030","article-title":"Indian siddis: African descendants with Indian admixture","volume":"89","author":"Shah","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1038\/jhg.2008.2","article-title":"The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system (cf. the erratum published in 2014 in the Journal of Human Genetics, 59:7, 415","volume":"54","author":"Sharma","year":"2009","journal-title":"J. Hum. Genet."},{"key":"B49","volume-title":"Hindu Tribes and Castes Vol III","author":"Sherring","year":"1881"},{"key":"B50","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1186\/s12862-017-0936-9","article-title":"A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals","volume":"17","author":"Silva","year":"2017","journal-title":"BMC Evol. Biol."},{"key":"B51","volume-title":"Census of India 1891 Volume XIII Madras - The Report of the Census","author":"Stuart","year":"1893"},{"key":"B52","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1080\/03014460.2019.1599067","article-title":"Maternal genetic link of a South Dravidian tribe with native Iranians indicating bidirectional migration","volume":"46","author":"Sylvester","year":"2019","journal-title":"Ann. Hum. Biol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/1471-2164-7-151","article-title":"In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup \u201cM\u201d in India","volume":"7","author":"Thangaraj","year":"2006","journal-title":"BMC Genomics"},{"key":"B54","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1126\/science.1109987","article-title":"Reconstructing the origin of Andaman Islanders","author":"Thangaraj","year":"2005","journal-title":"Sci."},{"key":"B55","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1002\/j.1939-4640.2002.tb02338.x","article-title":"CAG repeat expansion in the androgen receptor gene is not associated with male infertility in Indian populations","volume":"23","author":"Thangaraj","year":"2002","journal-title":"J. Androl."},{"key":"B56","doi-asserted-by":"publisher","first-page":"1743","DOI":"10.1002\/(SICI)1522-2683(19990101)20:8<1743::AID-ELPS1743>3.0.CO;2-V","article-title":"Y\u2010chromosome and mitochondrial DNA polymorphisms in Indian populations","volume":"20","author":"Thangaraj","year":"1999","journal-title":"Electrophoresis"},{"key":"B57","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1471-2156-7-42","article-title":"Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA","volume":"7","author":"Thanseem","year":"2006","journal-title":"BMC Genet."},{"key":"B58","volume-title":"Castes and Tribes of Southern India vol-III","author":"Thurston","year":"1909"},{"key":"B59","doi-asserted-by":"publisher","first-page":"e1010243","DOI":"10.1371\/journal.pgen.1010243","article-title":"Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals","volume":"18","author":"Tournebize","year":"2022","journal-title":"PLOS Genet."},{"key":"B60","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1080\/09723757.2008.11886023","article-title":"Genetic imprints of Pleistocene origin of Indian populations: a comprehensive phylogeographic sketch of Indian Y-chromosomes","volume":"8","author":"Trivedi","year":"2008","journal-title":"Int. J. Hum. Genet."},{"key":"B61","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1163\/2405478x-90000111","article-title":"East asian ethnolinguistic phylogeography","volume":"7","author":"van Driem","year":"2013","journal-title":"Bull. Chin. Linguist."},{"key":"B62","first-page":"60","article-title":"A prehistoric thoroughfare between the Ganges and the Himalayas","volume-title":"50 Years after Daojali-Hading: Emerging Perspectives in the Archaeology of Northeast India","author":"van Driem","year":"2014"},{"key":"B63","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1515\/9783110275681.335","article-title":"Etyma, shouldered adzes and molecular variants","author":"van Driem","year":"2012","journal-title":"Methods in Contemporary Linguistics"},{"key":"B64","doi-asserted-by":"crossref","DOI":"10.1163\/9789004448377","volume-title":"Ethnolinguistic Prehistory","author":"van Driem","year":"2021"},{"key":"B65","doi-asserted-by":"publisher","first-page":"E386","DOI":"10.1002\/humu.20921","article-title":"Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation","volume":"30","author":"van Oven","year":"2009","journal-title":"Hum. Mutat."},{"key":"B66","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1046\/j.1529-8817.2003.00083.x","article-title":"Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers","volume":"68","author":"Vishwanathan","year":"2004","journal-title":"Ann. Hum. Genet."},{"key":"B67","doi-asserted-by":"publisher","first-page":"369","DOI":"10.2307\/2840981","article-title":"Some account of a leaf-wearing tribe on the western coast of India","volume":"4","author":"Walhouse","year":"1875","journal-title":"J. Anthropol. Inst. G. B. Irel."},{"key":"B68","first-page":"1174","article-title":"Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis","volume":"60","author":"Zerjal","year":"1997","journal-title":"Am. J. Hum. Genet."},{"key":"B69","volume-title":"Dravidian Linguistics: An Introduction","author":"Zvelebil","year":"1990"},{"key":"B70","doi-asserted-by":"publisher","first-page":"523","DOI":"10.2307\/602307","article-title":"B\u00eb\u1e6d\u1e6d\u0289 Ku\u1e5fumba: first report on a tribal language","volume":"102","author":"Zvelebil","year":"1982","journal-title":"J. Am. Orient Soc."},{"key":"B71","doi-asserted-by":"publisher","first-page":"297","DOI":"10.2307\/603656","article-title":"J\u0113nu Ku\u1e5fumba: Brief report on a \u201ctribal\u201d language of the Nilgiri area","volume":"108","author":"Zvelebil","year":"1988","journal-title":"J. Am. Orient Soc."}],"updated-by":[{"DOI":"10.3389\/fgene.2024.1384937","type":"corrigendum","label":"Corrigendum","source":"publisher","updated":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T00:00:00Z","timestamp":1710201600000}}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2023.1303628\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T15:55:41Z","timestamp":1710172541000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2023.1303628\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,7]]},"references-count":71,"alternative-id":["10.3389\/fgene.2023.1303628"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2023.1303628","relation":{"corrigendum":[{"id-type":"doi","id":"10.3389\/fgene.2024.1384937","asserted-by":"object"}]},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,7]]},"article-number":"1303628"}}