Abstract
There is no indication from the previous mtDNA studies that west Eurasian-specific subclades have evolved within India and played a role in the spread of languages and the origins of the caste system. To address these issues, we have screened 14,198 individuals (4208 from this study) and analyzed 112 mitogenomes (41 new sequences) to trace west Eurasian maternal ancestry. This has led to the identification of two autochthonous subhaplogroupsāHV14a1 and U1a1a4, which are likely to have originated in the Dravidian-speaking populations approximately 10.5ā17.9 thousand years ago (kya). The carriers of these maternal lineages might have settled in South India during the time of the spread of the Dravidian language. In addition to this, we have identified several subsets of autochthonous U7 lineages, including U7a1, U7a2b, U7a3, U7a6, U7a7, and U7c, which seem to have originated particularly in the higher-ranked caste populations in relatively recent times (2.6ā8.0Ā kya with an average of 5.7Ā kya). These lineages have provided crucial clues to the differentiation of the caste system that has occurred during the recent past and possibly, this might have been influenced by the Indo-Aryan migration. The remaining west Eurasian lineages observed in the higher-ranked caste groups, like the Brahmins, were found to cluster with populations who possibly arrived from west Asia during more recent times.
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References
Abu-Amero KK, Larruga JM, Cabrera VM, GonzƔlez AM (2008) Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol Biol 8:45
Achilli A, Rengo C, Magri C et al (2004) The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75:910ā918
Al-Abri A, PodgornĆ” E, Rose JI et al (2012) Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation. Am J Phys Anthropol 149:291ā298
Al-Zahery N, Semino O, Benuzzi G et al (2003) Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations. Mol Phylogenet Evol 28:458ā472
Al-Zahery N, Pala M, Battaglia V et al (2011) In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq. BMC Evol Biol 11:288
Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147
Arunkumar G, Soria-Hernanz DF, Kavitha VJ et al (2012) Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS One 7:e50269
Bamshad MJ, Watkins WS, Dixon ME et al (1998) Female gene flow stratifies Hindu castes. Nature 395:651ā652
Bamshad M, Kivisild T, Watkins WS et al (2001) Genetic evidence on the origins of Indian caste populations. Genome Res 11:994ā1004
Basu A, Mukherjee N, Roy S et al (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res 13:2277ā2290
Behar DM, van Oven M, Rosset S et al (2012) A āCopernicanā reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90:675ā684
CernĆ½ V, Mulligan CJ, Fernandes V et al (2011) Internal diversification of mitochondrial haplogroup R0a reveals post-last glacial maximum demographic expansions in South Arabia. Mol Biol Evol 28:71ā78
Chaubey G, Metspalu M, Kivisild T, Villems R (2007) Peopling of South Asia: investigating the caste-tribe continuum in India. Bioessays 29:91ā100
Coble MD, Just RS, OāCallaghan JE et al (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 118:137ā146
Comas D, Calafell F, Mateu E et al (1998) Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations. Am J Hum Genet 63:1824ā1838
Comas D, Calafell F, Bendukidze N, FaƱanĆ”s L, Bertranpetit J (2000) Georgian and kurd mtDNA sequence analysis shows a lack of correlation between languages and female genetic lineages. Am J Phys Anthropol 112:5ā16
Comas D, Plaza S, Wells RS et al (2004) Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet 12:495ā504
Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking M (2003) Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet 11:253ā264
Cordaux R, Aunger R, Bentley G, Nasidze I, Sirajuddin SM, Stoneking M (2004) Independent origins of Indian caste and tribal paternal lineages. Curr Biol 14:231ā235
Derenko M, Malyarchuk B, Bahmanimehr A et al (2013) Complete mitochondrial DNA diversity in Iranians. PLoS One 8:e80673
Derenko M, Malyarchuk B, Denisova G et al (2014) Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evol Biol 14:217
Fedorova SA, Reidla M, Metspalu E et al (2013) Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evol Biol 13:127
Fernandes V, Alshamali F, Alves M et al (2012) The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. Am J Hum Genet 90:347ā355
Forster P, Torroni A, Renfrew C, Rƶhl A (2001) Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol Biol Evol 18:1864ā1881
Gaikwad S, Kashyap VK (2005) Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across non-recombinant and recombinant regions in genome. Genome Biol 6:P10
Grugni V, Battaglia V, Hooshiar Kashani B et al (2012) Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One 7:e41252
Hartmann A, Thieme M, Nanduri LK et al (2009) Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum Mutat 30:115ā122
Ingman M, Gyllensten U (2003) Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res 13:1600ā1606
Kivisild T, Bamshad MJ, Kaldma K et al (1999a) Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr Biol 9:1331ā1334
Kivisild T, Kaldma K, Metspalu M, Parik J, Papiha S, Villems R (1999b) The place of the Indian mtDNA variants in the global network of maternal lineages and the peopling of the Old World. In: Deka R, Papiha SS (eds) Genomic diversity. Kluwer Academic/Plenum Publishers, New York
Kivisild T, Papiha SS, Rootsi S et al (2000) An indian ancestry: a key for understanding human diversity in Europe and beyond. In: Renfrew C, Boyle K (eds) Archaeogenetics: DNA and the population history of Europe. McDonald Institute for Archaeological Research, Cambridge
Kivisild T, Rootsi S, Metspalu M et al (2003a) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72:313ā332
Kivisild T, Rootsi S, Metspalu M et al (2003b) The genetics of language and farming spread in India. In: Bellwood P, Renfrew C (eds) Examining the farming/language dispersal hypothesis. McDonald Institute Monographs, Cambridge
Kivisild T, Shen P, Wall DP et al (2006) The role of selection in the evolution of human mitochondrial genomes. Genetics 172:373ā387
LoogvƤli EL, Roostalu U, Malyarchuk BA et al (2004) Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol 21:2012ā2021
LoogvƤli EL, Kivisild T, Margus T, Villems R (2009) Explaining the imperfection of the molecular clock of Hominid mitochondria. PLoS One 4:e8260
Macaulay V, Richards M, Hickey E et al (1999) The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am J Hum Genet 64:232ā249
Malyarchuk B, Grzybowski T, Derenko M et al (2008) Mitochondrial DNA phylogeny in Eastern and Western Slavs. Mol Biol Evol 25:1651ā1658
Malyarchuk B, Derenko M, Grzybowski T et al (2010) The peopling of Europe from the mitochondrial haplogroup U5 perspective. PLoS One 5:e10285
Metspalu M, Kivisild T, Metspalu E et al (2004) 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 5:26
Mishmar D, Ruiz-Pesini E, Golik P et al (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci 100:171ā176
Nasidze I, Stoneking M (2001) Mitochondrial DNA variation and language replacements in the Caucasus. Proc Biol Sci 268:1197ā1206
Nasidze I, Ling EY, Quinque D et al (2004) Mitochondrial DNA and Y-chromosome variation in the Caucasus. Ann Hum Genet 68:205ā221
Nasidze I, Quinque D, Rahmani M, Alemohamad SA, Stoneking M (2006) Concomitant replacement of language and mtDNA in South Caspian populations of Iran. Curr Biol 16:668ā673
Nasidze I, Quinque D, Rahmani M, Alemohamad SA, Stoneking M (2008) Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran. Ann Hum Genet 72:241ā252
Olivieri A, Pala M, Gandini F et al (2013) Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and Neolithic dispersals within Europe. PLoS One 8:e70492
Pagel M, Atkinson QD, Calude AS, Meade A (2013) Ultra conserved words point to deep language ancestry across Eurasia. Proc Natl Acad Sci 110:8471ā8476
Pala M, Olivieri A, Achilli A et al (2012) Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. Am J Hum Genet 90:915ā924
Palanichamy MG, Sun C, Agrawal S et al (2004) Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 75:966ā978
Palanichamy MG, Zhang CL, Mitra B et al (2010) Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers. BMC Evol Biol 10:304
Perego UA, Achilli A, Angerhofer N et al (2009) Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 19:1ā8
Quintana-Murci L, Chaix R, Wells RS et al (2004) Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. Am J Hum Genet 74:827ā845
Rajkumar R, Kashyap VK (2003) Haplotype diversity in mitochondrial DNA hypervariable regions I and II in three communities of Southern India. Forensic Sci Int 136:79ā82
Rakha A, Shin KJ, Yoon JA et al (2011) Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 125:841ā848
Ranaweera L, Kaewsutthi S, Win Tun A, Boonyarit H, Poolsuwan S, Lertrit P (2014) Mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations. J Hum Genet 59:28ā36
Richards M, Macaulay V, Hickey E et al (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67:1251ā1276
Roostalu U, Kutuev I, LoogvƤli EL et al (2007) Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol 24:436ā448
Sahoo S, Singh A, Himabindu G et al (2006) A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci 103:843ā848
Saillard J, Forster P, Lynnerup N, Bandelt HJ, NĆørby S (2000) mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet 67:718ā726
Scheible M, Alenizi M, Sturk-Andreaggi K, Coble MD, Ismael S, Irwin JA (2011) Mitochondrial DNA control region variation in a Kuwaiti population sample. Forensic Sci Int Genet 5:e112āe113
Schƶnberg A, Theunert C, Li M, Stoneking M, Nasidze I (2011) High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. Eur J Hum Genet 19:988ā994
Sengupta S, Zhivotovsky LA, King R et al (2006) Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 78:202ā221
Soares P, Ermini L, Thomson N et al (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84:740ā759
Tamang R, Thangaraj K (2012) Genomic view on the peopling of India. Investig Genet 3:20
Terreros MC, Rowold DJ, Mirabal S, Herrera RJ (2011) Mitochondrial DNA and Y-chromosomal stratification in Iran: relationship between Iran and the Arabian Peninsula. J Hum Genet 56:235ā246
van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:e386āe394
Acknowledgments
This work was supported by Yunnan University, the Yunnan provincial Science and Technology Department and from Grants from the National Natural Science Foundation of China (31060156 and 31240018).
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439_2015_1547_MOESM1_ESM.xls (download XLS )
Supplementary material 1 (XLS 279 kb) Supplementary Table S1. Distribution of west Eurasian haplogroups in India. Supplementary Table S2. List of samples screened for west Eurasian haplogroups. Supplementary Table S3. West Eurasian haplogroup frequencies (%) in Regional, Social and Linguistic-subgroups of Indian populations
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Supplementary material 2 (PPT 290 kb) Supplementary Figures S1-S6: Phylogenetic tree of west Eurasian haplogroups H*, H2, H3 g, H5a1, H7b, H9, H13a, H15a1a, H103, V2, HV*, HV2a, HV6b, HV12b1, R0a2, JT, K1, U2e, U3-U5a1, R1, R2, W, and N1a. Mutations are scored relative to the revised Cambridge reference sequence (rCRS) (Andrews et al. 1999) and displayed along the branches. The prefix āā@āā indicates back mutation, recurrent mutations are underlined, transversions have a base suffix, āādāā deletions and āā+āā insertions, and the poly(C) region in HVS-I and -II as well as 16519 is excluded. The geographic origin of the sample and the accession number which is retrieved from the publication are given above the branches
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Palanichamy, M.G., Mitra, B., Zhang, CL. et al. West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system. Hum Genet 134, 637ā647 (2015). https://doi.org/10.1007/s00439-015-1547-4
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DOI: https://doi.org/10.1007/s00439-015-1547-4
