Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

详细信息    查看全文

• 作者：Gyaneshwer Chaubey (1) (2)
  Monika Karmin (1)
  Ene Metspalu (1)
  Mait Metspalu (1)
  Deepa Selvi-Rani (2)
  Vijay Kumar Singh (2)
  Jüri Parik (1)
  Anu Solnik (1)
  B Prathap Naidu (2)
  Ajay Kumar (2) (5)
  Niharika Adarsh (2) (5)
  Chandana Basu Mallick (2) (5)
  Bhargav Trivedi (2) (5)
  Swami Prakash (2) (5)
  Ramesh Reddy (2) (5)
  Parul Shukla (2) (5)
  Sanjana Bhagat (2) (5)
  Swati Verma (2) (5)
  Samiksha Vasnik (2) (5)
  Imran Khan (2) (5)
  Anshu Barwa (2) (5)
  Dipti Sahoo (2) (5)
  Archana Sharma (2) (5)
  Mamoon Rashid (2) (5)
  Vishal Chandra (2) (5)
  Alla G Reddy (2)
  Antonio Torroni (3)
  Robert A Foley (4)
  Kumarasamy Thangaraj (2)
  Lalji Singh (2)
  Toomas Kivisild (1) (4)
  Richard Villems (1)
  
• 刊名：BMC Evolutionary Biology
• 出版年：2008
• 出版时间：December 2008
• 年：2008
• 卷：8
• 期：1
• 全文大小：1279KB
• 参考文献：1. Papiha SS: "Genetic variation in India". / Hum Biol 1996, 68 (5) : 607-8.
  2. Singh KS, Ed: The Scheduled Tribes. / People of India Oxford, Oxford University Press 1997.
  3. Singh KS, Ed: The Scheduled Castes. / People of India New Dehli, Oxford University Press 2002.
  4. Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F, Wang CY, Chaudhuri TK, Palla V, Zhang YP: Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of Indian subcontinent. / Am J Hum Genet 2004, 75 (6) : 966-78. CrossRef
  5. Forster P, Matsumura S: Evolution. Did early humans go north or south? / Science 2005, 308 (5724) : 965-66. CrossRef
  6. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, Taha A, Shaari NK, Raja JM, Ismail P, Zainuddin Z, Goodwin W, Bulbeck D, Bandelt HJ, Oppenheimer S, Torroni A, Richards M: Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. / Science 2005, 308 (5724) : 1034-036. CrossRef
  7. Thangaraj K, Sridhar V, Kivisild T, Reddy AG, Chaubey G, Singh VK, Kaur S, Agarawal P, Rai A, Gupta J, Mallick CB, Kumar N, Velavan TP, Suganthan R, Udaykumar D, Kumar R, Mishra R, Khan A, Annapurna C, Singh L: Different population histories of the Mundari-and Mon–Khmer–speaking Austro–Asiatic tribes inferred from the mtDNA 9–bp deletion/insertion polymorphism in Indian populations. / Hum Genet 2005, 116 (6) : 507-17. CrossRef
  8. Thangaraj K, Chaubey G, Singh VK, Vanniarajan A, Thanseem I, Reddy AG, Singh L: In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India. / BMC Genomics 2006, 7: 151. CrossRef
  9. Thangaraj K, Chaubey G, Kivisild T, Selvi Rani D, Singh VK, Ismail T, Carvalho–Silva D, Metspalu M, Bhaskar LV, Reddy AG, Chandra S, Pande V, Prathap Naidu B, Adarsh N, Verma A, Jyothi IA, Mallick CB, Shrivastava N, Devasena R, Kumari B, Singh AK, Dwivedi SK, Singh S, Rao G, Gupta P, Sonvane V, Kumari K, Basha A, Bhargavi KR, Lalremruata A, Gupta AK, Kaur G, Reddy KK, Rao AP, Villems R, Tyler–Smith C, Singh L: Maternal footprints of Southeast Asians in North India. / Hum Hered 2008, 66 (1) : 1-. CrossRef
  10. Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, Yao YG, Khan F, Zhu CL, Chaudhuri TK, Zhang YP: The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. / Mol Biol Evol 2006, 23 (3) : 683-90. CrossRef
  11. Petraglia M, Allchin B: Human evolution and culture change in the Indian subcontinent. / The Evolution and History of Human Populations in Indian subcontinent / (Edited by: Petraglia M, Allchin B). Springer, Netherlands 2007, 393-43.
  12. Kivisild T, Bamshad MJ, Kaldma K, Metspalu M, Metspalu E, Reidla M, Laos S, Parik J, Watkins WS, Dixon ME, Papiha SS, Mastana SS, Mir MR, Ferak V, Villems R: Deep common ancestry of indian and western–Eurasian mitochondrial DNA lineages. / Curr Biol 1999, 9 (22) : 1331-334. CrossRef
  13. Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, Parik J, Metspalu E, Adojaan M, Tolk HV, Stepanov V, Golge M, Usanga E, Papiha SS, Cinnioglu C, King R, Cavalli–Sforza L, Underhill PA, Villems R: The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. / Am J Hum Genet 2003, 72 (2) : 313-32. CrossRef
  14. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, Karmin M, Behar DM, Gilbert MT, Endicott P, Mastana S, Papiha SS, Skorecki K, Torroni A, Villems R: 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. CrossRef
  15. Chaubey G, Metspalu M, Kivisild T, Villems R: Peopling of Indian subcontinent: investigating the caste–tribe continuum in India. / Bioessays 2007, 29 (1) : 91-00. CrossRef
  16. Chaubey G, Metspalu M, Karmin M, Thangaraj K, Rootsi S, Parik J, Solnik A, Selvi Rani D, Singh VK, Naidu BP, Reddy AG, Metspalu E, Singh L, Kivisild T, Villems R: Language shift by indigenous population: A Model Genetic Study in Indian subcontinent. / Int J Hum Genet 2008, 8: 41-0.
  17. Sahoo S, Singh A, Himabindu G, Banerjee J, Sitalaximi T, Gaikwad S, Trivedi R, Endicott P, Kivisild T, Metspalu M, Villems R, Kashyap VK: A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. / Proc Natl Acad Sci USA 2006, 103 (4) : 843-48. CrossRef
  18. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE, Lin AA, Mitra M, Sil SK, Ramesh A, Usha Rani MV, Thakur CM, Cavalli–Sforza LL, Majumder PP, Underhill PA: 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 2006, 78 (2) : 202-21. CrossRef
  19. Watkins WS, Prasad BV, Naidu JM, Rao BB, Bhanu BA, Ramachandran B, Das PK, Gai PB, Reddy PC, Reddy PG, Sethuraman M, Bamshad MJ, Jorde LB: Diversity and divergence among the tribal populations of India. / Ann Hum Genet 2005, 69 (Pt 6) : 680-92. CrossRef
  20. Rosenberg NA, Mahajan S, Gonzalez–Quevedo C, Blum MG, Nino–Rosales L, Ninis V, Das P, Hegde M, Molinari L, Zapata G, Weber JL, Belmont JW, Patel PI: Low levels of genetic divergence across geographically and linguistically diverse populations from India. / PLoS Genet 2006, 2 (12) : e215. CrossRef
  21. Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking M: Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. / Eur J Hum Genet 2003, 11 (3) : 253-64. CrossRef
  22. Quintana–Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R, Rengo C, Al–Zahery N, Semino O, Santachiara–Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler–Smith C, Qasim Mehdi S, Torroni A, McElreavey K: Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. / Am J Hum Genet 2004, 74 (5) : 827-45. CrossRef
  23. Atkinson QD, Gray RD, Drummond AJ: mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. / Mol Biol Evol 2008, 25 (2) : 468-74. CrossRef
  24. Higham CFW, Thosarat R: Prehistoric Thailand: From early settlement to Sukothai. River Books, Bangkok 1998.
  25. Diamond J, Bellwood P: Farmers and their languages: the first expansions. / Science 2003, 300: 597-03. CrossRef
  26. Diffloth G: Austroasiatic languages. [http://www.britannica.com/eb/article-9109792] / Encyclopedia Britannica, online edition 2005.
  27. Fuller DQ: Non–human genetics, agricultural origins and historical linguistics in Indian subcontinent. / The Evolution and History of Human Populations in Indian subcontinent / (Edited by: Petraglia M, Allchin B). Springer, Netherlands 2007, 393-43. CrossRef
  28. Witzel M: Central Asian roots and acculturation in Indian subcontinent: linguistic and archaeological evidence from Western Central Asia, the Hindukush and northwestern Indian subcontinent for early Indo–Aryan language and religion. / Liguistics, Archaeology and the Human Past / (Edited by: Osada T). Research Institute for Humanity and Nature, Kyoto 2005, 87-11.
  29. Basu A, Mukherjee N, Roy S, Sengupta S, Banerjee S, Chakraborty M, Dey B, Roy M, Roy B, Bhattacharyya NP, Roychoudhury S, Majumder PP: Ethnic India: a genomic view, with special reference to peopling and structure. / Genome Res 2003, 13 (10) : 2277-290. CrossRef
  30. Black ML, Dufall K, Wise C, Sullivan S, Bittles AH: Genetic ancestries in northwest Cambodia. / Ann Hum Biol 2006, 33 (5-) : 620-27. CrossRef
  31. Forster P, Harding R, Torroni A, Bandelt HJ: Origin and evolution of Native American mtDNA variation: a reappraisal. / Am J Hum Genet 1996, 59 (4) : 935-45.
  32. Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli–Sforza LL, Oefner PJ: The role of selection in the evolution of human mitochondrial genomes. / Genetics 2006, 172 (1) : 373-87. CrossRef
  33. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N: Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. / Nat Genet 1999, 23 (2) : 147. CrossRef
  34. Bandelt HJ, Forster P, Rohl A: Median–joining networks for inferring intraspecific phylogenies. / Mol Biol Evol 1999, 16 (1) : 37-8.
  35. Saillard J, Forster P, Lynnerup N, Bandelt HJ, Norby S: mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. / Am J Hum Genet 2000, 67 (3) : 718-26. CrossRef
  36. Sokal RR, Oden NL: Spatial autocorrelation in biology. / Biol J Linn Soc 1978, 10: 199-49. CrossRef
  37. Mantel NA: The detection of disease clustering and a generalized regression approach. / cer Res 1967, 27: 209-20.
  38. Schneider S, Roessli D, Excoffier L: Arlequin ver. 2.000: A software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland 2000.
  39. Krishnamurti B: The Dravidian Languages. Cambridge University Press 2003, 1-74. CrossRef
  40. Driem G: Languages of the Himalayas. / an ethnolinguistic handbook Leiden New York; K?ln : Brill 1997.
  41. Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB: Genetic evidence on the origins of Indian caste populations. / Genome Res 2001, 11 (6) : 994-004. CrossRef
  42. Rajkumar R, Kashyap VK: Haplotype diversity in mitochondrial DNA hypervariable regions I and II in three communities of Southern India. / Forensic Sci Int 2003, 136 (1-) : 79-2. CrossRef
  43. Roychoudhury S, Roy S, Basu A, Banerjee R, Vishwanathan H, Usha Rani MV, Sil SK, Mitra M, Majumder PP: Genomic structures and population histories of linguistically distinct tribal groups of India. / Hum Genet 2001, 109 (3) : 339-50. CrossRef
  44. Baig MM, Khan AA, Kulkarni KM: Mitochondrial DNA diversity in tribal and caste groups of Maharashtra (India) and its implication on their genetic origins. / Ann Hum Genet 2004, 68 (Pt 5) : 453-60. CrossRef
  45. Banerjee J, Trivedi R, Kashyap VK: Mitochondrial DNA control region sequence polymorphism in four indigenous tribes of Chotanagpur plateau, India. / Forensic Sci Int 2005, 149 (2-) : 271-74. CrossRef
  46. Thanseem I, Thangaraj K, Chaubey G, Singh VK, Bhaskar LV, Reddy BM, Reddy AG, Singh L: Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA. / BMC Genet 2006, 7: 42. CrossRef
  
• 作者单位：Gyaneshwer Chaubey (1) (2)
  Monika Karmin (1)
  Ene Metspalu (1)
  Mait Metspalu (1)
  Deepa Selvi-Rani (2)
  Vijay Kumar Singh (2)
  Jüri Parik (1)
  Anu Solnik (1)
  B Prathap Naidu (2)
  Ajay Kumar (2) (5)
  Niharika Adarsh (2) (5)
  Chandana Basu Mallick (2) (5)
  Bhargav Trivedi (2) (5)
  Swami Prakash (2) (5)
  Ramesh Reddy (2) (5)
  Parul Shukla (2) (5)
  Sanjana Bhagat (2) (5)
  Swati Verma (2) (5)
  Samiksha Vasnik (2) (5)
  Imran Khan (2) (5)
  Anshu Barwa (2) (5)
  Dipti Sahoo (2) (5)
  Archana Sharma (2) (5)
  Mamoon Rashid (2) (5)
  Vishal Chandra (2) (5)
  Alla G Reddy (2)
  Antonio Torroni (3)
  Robert A Foley (4)
  Kumarasamy Thangaraj (2)
  Lalji Singh (2)
  Toomas Kivisild (1) (4)
  Richard Villems (1)
  
  1. Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
  2. Centre for Cellular and Molecular Biology, Hyderabad, India
  5. Students of different Universities and Colleges of India studied (as a part of their curriculum), CCMB, Hyderabad, India
  3. Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, Pavia, 27100, Italy
  4. Leverhulme Centre of Human Evolutionary Studies, The Henry Wellcome Building, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, UK
  

文摘

Background Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East. Results Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of ~12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages. Conclusion Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.