Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  ArunKumar, GaneshPrasad ^a,m   Soria Hernanz, David F ^b,c   Kavitha, Valampuri John ^a,d   Arun, Varatharajan Santhakumari ^a   Syama, Adhikarla ^a   Ashokan, Kumaran Samy ^e   Gandhirajan, Kavandanpatti Thangaraj ^f   Vijayakumar, Koothapuli ^e   Narayanan, Muthuswamy ^g   Jayalakshmi, Mariakuttikan ^a   Ziegle, Janet S ^h   Royyuru, Ajay K ⁱ   Parida, Laxmi ⁱ   Wells, R Spencer ^b   Renfrew, Colin ^j   Schurr, Theodore G ^k   Smith, Chris Tyler ^l   Platt, Daniel E ⁱ   Pitchappan, Ramasamy ^a,m  

^a MADURAI KAMARAJ UNIVERSITY   (India)

^b NATIONAL GEOGRAPHIC SOCIETY   (United States)

^c UNIVERSITAT POMPEU FABRA   (Spain)

^d MOTHER TERESA WOMEN S UNIVERSITY   (India)

^e Nilgiri Adivasi Welfare Association   (India)

^f Government College of Fine Arts   (India)

^g ST XAVIER S COLLEGE AUTONOMOUS   (India)

^h APPLIED BIOSYSTEMS   (United States)

ⁱ IBM T J WATSON RESEARCH CENTER   (United States)

^j UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^k UNIVERSITY OF PENNSYLVANIA   (United States)

^l WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^m CHETTINAD HOSPITAL AND RESEARCH INSTITUTE   (India)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURE; ARTICLE; CASTE SYSTEM; CHROMOSOME ANALYSIS; CULTURAL FACTOR; DEMOGRAPHY; ETHNIC GROUP; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; INDIAN; INHERITANCE; MALE; NEOLITHIC; PLEISTOCENE; POPULATION DIFFERENTIATION; POPULATION GENETIC STRUCTURE; POPULATION MIGRATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOCIAL STATUS; SOCIOBIOLOGY; SPECIES DIVERSITY; Y CHROMOSOME;

AGRICULTURE; CHROMOSOMES, HUMAN, Y; DEMOGRAPHY; DNA, MITOCHONDRIAL; ETHNIC GROUPS; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; HUMAN MIGRATION; HUMANS; INDIA; MALE; MICROSATELLITE REPEATS; MODELS, STATISTICAL; MUTATION; PHYLOGENY; SOCIAL CLASS;

EID: 84870311462     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050269     Document Type: Article

References (70)

1. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The History and Geography of Human Genes. Princeton, NJ.: Princeton University Press.
2. Majumder PP, (2010) The human genetic history of South Asia. Curr Biol 20: R184-187.
3. Singh KS (2002) People of India: An Introduction, Revised edition: Oxford Uniersity Press.
4. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, 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 genetics 5: 26.
5. Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, et al. (2003) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72: 313-332.
6. Sahoo S, Singh A, Himabindu G, Banerjee J, Sitalaximi T, et al. (2006) A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci U S A 103: 843-848.
7. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, 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: 202-221.
8. Chaubey G, Metspalu M, Kivisild T, Villems R, (2007) Peopling of South Asia: investigating the caste-tribe continuum in India. Bioessays 29: 91-100.
9. Quintana-Murci L, Semino O, Bandelt HJ, Passarino G, McElreavey K, et al. (1999) Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat Genet 23: 437-441.
10. Cordaux R, Aunger R, Bentley G, Nasidze I, Sirajuddin SM, et al. (2004) Independent origins of Indian caste and tribal paternal lineages. Curr Biol 14: 231-235.
11. Indian Genome Variation Consortium (2008) Genetic landscape of the people of India: a canvas for disease gene exploration. Journal of genetics 87: 3-20.
12. Majumder PP, (2008) Genomic inferences on peopling of south Asia. Current opinion in genetics & development 18: 280-284.
13. Basu A, Mukherjee N, Roy S, Sengupta S, Banerjee S, et al. (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome research 13: 2277-2290.
14. Dirks NB (2001) Castes of Mind: Colonialism and the Making of Modern India. Princeton, NJ: Princeton University Press.
15. Sanghvi LD, Balakrishnan V, Karve I (1981) Biology of the People of Tamil Nadu.; Prune, editor. Calcutta: Indian Society of Human Genetics and Indian Anthropological Society.
16. Sharma S, Rai E, Sharma P, Jena M, Singh S, et al. (2009) The Indian origin of paternal haplogroup R1a1(*) substantiates the autochthonous origin of Brahmins and the caste system. J Hum Genet 54: 47-55.
17. Champaklakshmi R (2001) Reappraisal of a Brahmanical Institution: The Brahmadeya and its Ramifications in Early Midieval South India. In: Hall KR, editor. Structure and Society in Early South India: Essays in Honour of Noboru Karashima. Delhi: Oxford University Press. pp. 59-84.
18. Krishnan KG (1984) Karandai Tamil Sangam Plates of Rajendrachola I. New Delhi: Archaeological Survey of India.
19. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, et al. (2001) The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A 98: 10244-10249.
20. Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, et al. (2001) Genetic evidence on the origins of Indian caste populations. Genome research 11: 994-1004.
21. Zhao Z, Khan F, Borkar M, Herrera R, Agrawal S, (2009) Presence of three different paternal lineages among North Indians: a study of 560 Y chromosomes. Annals of human biology 36: 46-59.
22. Shastri KAN (1976) A history of South India: from prehistoric times to the fall of Vijayanagar. Madras: Oxford University Press. xii, 521 p., [512] leaves of plates p.
23. Trivedi R, Sahoo S, Singh A, Bindu GH, Banerjee J, et al. (2008) Genetic Imprints of Pleistocene Origin of Indian Populations: A Comprehensive Phylogeographic Sketch of Indian Y-Chromosomes. Internation Journal of Human Genetics 8 (1-2):: 97-118.
24. Carvalho-Silva DR, Tyler-Smith C, (2008) The Grandest Genetic Experiment Ever Performed on Man?- A Y-Chromosomal Perspective on Genetic Variation in India. International journal of human genetics 8: 21-29.
25. Thanseem I, Thangaraj K, Chaubey G, Singh VK, Bhaskar LV, et al. (2006) Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA. BMC genetics 7: 42.
26. McCrindle JW (2000) Ancient India as described by Megasthenes and Arrian: Munshirm Manoharial Pub Pvt Ltd.
27. Silverberg J, (1969) Social Mobility in the Caste System in India: An Interdisciplinary Symposium. The American Journal of Sociology 75: 443-444.
28. Srinivas MN (1952) Religion and Society among the Coorgs of South India. Oxford: Clarendon Press.
29. Pappu S, Gunnell Y, Taieb M, Brugal J-P, Touchard Y, (2003) Excavations at the Paleolithic Site of Attirampakkam, South India: Preliminary Findings. Current Antrhopology 44: 591-598.
30. Fuller DQ, (2006) Agricultural origins and frontiers in South Asia: a working synthesis. J World Prehist 20: 1-86.
31. Fuller DQ (2007) Non-human genetics, agricultural origins and historical linguistics in South Asia. In: Petraglia MD, Allchin B, editors. The Evolution and History of Human Populations in South Asia. Dordrecht, The Netherlands: Springer. pp. 393-443.
32. Haslam M, Korisettar R, Petraglia M, Smith T, Shipton C, et al. (2010) In Foote's Steps: The History, Significance and Recent Archaeological Investigation of the Billa Surgam Caves in South India. South Asian Studies 26: 1-19.
33. Misra VN, (2001) Prehistoric human colonization of India. J Biosci 26: 491-531.
34. Morrison KD (2007) Non-human genetics, agricultural origins and historical linguistics in South Asia. In: Petraglia MD, Allchin B, editors. The Evolution and History of Human Populations in South Asia. Dordrecht, The Netherlands: Springer. pp. 321-339.
35. Selvakumar V, (2002) Hunter-Gatherer Adaptations in Madurai Region, Tamil Nadu, India: From c. 10,000 BP to c. A.D. 500. Asians Perspectives 40: 71-102.
36. Ramaswamy V, (1994) Matallurgy and traditional metal crafts in Tamil Nadu (with special reference to bronze). Indian Journal of History of Science 29: 445-476.
37. Kanakasabhai V (1904) The Tamils Eighteen Hundred Years Ago. Madras and Bangalore: Higginbotham and Co.
38. Thurston E, Rangachari K (1909) Castes and tribes of southern India. Madras: Government Press.
39. Keay J (2001) India: a history. New York: Grove Press.
40. Pitchappan RM, Kakkanaiah VN, Rajashekar R, Arulraj N, Muthukkaruppan VR, (1984) HLA antigens in South India: I. Major groups of Tamil Nadu. Tissue antigens 24: 190-196.
41. Rajasekar R, Kakkanaiah VN, Pitchappan R, (1987) HLA antigens in South India. II: Selected caste groups of Tamil Nadu. Tissue antigens 30: 113-118.
42. Pitchappan RM, Balakrishnan K, Sudarsen V, Brahmajothi V, Mahendran V, et al. (1997) Sociobiology and HLA genetic polymorphism in hill tribes, the Irula of the Nilgiri hills and the Malayali of the Shevroy hills, south India. Human biology 69: 59-74.
43. Balakrishnan K, Pitchappan RM, Suzuki K, Kumar US, Santhakumari R, et al. (1996) HLA affinities of Iyers, a Brahmin population of Tamil Nadu, South India. Human biology 68: 523-537.
44. Watkins WS, Thara R, Mowry BJ, Zhang Y, Witherspoon DJ, et al. (2008) Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms. BMC genetics 9: 86.
45. Ramana GV, Su B, Jin L, Singh L, Wang N, et al. (2001) Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. European journal of human genetics: EJHG 9: 695-700.
46. Kumar V, Reddy AN, Babu JP, Rao TN, Langstieh BT, et al. (2007) Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations. BMC Evol Biol 7: 47.
47. Lokur Committee (1965) The Advisory Committee on the Revision of the Lists of Scheduled Castes and Scheduled Tribes (Lokur Committee). New Delhi: India, Government of.
48. Constituent Assembly (1949) Constitution of India. In: Ministry of Law and Justice, editor. New Delhi, India: Ministry of Law and Justice, India.
49. Mandal BP (1979) Mandal Commission,. New Delhi.
50. Kalelkar K (1955) First Backward Classes Commission. New Delhi.
51. Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, et al. (2011) Parallel Evolution of Genes and Languages in the Caucasus Region. Molecular biology and evolution 28: 2905-2920.
52. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, et al. (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome research 18: 830-838.
53. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
54. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
55. Jolliffe I (1986) Principal Coponents Analysis, Second Edition. New York, NY: Springer.
56. Nelson MR, Bryc K, King KS, Indap A, Boyko AR, et al. (2008) The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 83: 347-358.
57. Cattell R, (1966) The scree test for the number of factors. Multiv Behav Res 1: 245-276.
58. Kruskal JB, (1964) Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29: 1-27.
59. Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular biology and evolution 16: 37-48.
60. Forster P, Röhl A, Lunnemann P, Brinkmann C, Zerjal T, et al. (2000) A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Genet 67: 182-196.
61. Wilson I, Balding D, Weale M, (2003) Inferences from DNA Data: Population Histories, Evolutionary Processes and Forensic Probabilities. Journal of the Royal Statistical Society: Series A (Statistics in Society) 166: 155-188.
62. Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, et al. (2011) Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. European journal of human genetics: EJHG 19: 334-340.
63. Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, et al. (2006) Male demography in East Asia: a north-south contrast in human population expansion times. Genetics 172: 2431-2439.
64. Zhivotovsky LA, Underhill PA, Cinnioglu C, Kayser M, Morar B, et al. (2004) The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet 74: 50-61.
65. Reich D, Thangaraj K, Patterson N, Price AL, Singh L, (2009) Reconstructing Indian population history. Nature 461: 489-494.
66. Sturrock K, Rocha J, (2000) A Multidimensional Scaling Stress Evaluation Table. Field Methods 12: 49-60.
67. Krithika S, Maji S, Vasulu TS, (2009) A microsatellite study to disentangle the ambiguity of linguistic, geographic, ethnic and genetic influences on tribes of India to get a better clarity of the antiquity and peopling of South Asia. American journal of physical anthropology 139: 533-546.
68. Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, et al. (2010) Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. European journal of human genetics: EJHG 18: 479-484.
69. Morrison KD (2007) Foragers and forager-traders in South Asian worlds: some thoughts from the last 10,000 years. In: Petraglia MD, Allchin B, editors. The Evolution and History of Human Populations in South Asia. Dordrecht, The Netherlands: Springer. pp. 321-339.
70. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, et al. (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. American journal of human genetics 74: 1023-1034.