Ethnic India: A genomic view, with special reference to peopling and structure

Genome Research

Volumn 13, Issue 10, 2003, Pages 2277-2290

  Basu, Analabha ^a   Mukherjee, Namita ^a   Roy, Sangita ^b   Sengupta, Sanghamitra ^a   Banerjee, Sanat ^a   Chakraborty, Madan ^a   Dey, Badal ^a   Roy, Monami ^a   Roy, Bidyut ^a   Bhattacharyya, Nitai P ^c   Roychoudhury, Susanta ^b   Majumder, Partha P ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

^b INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^c SAHA INSTITUTE OF NUCLEAR PHYSICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER; MITOCHONDRIAL DNA;

ARTICLE; ASIA; ASIAN; AUSTRALIA; AUTOSOME; CHINA; CONTROLLED STUDY; CULTURAL ANTHROPOLOGY; CULTURAL FACTOR; DATA ANALYSIS; ETHNOLOGY; EUROPE; FEMALE; FOUNDER EFFECT; GENE FLOW; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC DRIFT; GENETIC LINE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME IMPRINTING; GEOGRAPHY; HABITAT STRUCTURE; HAPLOTYPE; HISTORY; HUMAN; INDIA; MALE; MYANMAR; NUCLEOTIDE SEQUENCE; POPULATION RESEARCH; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOCIAL ASPECT; STATISTICAL ANALYSIS; Y CHROMOSOME;

CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; ETHNIC GROUPS; FEMALE; FOUNDER EFFECT; GENE FREQUENCY; GENETIC MARKERS; GENETICS, POPULATION; GENOMICS; HAPLOTYPES; HUMANS; INDIA; LANGUAGE; PHYLOGENY;

EID: 10744228209     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1413403     Document Type: Article

References (60)

1. Bamshad, M.J., Watkins, W.S., Dixon, M.E., Jorde, L.B., Rao, B.B., Naidu, J.M., Prasad, B.V.R., Rasanayagam, A., and Hammer, M.F. 1998. Female gene flow stratifies Hindu castes. Nature 395: 851-852.
2. Bamshad, M.J., Kivisild, T., Watkins, W.S., Dixon, M.P., Ricker, L.E., Rao, B.B., Naidu, M., Prasad, B.V.R., Reddy, P.G., Rasanayagam, A., et al. 2001. Genetic evidence on the origins of Indian caste populations. Genome Res. 11: 994-1004.
3. Bandelt, H.J., Forster, P., and Rohl, A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: 37-48.
4. Beteille, A. 1998. The Indian heritage - A sociological perspective. In The Indian human heritage (eds. D. Balasubramian and N. Appaji Rao), pp. 87-94. University Press, Hyderabad, India.
5. Bhattacharyya, N., Basu, P., Das, M., Pramanik, S., Banerjee, R., Roy, B., Roychoudhury, S., and Majumder, P.P. 1999. Negligible gene-flow across ethnic boundaries in India, revealed by analysis of Y-chromosomal DNA polymorphisms. Genome Res. 9: 711-719.
6. Bonatto, S.L. and Salzano, F.M. 1997. A single and early origin for the peopling of the Americas supported by mitochondrial DNA sequence data. Proc. Natl. Acad. Sci. 94: 1866-1871.
7. Calafell, F., Underhill, P., Tolun, A., Angelicheva, D., and Kalaydjieva, L. 1996. From Asia to Europe: Mitochondrial DNA sequence variability in Bulgarians and Turks. Ann. Hum. Genet. 60: 35-49.
8. Cann, R.L. 2001. Genetic clues to dispersal of human populations: Retracing the past from the present. Science 291: 1742-1748.
9. Casanova, M., Leroy, P., Boucekkine, C., Weissenbach, J., Bishop, C., Fellous, M., Purrello, M., Fiori, G., and Siniscalco, M. 1985. A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance. Science 230: 1403-1406.
10. Comas, D., Calafell, F., Mateu, E., Perez-Lezaun, A., Bosch, E., Martinez-Arias, R., Clarimon, J., Facchini, F., Fiori, G., Luiselli, D., et al. 1998. Trading genes along the silk road: mtDNA sequences and the origin of Central Asian populations. Am. J. Hum. Genet. 63: 1824-1838.
11. Cruciani, F., Santolamazza, P., Shen, P., Macaulay, V., Moral, P., Olckers, A., Modiano, D., Holmes, S., Destro-Bisol, G., Coia, V., et al. 2002. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am. J. Hum. Genet. 70: 1197-1214.
12. Diamond, J. 1997. Guns, germs and steel: The fates of human societies. Jonathan Cape, London.
13. Forster, P., Torroni, A., Renfrew, C., and Rohl, A. 2001. Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol. Biol. Evol. 18: 1864-1881.
14. Grimes, B.F. 1999. The ethnologue: Languages of the world. Summer Institute of Linguistics, California.
15. Guha, B.S. 1935. The racial affinities of the people of India. In Census of India, 1931, Part III - Ethnographical. Government of India Press, Simla, India.
16. Hammer, M.F., Redd, A.J., Wood, E.T., Bonner, M.R., Jarjanazi, H., Karafet, T., Santachiara-Benerecetti, S., Oppenheim, A., Jobling, M.A., Jenkins, F., et al. 2000. Jewish and middle eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes. Proc. Natl. Acad. Sci. 97: 6769-6774.
17. Jorde, L.B., Bamshad, M.J., Watkins, W.S., Zenger, R., Fraley, A.E., Krakowiak, P.A., Carpenter, K.D., Soodyall, H., Jenkins, T., and Rogers, A.R. 1995. Origins and affinities of modern humans: A comparison of mitochondrial and nuclear genetic data. Am. J. Hum. Genet. 57: 523-538.
18. Karve, I. 1961. Hindu society: An interepretation. Deshmukh Prakashan, Poona, India.
19. Keith, A. 1936. Review of B.S. Guha's "Racial affinities of the peoples of India." Man 29: 37.
20. Kivisild, T., Bamshad, M.J., Kaldma, K., Metspalu, M., Metspalu, E., Reidla, M., Laos, S., Parik, J., Watkins, W.S., Dixon, M.E., et al. 1999a. Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr. Biol. 9: 1331-1334.
21. Kivisild, T., Kaldma, K., Metspalu, M., Parik, J., Papiha, S., and Villems, R. 1999b. The place of the Indian mitochondrial DNA variants in the global network of the maternal lineages and the peopling of the old world. In Genome diversity: Applications in human population genetics (eds. S.S. Papiha et al.), pp. 135-152. Kluwer, New York.
22. Kosambi, D.D. 1991. The culture and civilisation of ancient India in historical outline. Vikas Publishing House, New Delhi, India.
23. Lundstrom, R.S., Tavare, S., and Ward, R.H. 1992. Estimating substitution rates from molecular data using the coalescent. Proc. Natl. Acad. Sci. 89: 5961-5965.
24. Maca-Meyer, N., Gonzalez, A.M., Larruga, J.M., Flores, C., and Cabrera, V.M. 2001. Major genomic mitochondrial lineages delineate early human expansions. BMC Genetics 2: 13-20.
25. Majumdar, P. and Majumder, P.P. 2000. HAPLOFREQ: A computer program package for maximum-likelihood estimation of haplotype frequencies in a population via the EM algorithm. Tech Rep AHGU-1/2000. Indian Statistical Institute, Calcutta, India.
26. Majumder, P.P. 1998. People of India: Biological diversity and affinities. Evol. Anthrop. 6: 100-110.
27. Majumder, P.P., Roy, B., Banerjee, S., Chakraborty, M., Dey, B., Mukherjee, N., Roy, M., Guha Thakurta, P., and Sil, S.K. 1999a. Human-specific insertion/deletion polymorphisms in Indian populations and their possible evolutionary implications. Eur. J. Hum. Genet. 7: 435-446.
28. Majumder, P.P., Roy, B., Balgir, R.S., and Dash, B.P. 1999b. Polymorphisms in the β-globin gene cluster in some ethnic populations of India and their implications on disease. In Molecular intervention in disease (eds. S. Gupta and O.P. Sood), pp. 75-83. Ranbaxy Science Foundation, New Delhi.
29. Meenakshi, K. 1995. Linguistics and the study of early Indian history. In Recent perspectives of early Indian history (ed. R. Thapar), pp. 53-79. Popular Prakashan, Bombay, India.
30. Misra, V.N. 1992. Stone age in India: An ecological perspective. Man and Env. 14: 17-64.
31. Mukherjee, N., Nebel, A., Oppenheim, A., and Majumder, P.P. 2001. High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India. J. Genet. 80: 125-135.
32. Nebel, A., Filon, D., Weiss, D.A., Weale, M., Faerman, M., Oppenheim, A., and Thomas, M.G. 2000. High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews. Hum. Genet. 107: 630-641.
33. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
34. Pattanayak, D.P. 1998. The language heritage of India. In The Indian human heritage (eds. D. Balasubramanian and N.A. Rao), pp. 95-99. Universities Press, Hyderabad, India.
35. Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
36. Qamar, R., Ayub, Q., Mohyuddin, A., Helgason, A., Mazhar, K., Mansoor, A., Zerjal, T., Tyler-Smith, C., and Mehdi, S.Q. 2002. Y-chromosomal DNA variation in Pakistan. Am. J. Hum. Genet. 70: 1107-1124.
37. Quintana-Murci, L., Krausz, C., Zerjal, T., Sayar, S.H., Hammer, M.F., Mehdi, S.Q., Ayub, Q., Qamar, R., Mohyuddin, A., Radhakrishna, U., et al. 2001. Y-chromosome lineages trace diffusion of people and languages in southwestern Asia. Am. J. Hum. Genet. 68: 537-542.
38. Ratnagar, S. 1995. Archaeological perspectives of early Indian societies. In Recent perspectives of early Indian history (ed. R. Thapar), pp. 1-52. Popular Prakashan, Bombay, India.
39. Ray, N. 1973. Nationalism in India. Aligarh Muslim University, Aligarh, India.
40. Renfrew, C. 1992. Archaeology, genetics and linguistic diversity. Man 27: 445-478.
41. Risley, H.H. 1915. The people of India. Thacker Spink, Calcutta, India.
42. Rosser, Z.H., Zerjal, T., Hurles, M.E., Adojaan, M., Alavantic, D., Amorim, A., Amos, W., Armenteros, M., Arroyo, E., Barbujani, G., et al. 2000. Y-chromosomal diversity in Europe is clinal and is influenced primarily by geography, rather than by language. Am. J. Hum. Genet. 67: 1526-1543.
43. Roychoudhury, S., Roy, S., Basu, A., Banerjee, R., Vishwanathan, H., Usha Rani, M.V., Sil, S.K., Mitra, M., and Majumder, P.P. 2001. Genomic structures and population histories of linguistically distinct tribal groups of India. Hum. Genet. 109: 339-350.
44. Rozas, J. and Rozas, R. 1999. DnaSP version 3: An integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
45. Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
46. Sarkar, S.S. 1958. Race and race movements in India. In The cultural heritage of India (ed. S.K. Chatterjee), Vol. 1, pp. 17-32. The Ramakrishna Mission Institute of Culture, Calcutta, India.
47. Schneider, S., Kueffer, J.-M., Roessli, D., and Excoffier, L. 2000. ARLEQUIN: A software for population genetic data analysis. University of Geneva, Geneva, Switzerland.
48. Singh, K.S. 1992. People of India: An introduction. Anthropological Survey of India, Calcutta, India.
49. Slatkin, M. and Hudson, R.R. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
50. Su, B., Xiao, C., Deka, R., Seielstad, M.T., Kangwanpong, D., Xiao, J., Lu, D., Underhill, P., Cavalli-Sforza, L.L., Chakraborty, R., et al. 2000. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107: 582-590.
51. Thapar, R. 1966. A history of India, Volume 1. Penguin, Middlesex, UK.
52. Thapar, R. 1995. The first millennium B.C. in northern India (up to the end of Mauryan period). In Recent perspectives of early Indian history (ed. R. Thapar), pp. 80-141. Popular Prakashan, Bombay, India.
53. Thapar, R. 2003. Early India: From the origins to AD 1300. University of California Press, Berkeley, CA.
54. Thomas, M., Bradman, N., and Flinn, H. 1999. High throughput analysis of 10 microsatellite and 11 diallelic polymorphisms on the human Y-chromosome. Hum. Genet. 105: 577-581.
55. Tishkoff, S.A., Ruano, G., Kidd, J.R., and Kidd, K.K. 1996. Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans. Hum. Genet. 97: 759-764.
56. Torroni, A., Schurr, T.B., Cabell, M.F., Brown, M.D., Neel, J.V., Larsen, M., and Smith, D.G. 1993. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am. J. Hum. Genet. 53: 563-590.
57. Torroni, A., Huoponen, K., Francalacci, P., Petrozzi, M., Morelli, L., Scozzari, R., Obinu, D., Savontaus, M.-L., and Wallace, D.C. 1996. Classification of European mtDNAs from an analysis of three European populations. Genetics 144: 1835-1850.
58. Vigilant, L.A., Wilson, A.C., and Harpending, H. 1991. African populations and the evolution of human mitochondrial DNA. Science 253: 1503-1507.
59. Chromosome Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12: 339-348.
60. Zerjal, T., Wells, R.S., Yuldasheva, N., Ruzibakiev, R., and Tyler-Smith, C. 2002. A genetic landscape reshaped by recent events: Y-chromosomal insights into Central Asia. Am. J. Hum. Genet. 71: 466-482.