Low levels of genetic divergence across geographically and linguistically diverse populations from India

PLoS Genetics

Volumn 2, Issue 12, 2006, Pages 2052-2061

  Rosenberg, Noah A ^a   Mahajan, Saurabh ^b   Gonzalez Quevedo, Catalina ^b   Blum, Michael G B ^a   Nino Rosales, Laura ^c   Ninis, Vasiliki ^c   Das, Parimal ^c   Hegde, Madhuri ^c,f   Molinari, Laura ^c   Zapata, Gladys ^c   Weber, James L ^d   Belmont, John W ^c   Patel, Pragna I ^b,e  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d MARSHFIELD CLINIC   (United States)

^e UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^f EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC DIFFERENCE; GENETIC HETEROGENEITY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HETEROZYGOSITY; HUMAN; HUMAN CELL; HUMAN EXPERIMENT; INDIA; LINGUISTICS; NORMAL HUMAN; POPULATION GENETICS; POPULATION RESEARCH; SOUTH ASIA; UNITED STATES; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; ETHNOLOGY; EUROPE; FAR EAST; GENE DELETION; GENETICS; LANGUAGE; MIDDLE EAST; TRANSPOSON;

MICROSATELLITE DNA;

ALLELES; CLUSTER ANALYSIS; DNA TRANSPOSABLE ELEMENTS; EUROPE; FAR EAST; GENE DELETION; GENE FREQUENCY; HUMANS; INDIA; LANGUAGE; MICROSATELLITE REPEATS; MIDDLE EAST; POLYMORPHISM, GENETIC; SOFTWARE; VARIATION (GENETICS);

EID: 33845994051     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020215     Document Type: Article

References (57)

1. Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5: 89-100.
2. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, et al. (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307: 1072-1079.
3. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
4. Devlin B, Roeder K, Wasserman L (2001) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60: 155-166.
5. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60: 227-237.
6. Thomas DC, Witte JS (2002) Population stratification: A problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 11: 505-512.
7. Ziv E, Burchard EG (2003) Human population structure and genetic association studies. Pharmacogenomics 4: 431-441.
8. Enas EA, Mehta J (1995) Malignant coronary artery disease in young Asian Indians: Thoughts on pathogenesis, prevention, and therapy. Clin Cardiol 18: 131-135.
9. Gupta R, Deedwania PC, Gupta A, Rastogi S, Panwar RB, et al. (2004) Prevalence of metabolic syndrome in an Indian urban population. Int J Cardiol 97: 257-261.
10. Ramachandran A, Snehalatha C, Latha E, Vijay V, Viswanathan M (1997) Rising prevalence of NIDDM in an urban population in India. Diabetologia 40: 232-237.
11. Uppaluri CR (2002) Heart disease and its related risk factors in Asian Indians. Ethn Dis 12: 45-53.
12. Venkataraman R, Nanda NC, Baweja G, Parikh N, Bhatia V (2004) Prevalence of diabetes mellitus and related conditions in Asian Indians living in the United States. Am J Cardiol 94: 977-980.
13. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, et al. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
14. The Indian Genome Variation Consortium (2005) The Indian Genome Variation database (IGVdb): A project overview. Hum Genet 118: 1-11.
15. 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 Res 13: 2277-2290.
16. Kashyap VK, Sarkar N, Sahoo S, Sarkar BN, Trivedi R (2003) Genetic variation at fifteen microsatellite loci in human populations of India. Curr Sci 85: 464-473.
17. Kashyap VK, Guha S, Sitalaximi T, Hima Bindu G, Hasnain SE, et al. (2005) Genetic structure of Indian populations based on fifteen autosomal microsatellite loci. BMC Genet 7: 28.
18. Cann HM, de Toma C, Cazes L, Legrand M-F, Morel V, et al. (2002) A human genome diversity cell line panel. Science 296: 261-262.
19. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et al. (2002) Genetic structure of human populations. Science 298: 2381-2385.
20. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A 102: 15942-15947.
21. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, et al. (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet 1: e70. doi:10.1371/journal.pgen.0010070
22. Prugnolle F, Manica A, Balloux F (2005) Geography predicts neutral genetic diversity of human populations. Curr Biol 15: R159-R160.
23. Thapar R (1990) A history of India: Volume I. London: Penguin Books. 384 p.
24. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, et al. (2003) Human population structure and inference of group membership. Am J Hum Genet 72: 578-589.
25. Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, et al. (2003) Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms. Genome Res 13: 1607-1618.
26. Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, et al. (2005) Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: Application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet 118: 382-392.
27. Shriver MD, Mei R, Parra EJ, Sonpar V, Halder I, et al. (2005) Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2: 81-89.
28. Li S-L, Yamamoto T, Yoshimoto T, Uchihi R, Mizutani M, et al. (2006) Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci. Hum Genet 118: 695-707.
29. Rosenberg N, Nordborg M (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations. Genetics 173: 1665-1678.
30. Roychoudhury S, Roy S, Dey B, Chakraborty M, Roy M, et al. (2000) Fundamental genomic unity of ethnic India is revealed by analysis of mitochondrial DNA. Curr Sci 79: 1182-1192.
31. Majumder PP (2001) Ethnic populations of India as seen from an evolutionary perspective. J Biosci 26: 533-545.
32. Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, et al. (2003) Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet 11: 253-264.
33. 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.
34. Cordaux R, Weiss G, Saha N, Stoneking M (2004) The northeast Indian passageway: A barrier or corridor for human migrations? Mol Biol Evol 21: 1525-1533.
35. Rajkumar R, Kashyap VK (2004) Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups. BMC Genet 5: 23.
36. Wooding S, Ostler C, Prasad BVR, Watkins WS, Sung S, et al. (2004) Directional migration in the Hindu castes: Inferences from mitochondrial, autosomal and Y-chromosomal data. Hum Genet 115: 221-229.
37. Sahoo S, Kashyap VK (2005) Influence of language and ancestry on genetic structure of contiguous populations: A microsatellite based study on populations of Orissa. BMC Genet 6: 4.
38. Watkins WS, Prasad BVR, Naidu JM, Rao BB, Bhanu BA, et al. (2005) Diversity and divergence among the tribal populations of India. Ann Hum Genet 69: 680-692.
39. Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, et al. (2001) Genetic evidence on the origins of Indian caste populations. Genome Res 11: 994-1004.
40. François O, Ancelet S, Guillot G (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics 174: 805-816.
41. Vishwanathan H, Edwin D, Usharani MV, Majumder PP (2003) Insertion/deletion polymorphisms in tribal populations of southern India and their possible evolutionary implications. Hum Biol 75: 873-887.
42. Vishwanathan H, Deepa E, Cordaux R, Stoneking M, Usha Rani MV, et al. (2004) Genetic structure and affinities among tribal populations of southern India: A study of 24 autosomal DNA markers. Ann Hum Genet 68: 128-138.
43. Boehnke M, Cox NJ (1997) Accurate inference of relationships in sib-pair linkage studies. Am J Hum Genet 61: 423-429.
44. Epstein M, Duren W, Boehnke M (2000) Improved inference of relationship for pairs of individuals. Am J Hum Genet 67: 1219-1231.
45. Anderson MA, Gusella JF (1984) Use of cyclosporin A in establishing Epstein-Barr virus-transformed human lympoblastoid cell lines. In Vitro 20: 856-858.
46. Ghebranious N, Vaske D, Yu A, Zhao C, Marth G, et al. (2003) STRP screening sets for the human genome at 5 cM density. BMC Genomics 4: 6.
47. Weber JL, David D, Heil J, Fan Y, Zhao C, et al. (2002) Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 71: 854-862.
48. Sokal RR, Rohlf FJ (1994) Biometry. 3rd edition. New York: W. H. Freeman. 880 p.
49. Rosenberg NA (2006) Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet 70: 841-847.
50. Nei M (1987) Molecular evolutionary genetics. New York: Columbia University Press. 512 p.
51. Weir BS (1996) Genetic data analysis II: Methods for discrete population genetic data. 2nd edition. Sunderland, MA: Sinauer Associates. 445 p.
52. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
53. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
54. Chen C (2006) TESS reference manual. Grenoble: Institut d'Informatique et Mathématiques Appliquées de Grenoble. Available: http://www-timc.imag.fr/Olivier.Francois/tess.html. Accessed 13 November 2006.
55. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
56. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.65. Seattle: Department of Genome Sciences, University of Washington. Available: http://evolution.genetics.washington.edu/phylip.html. Accessed 13 November 2006.
57. Mountain JL, Cavalli-Sforza LL (1997) Multilocus genotypes, a tree of individuals, and human evolutionary history. Am J Hum Genet 61: 705-718.