The Soliga, an isolated tribe from Southern India: Genetic diversity and phylogenetic affinities

Journal of Human Genetics

Volumn 56, Issue 4, 2011, Pages 258-269

  Morlote, Diana M ^a   Gayden, Tenzin ^a   Arvind, Prathima ^b   Babu, Arvind ^c   Herrera, Rene J ^a  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b Multispecialty Hospital Shaw Mazumdar Medical Centre   (India)

^c RK Lakeview   (India)

Author keywords

Australia; autosomal STRs; India; Soliga

Indexed keywords

ARTICLE; AUSTRALIA; GENE FREQUENCY; GENE LOCUS; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; INDIA; INDIAN; MIGRATION; PHYLOGENY; SHORT TANDEM REPEAT; SOLIGA;

EMIGRATION AND IMMIGRATION; ETHNIC GROUPS; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; HISTORY, ANCIENT; HUMANS; INDIA; MICROSATELLITE REPEATS; OCEANIC ANCESTRY GROUP; PHYLOGENY;

EID: 79955517865     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1038/jhg.2010.173     Document Type: Article

References (86)

1. Quintana-Murci, L., Semino, O., Bandelt, H. J., Passarino, G., McElreavey, K. & Santachiara-Benerecetti, A. S. Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat. Genet. 23, 437-441 (1999).
2. Redd, A. J. & Stoneking, M. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua new Guinean populations. Am. J. Hum. Genet. 65, 808-828 (1999). (Pubitemid 30468727)
3. Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708-713 (2000). (Pubitemid 32015984)
4. Redd, A. J., Roberts-Thomson, J., Karafet, T., Bamshad, M., Jorde, L. B., Naidu, J. M. et al. Gene flow from the Indian subcontinent to Australia evidence from the Y chromosome. Curr. Biol. 12, 673-677 (2002). (Pubitemid 34315853)
5. Basu, A., Mukherjee, N., Roy, S., Sengupta, S., Banerjee, S., Chakraborty, M. et al. Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res. 13, 2277-2290 (2003). (Pubitemid 37265994)
6. Cordaux, R., Aunger, R., Bentley, G., Nasidze, I., Sirajuddin, S. M. & Stoneking, M. Independent origins of Indian caste and tribal paternal lineages. Curr. Biol. 14, 231-235 (2004). (Pubitemid 38215351)
7. Macaulay, V., Hill, C., Achilli, A., Rengo, C., Clarke, D., Meehan, W. et al. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308, 1034-1036 (2005). (Pubitemid 40664416)
8. Thangaraj, K., Chaubey, G., Kivisild, T., Reddy, A. G., Singh, V. K., Rasalkar, A. A. et al. Reconstructing the origin of Andaman islanders. Science 308, 996 (2005). (Pubitemid 40664404)
9. Sun, C., Kong, Q. P., Palanichamy, M., Agrawal, S., Bandelt, H. J., Yao, Y. G. et al. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol. Biol. Evol. 23, 683-690 (2006). (Pubitemid 43278280)
10. Majumder, P. P. The human genetic history of South Asia. Curr. Biol. 20, 184-187 (2010).
11. Kennedy, K. A. R., Deraniyagala, S. U., Roertgen, W. J., Chiment, J. & Disotell, T. Upper Pleistocene fossil hominids from Sri Lanka. Am. J. Phys. Anthropol. 72, 441-461 (1987). (Pubitemid 17062887)
12. Cavalli-Sforza, L. L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton University Press, Princeton, NJ, USA, 1994).
13. Lahr, M. M. & Foley, R. Multiple dispersals and modern human origins. Evol. Anthropol. 3, 48-60 (1994). (Pubitemid 124006878)
14. Stringer, C. Palaeoanthropology: coasting out of Africa. Nature 405, 24-27 (2000).
15. Cann, R. L. Genetic clues to dispersal in human populations: retracing the past from the present. Science. 291, 1742-1748 (2001). (Pubitemid 32198972)
16. Maca-Meyer, N., González, A. M., Larruga, J. M., Flores, C. & Cabrera, V. M. Major genomic mitochondrial lineages delineate early human expansions. BMC. Genet. 2, 1471-2156 (2001).
17. Lewin, R. & Foley, R. Principles of Human Evolution 2nd edn.(Blackwell Publishing, MA, USA, 2004).
18. Palanichamy, M., Sun, C., Agrawal, S., Bandelt, H. J., Kong, Q. P. & Khan, F. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of south Asia. Am. J. Hum. Genet. 75, 966-978 (2004). (Pubitemid 39532067)
19. Tanaka, M., Cabrera, V. M., Gonzalez, A. M., Larruga, J. M., Takeyasu, T., Fuku, N. et al. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome. Res. 14, 1832-1850 (2004). (Pubitemid 39386497)
20. Kong, Q. P., Bandelt, H. J., Sun, C., Yao, Y. G., Salas, A. & Achilli, A. Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum. Mol. Genet. 15, 2076-2086 (2006). (Pubitemid 43923397)
21. Huxley, T. H. On the geographical distribution of the chief modifications of mankind. J. Ethnol. Soc. London. 2, 404-412 (1870).
22. Birdsell, J. B. Microevolutionary Patterns in Aboriginal Australia: A Gradient Analysis of Clines (Oxford University Press, New York, 1993).
23. Gollan, K. Prehistoric dogs in Australia: an Indian origin? in Recent Advances in Indo-Pacific Prehistory (eds Misra, V.N. & Bellwood, P.) 439-443 (Oxford and IBH Publishing Co, New Delhi, 1985).
24. Glover, I. C. & Presland, G. Microliths in Indonesian flaked stone industries in Recent Advances in Indo-Pacific Prehistory (eds Misra, V.N. & Bellwood, P.) 185-195 (Oxford and IBH Publishing Co, New Delhi, 1985).
25. Beaton, J. M. Dangerous harvest: investigations in the late prehistoric occupation of upland south-east central Queensland PhD Thesis, Australian National University, Canberra (1977).
26. Evans, N. & Jones, R. The cradle of the Pama-Nyungans: archaeological and linguistic speculations in Archaeology and Linguistics: Aboriginal Australia in Global Perspective (eds McConvell, P & Evans, N.) 385-417 (Oxford University Press, Melbourne, 1997).
27. Dixon, R. M. W. The Languages of Australia (Cambridge University Press, New York, 1980).
28. Hudjashov, G., Kivisild, T., Underhill, P. A., Endicott, P., Sanchez, J. J., Lin, A. A. et al. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc. Natl Acad. Sci. 104, 8726-8730 (2007). (Pubitemid 47175379)
29. Kirk, R. L. & Thorne, A. G. The Origin of the Australians (Humanities Press, New Jersey, 1976).
30. Nei, M. & Roychoudhury, A. K. Evolutionary relationships of human populations on a global scale. Mol. Biol. Evol. 10, 927-943 (1993). (Pubitemid 23260604)
31. Alfonso-Sanchez, M. A., Perez-Miranda, A. M. & Herrera, R. J. Autosomal microsatellite variability of the Arrernte people of Australia. Am. J. Hum. Biol. 20, 91-99 (2008).
32. Bamshad, M., Kivisild, T., Watkins, W. S., Dixon, M. E., Ricker, C. E., Rao, B. B. et al. Genetic evidence on the origins of Indian caste populations. Genome. Res. 11, 994-1004 (2001). (Pubitemid 32834545)
33. Sahoo, S., Singh, A., Himabindu, G., Banerjee, J., Sitalaximi, T., Gaikwad, S. et al. A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc. Natl Acad. Sci. 103, 843-848 (2006). (Pubitemid 43212185)
34. Sengupta, S., Zhivotovsky, L. A., King, R., Mehdi, S. Q., Edmonds, C. A., Chow, C. E. et al. 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. 2, 202-221 (2006). (Pubitemid 43157561)
35. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature. 461, 489-494 (2009).
36. Thapar, R. A History of India: Volume 1 (Penguin Books, London, 1966).
37. Ray, N. Nationalism in India (Aligarh Muslim University, Aligarh, India, 1973).
38. Majumder, P. P. Genomic inferences on peopling of south Asia. Curr. Opin. Genet. Dev. 18, 280-284 (2008).
39. Chopra, P. N. The Gazetteer of India (Ministry of Education and Social Welfare, India, 1965).
40. Morab, S. G. The Soliga of Biligiri Rangana Hills (Anthropological Survey of India, India, 1977).
41. Majumder, P. P. People of India: biological diversity and affinities. Evol. Anthropol. 6, 100-110 (1998).
42. Zaraska, N. A. Health Behaviors of the Soliga Tribe Women Master's Thesis, Queen's University, Canada 1997.
43. Gordon, R. G. Ethnologue: Languages of the World 15th edn. (SIL International, Texas, 2005).
44. Sujatha, K. Education among scheduled tribes in India Education Report 1st edn (eds Govinda, R.) 87-94 (Oxford University Press, New Delhi, 2002).
45. Sarkar, S. S. The Aboriginal Races of India 1st edn. (Bookland Ltd, Calcutta, 1954).
46. Rowold, D. J. & Herrera, R. J. Inferring recent human phylogenies using forensic STR technology. Forensic Sci. Int. 133, 260-265 (2003). (Pubitemid 36638307)
47. Shepard, E. M., Chow, R. A., Suafo'a, E., Addison, D., Perez-Miranda, A. M., Garcia- Bertrand, R. L. et al. Autosomal STR variation in five Austronesian populations. Hum. Biol. 77, 825-851 (2005). (Pubitemid 43727750)
48. Perez-Miranda, A. M., Alfonso-Sanchez, M. A., Pena, J. A. & Herrera, R. J. Qatari DNA variation at a crossroad of human migrations. Hum. Hered. 61, 67-79 (2006). (Pubitemid 43883124)
49. Shepard, E. M. & Herrera, R. J. Genetic encapsulation among Near Eastern populations. J. Hum. Genet. 51, 467-476 (2006a). (Pubitemid 43863784)
50. Shepard, E. M. & Herrera, R. J. Iranian STR variation at the fringes of biogeographical demarcation. Forensic Sci. Int. 158, 140-148 (2006b).
51. Applied Biosystems. AmpFlSTR Identifiler PCR Amplification Kit User's Manual (Applied Biosystems, Foster City, CA, USA, 2001).
52. Raymond, M. & Rousset, F. Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248-249 (1995).
53. Jones, D. A. Blood samples: probability of discrimination. J. Forensic Sci. Soc. 12, 355-359 (1972).
54. Brenner, C. H. & Morris, J. W. Proceedings for the International Symposium on Human Identification (Promega Corporation, Madison, 1990).
55. Tereba, A. Profiles in DNA (Promega Corporation, Madison, 1999).
56. Schneider, S., Kueffer, J. M., Roessli, D. & Excoffier, L. Arlequin v. 2.000: A Software for Population Genetic Analysis (Genetics and Biometry Laboratory, University of Geneva, Geneva, 2000).
57. Alves, C., Gusmão, L., Damasceno, A., Soares, B. & Amorim, A. Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 system) and a report on genotypic variations. Forensic Sci. Int. 139, 201-205 (2004). (Pubitemid 38201123)
58. Beleza, S., Alves, C., Reis, F., Amorim, A., Carracedo, A. & Gusmão, L. 17 STR data (AmpF/STR Identifiler and Powerplex 16 system) from Cabinda (Angola). Forensic Sci. Int. 141, 193-196 (2004). (Pubitemid 38446827)
59. Kido, A., Dobashi, Y., Fujitani, N., Hara, M., Susukida, R., Kimura, H. et al. Population data on the AmpFlSTR identifiler loci in Africans and Europeans from South Africa. Forensic Sci. Int. 168, 232-235 (2007). (Pubitemid 46621213)
60. Forward, B.W., Eastman, M. W.,Nyambo, T. B. & Ballard, R. E. AMPF/STRsidentifilert STR allele frequencies in Tanzania, Africa. J. Forensic Sci. 53, 245-247 (2008). (Pubitemid 351239250)
61. Regueiro, M., Mirabal, S., Lacau, H., Caeiro, J. L., Garcia-Bertrand, R. L. & Herrera, R. J. Austronesian genetic signature in east African Madagascar and Polynesia. J. Hum. Genet. 53, 106-120 (2008).
62. Barni, F., Berti, A., Pianese, A., Boccellino, A., Miller, M. P., Caperna, A. et al. Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region. Forensic Sci. Int. 167, 87-92 (2007). (Pubitemid 46420633)
63. Bindu, H. G., Trivedi, R. & Kashyap, V. K. Allele frequency distribution based on 17 STR markers in three major Dravidian linguistic populations of Andhra Pradesh, India. Forensic Sci. Int. 170, 76-85 (2007). (Pubitemid 47007679)
64. Banerjee, J., Trivedi, R. & Kashyap, V. K. Polymorphism at 15 short tandem repeat AmpFlSTR Identifiler TM loci in three aboriginal populations of India: an assessment in human identification. J. Forensic Sci. 50, 1229-1234 (2005). (Pubitemid 41279182)
65. Roy, S., Eaaswarkhanth, M., Dubey, B. & Haque, I. Autosomal STR variations in three endogamous populations of West Bengal, India. Leg. Med. 10, 326-332 (2008).
66. Dobashi, Y., Kido, A., Fujitani, N., Hara, M., Susukida, R. & Oya, M. STR data for the AmpFLSTR Identifiler loci in Bangladeshi and Indonesian populations. Leg. Med. 7, 222-226 (2005). (Pubitemid 40828860)
67. Wang, Z. Y., Yu, R. J., Wang, F., Li, X. S. & Jin, T. B. Genetic polymorphisms of 15 STR loci in Han population from Shaanxi (NW china). Forensic Sci. Int. 147, 89-91 (2005). (Pubitemid 39488114)
68. Kim, Y. L., Hwang, J. Y., Kim, Y. J., Lee, S., Chung, N. G., Goh, H. G. et al. Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population. Forensic Sci. Int. 136, 92-95 (2003). (Pubitemid 37101302)
69. Hashiyada, M., Itakura, Y., Nagashima, T., Nata, M. & Funayama, M. Polymorphism of STRs by multiplex analysis in japanese population. Forensic Sci. Int. 133, 250-253 (2003). (Pubitemid 36638304)
70. De Ungria, M. C. A., Roby, R. K., Tabbada, K. A., Rao-Coticone, S., Tan, M. M. M. & Hernandez, K. N. Allele frequencies of 19 STR loci in a Philippine population generated using AmpFlSTR multiplex and ALF singleplex systems. Forensic Sci. Int. 152, 281 (2005).
71. Rerkamnuaychoke, B., Rinthachai, T., Shotivaranon, J., Jomsawat, U., Siriboonpiputtana, T., Chaiatchanarat, K. et al. Thai population data on 15 tetrameric STR loci- D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA. Forensic Sci. Int. 158, 234-237 (2006).
72. Seah, L. H., Jeevan, N. H., Othman, M. I., Jaya, P., Ooi, Y. S., Wong, P. C. et al. STR data for the AmpF/STR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population. Forensic Sci. Int. 138, 134-137 (2003). (Pubitemid 37464745)
73. Eckhoff, C., Walsh, S. J. & Buckleton, J. S. Population data from sub-populations of the northern territory of Australia for 15 autosomal short tandem repeat (STR) loci. Forensic Sci. Int. 171, 237-249 (2007). (Pubitemid 47211734)
74. Rohlf, F. NTSYSpc (Exter Publishing, Setauket, NY, 2002).
75. Felsentein, J. Phylogeny Inference Package (PHYLIP) Version 3.6a3 (Department of Genetics, University of Washington, Seattle, 2002).
76. Ota, T. DISPAN: Genetic Distance and Phylogenetic Analysis (Institute of Molecular Evolutionary Genetics, Pennsylvania State University, Pennsylvania, 1993).
77. Carmody, G. G-test (Carleton University, Ottawa, 1990).
78. Long, J. C., Williams, R. C., McAuley, J. E., Medis, R., Partel, R., Tregellas, W. M. et al. Genetic variation in Arizona Mexican Americans: estimation and interpretation of admixture proportions. Am. J. Phys. Anthropol. 84, 141-157 (1991).
79. Ayres, K. L., Chaseling, J. & Balding, D. J. Implications for DNA identification arising from an analysis of Australian forensic databases. Forensic Sci. Int. 129, 90-98 (2002). (Pubitemid 35286778)
80. Allor, C., Einum, D. D. & Scarpetta, M. Identification and characterization of variant alleles at CODIS STR loci. J. Forensic Sci. 50, 1128-1133 (2005). (Pubitemid 41279164)
81. Ferdous, A., Eunus Ali, M., Alam, S., Hossai, T., Hany, U., Dissing, J. et al. Genetic data on 10 autosomal STR loci in the Bangladeshi population. Leg. Med. 8, 297-299 (2006). (Pubitemid 44667600)
82. Ali, M. E., Ferdous, A., Alam, S., Hany, U., Hossain, T., Hasan, M. et al. Identification of variant alleles at AmpFlSTR SGM plus STR loci in a sample population of Bangladesh. Afr. J. Biotechnol. 7, 3603-3605 (2008).
83. Short Tandem Repeat DNA Internet Database, http://www.cstl.nist.gov/ biotech/strbase/.
84. Kashyap, V. K., Guha, S., Sitalaximi, T., Bindu, G. H., Hasnain, S. E. & Trivedi, R. Genetic structure of Indian populations based on fifteen autosomal microsatellite loci. BMC. Genet. 7, 28 (2006).
85. Jobling, M. A. & Tyler-Smith, C. The human Y chromosome: an evolutionary marker comes of age. Nat. Rev. Genet. 4, 598-612 (2003). (Pubitemid 36917502)
86. Walsh, S. J., Mitchell, R. J., Watson, N. & Buckleton, J. S. A comprehensive analysis of microsatellite diversity in Aboriginal Australians. J. Hum. Genet. 52, 712-728 (2007). (Pubitemid 47389619)