Revisiting the role of the Himalayas in peopling Nepal: Insights from mitochondrial genomes

Journal of Human Genetics

Volumn 57, Issue 4, 2012, Pages 228-234

  Wang, Hua Wei ^a,b   Li, Yu Chun ^a   Sun, Fei ^c   Zhao, Mian ^a,d   Mitra, Bikash ^b,e   Chaudhuri, Tapas Kumar ^e   Regmi, Pasupati ^f   Wu, Shi Fang ^a,d   Kong, Qing Peng ^a,d   Zhang, Ya Ping ^a,b,d  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b YUNNAN UNIVERSITY   (China)

^c XINXIANG MEDICAL UNIVERSITY   (China)

^d KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases   (China)

^e UNIVERSITY OF NORTH BENGAL   (India)

^f Little Angel's College Hattiban   (Nepal)

Author keywords

mtDNA; Nepalese; origin

Indexed keywords

MITOCHONDRIAL DNA;

ARCHEOLOGY; ARTICLE; CHINA; GENE FLOW; GENETIC ANALYSIS; HAPLOTYPE; HUMAN; INDIA; LINGUISTICS; MITOCHONDRIAL GENOME; NEPAL; NUCLEOTIDE SEQUENCE; PHYLOGENY; Y CHROMOSOME;

ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; GENE FLOW; GENETICS, POPULATION; GENOME, HUMAN; GENOME, MITOCHONDRIAL; HAPLOTYPES; HUMANS; INDIA; MITOCHONDRIA; NEPAL; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; TIBET; TIME FACTORS;

EID: 84860305689     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/jhg.2012.8     Document Type: Article

References (50)

1. Zhao, M., Kong, Q. P., Wang, H. W., Peng, M. S., Xie, X. D., Wang, W. Z. et al. Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau. Proc. Natl. Acad. Sci. USA 106, 21230-21235 (2009).
2. Wang, H. W. Nepal (Social Sciences Documentation Publishing House, Beijing, China, 2004).
3. Xue, K. Q., Zhao, C. Q., Sun, S. H., Ge, W. J., Liu, Y., Xing, G. C. et al. Concise Encyclopaedia Of South Asia and Central Asia (China Social Science Press, Beijing, China, 2004).
4. Gayden, T., Cadenas, A. M., Regueiro, M., Singh, N. B., Zhivotovsky, L. A., Underhill, P. A. et al. The Himalayas as a directional barrier to gene flow. Am. J. Hum. Genet. 80, 884-894 (2007). (Pubitemid 46668457)
5. Fornarino, S., Pala, M., Battaglia, V., Maranta, R., Achilli, A., Modiano, G. et al. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): A reservoir of genetic variation. BMC Evol. Biol. 9, 154 (2009).
6. Gayden, T., Mirabal, S., Cadenas, A. M., Lacau, H., Simms, T. M., Morlote, D. et al. Genetic insights into the origins of Tibeto-Burman populations in the Himalayas. J. Hum. Genet. 54, 216-223 (2009).
7. Thangaraj, K., Chaubey, G., Kivisild, T., Rani, D. S., Singh, V. K., Ismail, T. et al. Maternal footprints of Southeast Asians in North India. Hum. Hered. 66, 1-9 (2008). (Pubitemid 351342229)
8. Su, B., Xiao, C. J., Deka, R., Seielstad, M. T., Kangwanpong, D., Xiao, J. H. et al. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107, 582-590 (2000). (Pubitemid 32010960)
9. Cordaux, R., Saha, N., Bentley, G. R., Aunger, R., Sirajuddin, S. M. & Stoneking, M. Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur. J. Hum. Genet. 11, 253-264 (2003). (Pubitemid 36519095)
10. Cordaux, R., Weiss, G., Saha, N. & Stoneking, M. The Northeast Indian passageway: A barrier or corridor for human migrations? Mol. Biol. Evol. 21, 1525-1533 (2004). (Pubitemid 38976555)
11. Metspalu, M., Kivisild, T., Metspalu, E., Parik, J., Hudjashov, G., Kaldma, K. et al. 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. 5, 26 (erratum 26:41) (2004).
12. Reddy, B. M., Langstieh, B. T., Kumar, V., Nagaraja, T., Reddy, A. N. S., Meka, A. et al. Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PLoS ONE 2, e1141 (2007).
13. Qin, Z. D., Yang, Y. J., Kang, L. L., Yan, S., Cho, K., Cai, X. Y. et al. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum. Am. J. Phys. Anthropol. 143, 555-569 (2010).
14. Kivisild, T., Bamshad, M. J., Kaldma, K., Metspalu, M., Metspalu, E., Reidla, M. et al. Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr. Biol. 9, 1331-1334 (1999).
15. Roychoudhury, S., Roy, S., Basu, A., Banerjee, R., Vishwanathan, H., Usha Rani, M. V. et al. Genomic structures and population histories of linguistically distinct tribal groups of India. Hum. Genet. 109, 339-350 (2001). (Pubitemid 32926929)
16. Banerjee, J., Trivedi, R. & Kashyap, V. K. Mitochondrial DNA control region sequence polymorphism in four indigenous tribes of Chotanagpur plateau, India. Forensic Sci. Int. Genet. 149, 271-274 (2005). (Pubitemid 40321068)
17. Kumar, V., Langstieh, B. T., Madhavi, K. V., Naidu, V. M., Singh, H. P., Biswas, S. et al. Global patterns in human mitochondrial DNA and Y-chromosome variation caused by spatial instability of the local cultural processes. PLoS Genet. 2, e53 (2006).
18. Wang, H. W., Jia, X. Y., Ji, Y. L., Kong, Q. P., Zhang, Q. J., Yao, Y. G. et al. Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A. Mutat. Res. 643, 48-53 (2008).
19. Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M. & Howell, N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147 (1999). (Pubitemid 29455385)
20. Kivisild, T., Tolk, H. V., Parik, J., Wang, Y. M., Papiha, S. S., Bandelt, H. J. et al. The emerging limbs and twigs of the East Asian mtDNA tree. Mol. Biol. Evol. 19, 1737-1751 (2002).
21. Kong, Q. P., Yao, Y. G., Sun, C., Bandelt, H. J., Zhu, C. L. & Zhang, Y. P. Phylogeny of east Asian mitochondrial DNA lineages inferred fromcomplete sequences. Am. J. Hum. Genet. 73, 671-676 (2003). (Pubitemid 37076281)
22. Tanaka, M., Cabrera, V. M., González, 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)
23. Kong, Q. P., Bandelt, H. J., Sun, C., Yao, Y. G., Salas, A., Achilli, A. et al. Updating the East Asian mtDNA phylogeny: A prerequisite for the identification of pathogenic mutations. Hum. Mol. Genet. 15, 2076-2086 (2006). (Pubitemid 43923397)
24. Derenko, M., Malyarchuk, B., Grzybowski, T., Denisova, G., Dambueva, I., Perkova, M. et al. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am. J. Hum. Genet. 81, 1025-1041 (2007). (Pubitemid 47580254)
25. Kong, Q. P., Sun, C., Wang, H. W., Zhao, M., Wang, W. Z., Zhong, L. et al. Large-scale mtDNA screening reveals a surprising matrilineal complexity in East Asia and its implications to the peopling of the region. Mol. Biol. Evol. 28, 513-522 (2011).
26. Palanichamy, M. G., Sun, C., Agrawal, S., Bandelt, H. J., Kong, Q. P., Khan, F. et al. 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)
27. Sun, C., Kong, Q. P., Palanichamy, M. G., 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)
28. Thangaraj, K., Chaubey, G., Singh, V. K., Vanniarajan, A., Thanseem, I., Reddy, A. G. et al. In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India. BMC Genomics 7, 151-156 (2006).
29. Chandrasekar, A., Kumar, S., Sreenath, J., Sarkar, B. N., Urade, B. P., Mallick, S. et al. Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: Dispersal of modern human in South Asian corridor. PLoS ONE 4, e7447 (2009).
30. Thangaraj, K., Chaubey, G., Kivisild, T., Reddy, A., Singh, V. K., Rasalkar, A. A. et al. Reconstructing the origin of Andaman Islanders. Science 308, 996 (2005). (Pubitemid 40664404)
31. Kivisild, T., Shen, P. D., Wall, D., Do, B., Sung, R., Davis, K. et al. The role of selection in the evolution of human mitochondrial genomes. Genetics 172, 373-387 (2006). (Pubitemid 43345499)
32. Maca-Meyer, N., González, A. M., Larruga, J. M., Flores, C. & Cabrera, V. M. Major genomicmitochondrial lineages delineate early human expansions. BMC Genet. 2, 13 (2001).
33. Ingman, M. & Gyllensten, U.Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13, 1600-1606 (2003). (Pubitemid 36874477)
34. 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)
35. Hill, C., Soares, P., Mormina, M., Macaulay, V., Meehan, W., Blackburn, J. et al. Phylogeography and ethnogenesis of aboriginal Southeast Asians. Mol. Biol. Evol. 23, 2480-2491 (2006). (Pubitemid 44737142)
36. Hill, C., Soares, P., Mormina, M., Macaulay, V., Clarke, D., Blumbach, P. B. et al. A mitochondrial stratigraphy for island southeast Asia. Am. J. Hum. Genet. 80, 29-43 (2007). (Pubitemid 46047648)
37. Peng, M. S., Quang, H. H., Dang, K. P., Trieu, A. V., Wang, H. W., Yao, Y. G. et al. Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA. Mol. Biol. Evol. 27, 2417-2430 (2010).
38. Tabbada, K. A., Trejaut, J., Loo, J. H., Chen, Y. M., Lin, M., Mirazón-Lahr, M. et al. Philippine mitochondrial DNA diversity: A populated viaduct between Taiwan and Indonesia? Mol. Biol. Evol. 27, 21-31 (2010).
39. Kong, Q. P., Salas, A., Sun, C., Fuku, N., Tanaka, M., Zhong, L. et al. Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS ONE 3, e3016 (2008).
40. Yao, Y. G., Kong, Q. P., Bandelt, H. J., Kivisild, T. & Zhang, Y. P. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am. J. Hum. Genet. 70, 635-651 (2002). (Pubitemid 34177919)
41. Excoffier, L., Laval, G. & Schneider, S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47-50 (2005).
42. 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).
43. Bandelt, H. J., Macaulay, V. & Richards, M. Median networks: Speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol. Phylogenet. Evol. 16, 8-28 (2000). (Pubitemid 30466873)
44. Forster, P., Harding, R., Torroni, A. & Bandelt, H. J. Origin and evolution of Native American mtDNA variation: A reappraisal. Am. J. Hum. Genet. 59, 935-945 (1996). (Pubitemid 26328092)
45. Saillard, J., Forster, P., Lynnerup, N., Bandelt, H. J. & Nørby, S. mtDNA variation among Greenland Eskimos: The edge of the Beringian expansion. Am. J. Hum. Genet. 67, 718-726 (2000). (Pubitemid 30659601)
46. Soares, P., Ermini, L., Thomson, N., Mormina, M., Rito, T., Röhl, A. et al. Correcting for purifying selection: An improved human mitochondrial molecular clock. Am. J. Hum. Genet. 84, 740-759 (2009).
47. Finnilä , S., Lehtonen, M. S. & Majamaa, K. Phylogenetic network for European mtDNA. Am. J. Hum. Genet. 68, 1475-1484 (2001). (Pubitemid 32510623)
48. Herrnstadt, C., Elson, J. L., Fahy, E., Preston, G., Turnbull, D. M., Anderson, C. et al. Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am. J. Hum. Genet. 70, 1152-1171 (2002). (Pubitemid 34450567)
49. Sharmai, D. R. Archaeological Remains of the Dang Valley. Ancient Nepal. 88, 8-15 (1988).
50. Peng, M. S., Palanichamy, M. G., Yao, Y. G., Mitra, B., Cheng, Y. T., Zhao, M. et al. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b. BMC Biol. 9, 2 (2011).