The Himalayas: Barrier and conduit for gene flow

American Journal of Physical Anthropology

Volumn 151, Issue 2, 2013, Pages 169-182

  Gayden, Tenzin ^a,b   Perez, Annabel ^a   Persad, Patrice J ^a   Bukhari, Areej ^a,b   Chennakrishnaiah, Shilpa ^a,b   Simms, Tanya ^a   Maloney, Trisha ^a   Rodriguez, Kristina ^a   Herrera, Rene J ^a,b  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b FLORIDA INTERNATIONAL UNIVERSITY   (United States)

Author keywords

MtDNA; Nepal; Tibet

Indexed keywords

GENOMIC DNA; MITOCHONDRIAL DNA;

ARTICLE; ASIA; BLOOD SAMPLING; CHINA; CHROMOSOME ANALYSIS; CLADISTICS; GENE FLOW; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC ELEVATION; HUMAN; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETICS; POPULATION STRUCTURE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS; Y CHROMOSOME;

ANALYSIS OF VARIANCE; ANTHROPOLOGY, PHYSICAL; ASIAN CONTINENTAL ANCESTRY GROUP; DNA, MITOCHONDRIAL; GENE FLOW; GENOMICS; HAPLOTYPES; HUMAN MIGRATION; HUMANS; NEPAL; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; TIBET;

EID: 84878111463     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.22240     Document Type: Article

References (73)

1. Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ,. 2008. The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS One 3: e1764.
2. Aldenderfer M, Z Yinong,. 2004. The prehistory of the Tibetan Plateau to the seventh century AD: perspectives and research from China and the West since 1950. J World Prehist 18: 1-55.
3. Antunez-de-Mayolo G, Antunez-de-Mayolo A, Antunez-de-Mayolo P, Papiha SS, Hammer M, Yunis JJ, Yunis EJ, Damodaran C, Martinez de Pancorbo M, Caeiro JL, Puzyrev VP, Herrera RJ,. 2002. Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. Electrophoresis 23: 3346-3356.
4. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG,. 1981. Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
5. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N,. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147.
6. Applied B,. 2001. AmpFlSTR identifiler PCR amplification kit user's manual. (Foster City, CA).
7. Ballinger SW, Schurr TG, Torroni A, Gan YY, Hodge JA, Hassan K, Chen KH, Wallace DC,. 1992. Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient mongoloid migrations. Genetics 130: 139-152.
8. Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli EL, Silva NM, Kivisild T, Torroni A, Villems R,. 2012. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90: 675-684.
9. Berreman GD,. 1963. People and cultures of the Himalayas. Asian Survey 3: 289-304.
10. Brantingham P, Haizhou M, Olsen J, Xing G, Madsen D, Rhode D,. 2003. Speculation on the timing and nature of Late Pleistocene hunter-gatherer colonization of the Tibetan Plateau. Chin Sci Bull 48: 1510-1516.
11. Cavalli-Sforza LL, Menozzi P, Piazza A,. 1994. The history and geography of human genes. Princeton, NJ: Princeton University Press.
12. Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking M,. 2003. Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet 11: 253-264.
13. Chandrasekar A, Kumar S, Sreenath J, Sarkar BN, Urade BP, Mallick S, Bandopadhyay SS, Barua P, Barik SS, Basu D, Kiran U, Gangopadhyay P, Sahani R, Prasad BV, Gangopadhyay S, Lakshmi GR, Ravuri RR, Padmaja K, Venugopal PN, Sharma MB, Rao VR,. 2009. Updating phylogeny of mitochondrial DNA macrohaplogroup M in India: dispersal of modern human in South Asian corridor. PLoS One 4: e7447.
14. Cheng B, Tang W, He L, Dong Y, Lu J, Lei Y, Yu H, Zhang J, Xiao C,. 2008. Genetic imprint of the Mongol: signal from phylogeographic analysis of mitochondrial DNA. J Hum Genet 53: 905-913.
15. Comas D, Calafell F, Mateu E, Pérez-Lezaun A, Bosch E, Martínez-Arias R, Clarimon J, Facchini F, Fiori G, Luiselli D, Pettener D, Bertranpetit J,. 1998. Trading genes along the Silk Road: mtDNA sequences and the origin of central Asian populations. Am J Hum Genet 63: 1824-1838.
16. Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, Calafell F, Bertranpetit J,. 2004. Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet 12: 495-504.
17. Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T, Villems R, Zakharov I,. 2007. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 81: 1025-1041.
18. Endicott P, Metspalu M, Stringer C, Macaulay V, Cooper A, Sanchez JJ,. 2006. Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PLoS One 1: e81.
19. Endicott P, Ho SY, Metspalu M, Stringer C,. 2009. Evaluating the mitochondrial timescale of human evolution. Trends Ecol Evol 24: 515-521.
20. Excoffier L, Laval LG, Schneider S,. 2007. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
21. Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, Torroni A, Semino O, Santachiara-Benerecetti SA,. 2009. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 9: 154.
22. Forster P, Harding R, Torroni A, Bandelt HJ,. 1996. Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet 59: 935-945.
23. Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, Underhill PA, Cavalli-Sforza LL, Herrera RJ,. 2007. The Himalayas as a directional barrier to gene flow. Am J Hum Genet 80: 884-894.
24. Gayden T, Regueiro M, Martinez L, Cadenas AM, Herrera RJ,. 2008. Human Y-chromosome haplotyping by allele-specific polymerase chain reaction. Electrophoresis 29: 2419-2423.
25. Gayden T, Mirabal S, Cadenas AM, Lacau H, Simms TM, Morlote D, Chennakrishnaiah S, Herrera RJ,. 2009. Genetic insights into the origins of Tibeto-Burman populations in the Himalayas. J Hum Genet 54: 216-223.
26. Hall TA,. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
27. Hammer MF, Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S,. 2006. Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. J Hum Genet 51: 47-58.
28. Henn BM, Gignoux CR, Feldman MW, Mountain JL,. 2009. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Mol Biol Evol 26: 217-230.
29. Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M,. 2007. A mitochondrial stratigraphy for island Southeast Asia. Am J Hum Genet 80: 29-43.
30. Huang W,. 1994. The prehistoric human occupation of the Qinghai-Xizang plateau. Gottinger Geographische Abhandlungen 95: 201-219.
31. Ingman M, Gyllensten U,. 2006. A recent genetic link between Sami and the Volga-Ural region of Russia. Eur J Hum Genet 15: 115-120.
32. Kang L, Li S, Gupta S, Zhang Y, Liu K, Zhao J, Jin L, Li H,. 2010. Genetic structures of the Tibetans and the Deng people in the Himalayas viewed from autosomal STRs. J Hum Genet 55: 270-277.
33. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, Bandelt HJ, Villems R,. 2002. The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19: 1737-1751.
34. Kong QP, Bandelt HJ, Sun C, Yao YG, Salas A, Achilli A, Wang CY, Zhong L, Zhu CL, Wu SF, Torroni A, Zhang YP,. 2006. Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15: 2076-2086.
35. Kolman CJ, Sambuughin N, Bermingham E,. 1996. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142: 1321-1334.
36. Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, Curran JE,. 2011. Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 11: 293.
37. Lee HY, Yoo JE, Park MJ, Chung U, Shin KJ,. 2006. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Int J Legal Med 120: 5-14.
38. Lewis TT, and, Shakya DR,. 1988. Contributions to the history of Nepal: eastern Newar diaspora settlements. Contrib Nepal Stud 15: 25-65.
39. Li H, Cai X, Winograd-Cort ER, Wen B, Cheng X, Qin Z, Liu W, Liu Y, Pan S, Qian J, Tan CC, Jin L,. 2007. Mitochondrial DNA diversity and population differentiation in southern East Asia. Am J Phys Anthropol 134: 481-488.
40. Malla KP,. 1981. Linguistic archaeology of the Nepal Valley. A preliminary report. Kailash 8: 5-23.
41. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, Karmin M, Behar DM, Gilbert MT, Endicott P, Mastana S, Papiha SS, Skorecki K, Torroni A, Villems R,. 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 Genet 5: 26.
42. Metspalu M, Kivisild T, Bandelt HJ, Richards M, Villems R,. 2006. The pioneer settlement of modern humans in Asia. In:, Bandelt HJ, Macaulay V, Richards M, editors. Human mitochondrial DNA and the evolution of Homo sapiens. Nucleic Acids and Molecular Biology, Vol. 18. Berlin; New York: Springer. p 181-199.
43. Nei M, Roychoudhury AK,. 1993. Evolutionary relationships of human populations on a global scale. Mol Biol Evol 10: 927-943.
44. Nohira C, Maruyama S, Minaguchi K,. 2010. Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences. Int J Legal Med 124: 7-12.
45. Peng MS, Palanichamy MG, Yao YG, Mitra B, Cheng YT, Zhao M, Liu J, Wang HW, Pan H, Wang WZ, Zhang AM, Zhang W, Wang D, Zou Y, Yang Y, Chaudhuri TK, Kong QP, Zhang YP,. 2011. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b. BMC Biol 9: 2.
46. Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, Yao YG, Kong QP, Zhang YP,. 2010. Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Mol Biol Evol 27: 2417-2430.
47. Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H,; Genographic Consortium. 2010. 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.
48. Rakha A, Shin KJ, Yoon JA, Kim NY, Siddique MH, Yang IS, Yang WI, Lee HY,. 2011. Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 125: 841-848.
49. Reddy BM, Langstieh BT, Kumar V, Nagaraja T, Reddy AN, Meka A, Reddy AG, Thangaraj K, Singh L,. 2007. Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PLoS One 2: e1141.
50. Regmi DR,. 1969. Ancient Nepal. K.L. Mukhopadhyay, Calcutta.
51. Richardson H,. 1962. A short history of Tibet. New York: E.P. Dutton & Co., Inc.
52. Rohlf FJ,. 2002. NTSYS pc: Numerical Taxonomy System, Version 2.1. Setauket, NY: Exeter Publishing.
53. Roostalu U, Kutuev I, Loogväli EL, Metspalu E, Tambets K, Reidla M, Khusnutdinova EK, Usanga E, Kivisild T, Villems R,. 2007. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol 24: 436-448.
54. Saillard J, Forster P, Lynnerup N, Bandelt HJ, Norby S,. 2000. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet 67: 718-726.
55. Schurr TG, Sukernik RI, Starikovskaya YB, Wallace DC,. 1999. Mitochondrial DNA variation in Koryaks and Itel'men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic. Am J Phys Anthropol 108: 1-39.
56. Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RZ, Xiao CJ, Wells RS, Jin L, Su B,. 2008. Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol 6: 45.
57. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB,. 2009. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740-759.
58. Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA,. 1991. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48: 370-382.
59. Tabbada KA, Trejaut J, Loo JH, Chen YM, Lin M, Mirazõn-Lahr M, Kivisild T, De Ungria MC,. 2010. Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia? Mol Biol Evol 27: 21-31.
60. Tambets K, Rootsi S, Kivisild T, Help H, Serk P, Loogväli EL, Tolk HV, Reidla M, Metspalu E, Pliss L, Balanovsky O, Pshenichnov A, Balanovska E, Gubina M, Zhadanov S, Osipova L, Damba L, Voevoda M, Kutuev I, Bermisheva M, Khusnutdinova E, Gusar V, Grechanina E, Parik J, Pennarun E, Richard C, Chaventre A, Moisan JP, Barác L, Pericic̈ M, Rudan P, Terzic̈ R, Mikerezi I, Krumina A, Baumanis V, Koziel S, Rickards O, De Stefano GF, Anagnou N, Pappa KI, Michalodimitrakis E, Ferák V, Füredi S, Komel R, Beckman L, Villems R,. 2004. The western and eastern roots of the Saami: the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 74: 661-682.
61. Thangaraj K, Chaubey G, Kivisild T, Selvi Rani D, Singh VK, Ismail T, Carvalho-Silva D, Metspalu M, Bhaskar LV, Reddy AG, Chandra S, Pande V, Prathap Naidu B, Adarsh N, Verma A, Jyothi IA, Mallick CB, Shrivastava N, Devasena R, Kumari B, Singh AK, Dwivedi SK, Singh S, Rao G, Gupta P, Sonvane V, Kumari K, Basha A, Bhargavi KR, Lalremruata A, Gupta AK, Kaur G, Reddy KK, Rao AP, Villems R, Tyler-Smith C, Singh L,. 2008. Maternal footprints of Southeast Asians in North India. Hum Hered 66: 1-9.
62. Thangaraj K, Chaubey G, Kivisild AG, Singh VK, Rasalkar AA, Singh L,. 2005. Reconstructing the origin of Andaman Islanders. Science 308(5724): 996.
63. Torroni A, Miller JA, Moore LG, Zamudio S, Zhuang J, Droma T, Wallace DC,. 1994. Mitochondrial DNA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude. Am J Phys Anthropol 93: 189-199.
64. van Oven M, and, Kayser M,. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386-394.
65. Vigilant L, Pennington R, Harpending H, Kocher TD, Wilson AC,. 1989. Mitochondrial DNA sequences in single hairs from a southern African population. Proc Natl Acad Sci U S A 86: 9350-9354.
66. Wang HW, Mitra B, Chaudhuri TK, Palanichamy MG, Kong QP, Zhang YP,. 2011. Mitochondrial DNA evidence supports Northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics 38: 117-122.
67. Wang HW, Li YC, Sun F, Zhao M, Mitra B, Chaudhuri TK, Regmi P, Wu SF, Kong QP, Zhang YP,. 2012. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes. J Hum Genet 57: 228-234.
68. Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, Gao Y, Mao X, Zhang L, Qian J, Tan J, Jin J, Huang W, Deka R, Su B, Chakraborty R, Jin L,. 2004. Genetic evidence supports demic diffusion of Han culture. Nature 431: 302-305.
69. Whelpton J,. 1990. World bibliographical series: Nepal. Denver: Clio Press.
70. Yan S, Wang C, Li H, Li S, Jin L, The Genographic Consortium. 2011. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. Eur J Hum Genet 19: 1013-1015.
71. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP,. 2002. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70: 635-651.
72. Zhao M, Kong QP, Wang HW, Peng MS, Xie XD, Wang WZ, Jiayang, Duan JG, Cai MC, Zhao SN, Cidanpingcuo, Tu YQ, Wu SF, Yao YG, Bandelt HJ, Zhang YP,. 2009. Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau. Proc Natl Acad Sci USA 106: 21230-21235.
73. Zhang YJ, Xu QS, Zheng ZJ, Lin HY, Lee JB,. 2005. Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in northeast China Han. Forensic Sci Int 149: 267-269.