Complete mitochondrial DNA analysis of eastern eurasian haplogroups rarely found in populations of Northern Asia and Eastern Europe

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Derenko, Miroslava ^a   Malyarchuk, Boris ^a   Denisova, Galina ^a   Perkova, Maria ^a   Rogalla, Urszula ^b   Grzybowski, Tomasz ^b   Khusnutdinova, Elza ^c   Dambueva, Irina ^d   Zakharov, Ilia ^e  

^a INSTITUTE OF BIOLOGICAL PROBLEMS OF THE NORTH   (Russian Federation)

^b NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^c INSTITUTE OF BIOCHEMISTRY AND GENETICS   (Russian Federation)

^d INSTITUTE OF GENERAL AND EXPERIMENTAL BIOLOGY   (Russian Federation)

^e VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ALTAIAN KAZAKHS; ARTICLE; ASIA; BARGHUTS; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; EASTERN EUROPE; ETHNIC GROUP; GENE INTERACTION; GENE POOL; GENEALOGY; GENETIC PARAMETERS; GENETIC VARIABILITY; HAPLOGROUP; HUMAN; MONGOLIA; PHYLOGEOGRAPHY; POPULATION GENETICS; REGULATOR GENE; RUSSIAN FEDERATION; ASIAN; CAUCASIAN; EUROPE; GENETICS; HAPLOTYPE; MOLECULAR GENETICS; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS;

ASIA; ASIAN CONTINENTAL ANCESTRY GROUP; DNA, MITOCHONDRIAL; ETHNIC GROUPS; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYLOGEOGRAPHY; PRINCIPAL COMPONENT ANALYSIS;

EID: 84857407586     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032179     Document Type: Article

References (92)

1. Pitulko VV, Nikolsky PA, Girya EY, Basilyan AE, Tumskoy VE, et al. (2004) The Yana RHS site: humans in the Arctic before the last glacial maximum. Science 303: 52-56.
2. Goebel T, Waters MR, O'Rourke DH, (2008) The late Pleistocene dispersal of modern humans in the Americas. Science 319: 1497-1502.
3. Schroeder KB, Schurr TG, Long JC, Rosenberg NA, Crawford MH, et al. (2007) A private allele ubiquitous in the Americas. Biol Lett 3: 218-223.
4. Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, et al. (2007) Beringian standstill and spread of Native American founders. PLoS One 2: e829.
5. Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, et al. (2008) The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS One 3: e1764.
6. Kitchen A, Miyamoto MM, Mulligan CJ, (2008) A three-stage colonization model for the peopling of the Americas. PLoS One 3: e1596.
7. Derbeneva OA, Sukernik RI, Volodko NV, Hosseini SH, Lott MT, et al. (2002) Analysis of mitochondrial DNA diversity in the Aleuts of the Commander Islands and its implications for the genetic history of Beringia. Am J Hum Genet 71: 415-421.
8. Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, et al. (2007) Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 81: 1025-1041.
9. Gilbert MT, Kivisild T, Grønnow B, Andersen PK, Metspalu E, et al. (2008) Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320: 1787-1789.
10. Volodko V, Starikovskaya EB, Mazunin IO, Eltsov NP, Naidenko PV, et al. (2008) Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am J Hum Genet 82: 1084-1100.
11. Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, et al. (2009) Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 19: 1-8.
12. Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, et al. (2010) Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLoS One 5: e15214.
13. Perego UA, Angerhofer N, Pala M, Olivieri A, Lancioni H, et al. (2010) The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia. Genome Res 20: 1174-1179.
14. Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, et al. (2008) Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: insights into Turkic population history. Am J Phys Anthropol 136: 278-293.
15. Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, et al. (2010) Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann Hum Genet 74: 539-546.
16. Derenko M, Malyarchuk B, Denisova GA, Wozniak M, Dambueva I, et al. (2006) Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions. Hum Genet 118: 591-604.
17. Renfrew C, (1994) World linguistic diversity. Sci Am 270: 104-110.
18. van Oven M, Kayser M, (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: 386-394.
19. Soares P, Ermini L, Thomson N, Mormina M, Rito T, et al. (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740-759.
20. Soares P, Rito T, Trejaut J, Mormina M, Hill C, et al. (2011) Ancient voyaging and Polynesian origins. Am J Hum Genet 88: 239-247.
21. Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, et al. (2004) Mitochondrial genome variation in Eastern Asia and the peopling of Japan. Genome Res 14: 1832-1850.
22. Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, et al. (2005) Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol 3: e247.
23. Tabbada KA, Trejaut J, Loo JH, Chen YM, Lin M, et al. (2010) Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia? Mol Biol Evol 27: 21-31.
24. Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, et al. (2010) Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Mol Biol Evol 27: 2417-2430.
25. Loo JH, Trejaut JA, Lin M, ChenYM, Lee CL, et al. (2011) Genetic affinities between populations of Batanes and Orchid Islands. BMC Genet 12: 21.
26. Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, et al. (2006) Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol 23: 1966-1975.
27. Starikovskaya YB, Sukernik RI, Derbeneva OA, Volodko NV, Torroni A, et al. (2005) Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of native American haplogroups. Ann Hum Genet 69: 67-89.
28. Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, et al. (2003) Phylogeny of East Asian mitochondrial DNA linerages inferred from complete sequences. Am J Hum Genet 73: 671-676.
29. Bandelt HJ, Herrnstadt C, Yao YG, Kong QP, Kivisild T, et al. (2003) Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet 67: 512-524.
30. Hill C, Soares P, Mormina M, Macaulay V, Clarke D, et al. (2007) A mitochondrial stratigraphy for island southeast Asia. Am J Hum Genet 80: 29-43.
31. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, et al. (2008) Climate change and post-glacial human dispersals in Southeast Asia. Mol Biol Evol 25: 1209-1218.
32. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, et al. (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.
33. Bodner M, Zimmermann B, Röck A, Kloss-Brandstätter A, Horst D, et al. (2011) Southeast Asian diversity: first insights into the complex mtDNA structure of Laos. BMC Evol Biol 11: 49.
34. Wen B, Li H, Gao S, Mao X, Gao Y, et al. (2005) Genetic structure of Hmong-Mien speaking populations in East Asia as revealed by mtDNA lineages. Mol Biol Evol 22: 725-734.
35. Chaix R, Quintana-Murci L, Hegay T, Hammer MF, Mobasher Z, et al. (2007) From social to genetic structures in central Asia. Curr Biol 17: 43-48.
36. Irwin JA, Ikramov A, Saunier J, Bodner M, Amory S, et al. (2010) The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns. Int J Legal Med 124: 195-204.
37. Bermisheva M, Tambets K, Villems R, Khusnutdinova E, (2002) Diversity of mitochondrial DNA haplotypes in ethnic populations of the Volga-Ural region of Russia. Mol Biol (Moscow) 36: 990-1001.
38. Malyarchuk B, Derenko M, Denisova G, Kravtsova O, (2010) Mitogenomic diversity in Tatars from the Volga-Ural region of Russia. Mol Biol Evol 27: 2220-2226.
39. Malyarchuk BA, (2002) Human mitochondrial genome variability with implication to genetic history of Slavs. Dr Sci Biol thesis. Magadan: Institute of Biological Problems of the North.
40. Malyarchuk BA, Vanecek T, Perkova MA, Derenko MV, Sip M, (2006) Mitochondrial DNA variability in the Czech population, with application to the ethnic history of Slavs. Hum Biol 78: 681-696.
41. Burger J, Kirchner M, Bramanti B, Haak W, Thomas MG, (2007) Absence of the lactase-persistence-associated allele in early Neolithic Europeans. Proc Natl Acad Sci USA 104: 3736-3741.
42. Guba Z, Hadadi E, Major A, Furka T, Juhász E, et al. (2011) HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary. J Hum Genet 56: 784-79.
43. Yao YG, Kong QP, Wang CY, Zhu CL, Zhang YP, (2004) Different matrilineal contributions to genetic structure of ethnic groups in the Silk Road region in China. Mol Biol Evol 21: 2265-2280.
44. Kong QP, Bandelt HJ, Sun C, Yao YG, Salas A, et al. (2006) Updating the East Asian mtDNA phylogeny: A prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15: 2076-2086.
45. Zhao M, Kong QP, Wang HW, Peng MS, Xie XD, et al. (2009) Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau. Proc Natl Acad Sci USA 106: 21230-21235.
46. Qin Z, Yang Y, Kang L, Yan S, Cho K, et al. (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.
47. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, et al. (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete human mitochondrial genomes. Science 308: 1034-1036.
48. Chandrasekar A, Kumar S, Sreenath J, Sarkar BN, Urade BP, et al. (2009) Updating phylogeny of mitochondrial DNA macrohaplogroup M in India: dispersal of modern human in South Asian corridor. PLoS One 4: e7447.
49. Grzybowski T, Malyarchuk BA, Derenko MV, Perkova MA, Bednarek J, et al. (2007) Complex interactions of the Eastern and Western Slavic populations with other European groups as revealed by mitochondrial DNA analysis. Forensic Sci Int Genet 1: 141-147.
50. Bilal E, Rabadan R, Alexe G, Fuku N, Ueno H, et al. (2008) Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan. PLoS ONE 3 (6): e2421.
51. 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.
52. Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, et al. (2009) Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 9: 154.
53. Peng MS, Palanichamy MG, Yao YG, Mitra B, Cheng YT, et al. (2011) Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b. BMC Biol 9: 2.
54. Okladnikov AP, (1981) The Paleolithic of Central Asia Novosibirsk Nauka.
55. Laukhin SA, (1993) A conception of step-by-step peopling of northern Asia by Paleolithic humans. Dokl Akad Nauk 332: 352-356.
56. Vasiliev SA, (1993) The Upper Paleolithic of northern Asia. Curr Anthropol 34: 82-92.
57. Goebel T, (1999) Pleistocene human colonization of Siberia and peopling of the Americas: an ecological approach. Evol Anthropol 8: 208-227.
58. Ingman M, Gyllensten U, (2007) A recent genetic link between Sami and the Volga-Ural region of Russia. Eur J Hum Genet 15: 115-120.
59. Palanichamy MG, Zhang CL, Mitra B, Malyarchuk B, Derenko M, et al. (2010) Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers. BMC Evol Biol 10: 304.
60. Dolukhanov P, Shukurov A, Gronenborn D, Sokoloff D, Tomofeev V, et al. (2005) The chronology of Neolithic dispersal in Central and Eastern Europe. J Archaeol Sci 32: 1441-1458.
61. Derenko MV, Shields GF, (1997) Diversity of mitochondrial DNA nucleotide sequences in three groups of aboriginal inhabitants of Northern Asia. Mol Biol (Moscow) 31: 784-789.
62. Derenko MV, Malyarchuk BA, Dambueva IK, Shaikhaev GO, Dorzhu CM, et al. (2000) Mitochondrial DNA variation in two South Siberian aboriginal populations: implications for the genetic history of North Asia. Hum Biol 72: 945-973.
63. Malyarchuk BA, Derenko MV, (2001) Mitochondrial DNA variability in Russians and Ukrainians: implication to the origin of the Eastern Slavs. Ann Hum Genet 65: 63-78.
64. Derenko MV, Grzybowski T, Malyarchuk BA, Dambueva IK, Denisova GA, et al. (2003) Diversity of mitochondrial DNA lineages in South Siberia. Ann Hum Genet 67: 391-411.
65. Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Woźniak M, et al. (2002) Mitochondrial DNA variability in Poles and Russians. Ann Hum Genet 66: 261-283.
66. Malyarchuk B, Derenko M, Grzybowski T, Lunkina A, Czarny J, et al. (2004) Differentiation of mitochondrial DNA and Y chromosomes in Russian populations. Hum Biol 76: 877-900.
67. Malyarchuk B, Grzybowski T, Derenko M, Perkova M, Vanecek T, et al. (2008) Mitochondrial DNA phylogeny in Eastern and Western Slavs. Mol Biol Evol 25: 1651-1658.
68. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, et al. (2001) Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 69: 1348-1356.
69. Andrews RM, Kubacka I, Chinnery PF, Lightowlers R, Turnbull D, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147.
70. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
71. Fu YX, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915925.
72. Schneider S, Roessli D, Excoffier L, (2000) Arlequin ver 2.0: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.
73. Comas D, Calafell F, Mateu E, Pérez-Lezaun A, Bosch E, 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.
74. Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, et al. (2004) Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet 12: 495-504.
75. Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, et al. (2004) Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. Am J Hum Genet 74: 827-845.
76. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, et al. (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19: 1737-1751.
77. 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.
78. Ingman M, Kaessmann H, Pääbo S, Gyllensten U, (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-713.
79. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, et al. (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA 100: 171-176.
80. Kazuno AA, Munakata K, Mori K, Tanaka M, Nanko S, et al. (2005) Mitochondrial DNA sequence analysis of patients with 'atypical psychosis'. Psychiatry Clin Neurosci 59: 497-503.
81. Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, et al. (2005) Reconstructing the origin of Andaman Islanders. Science 308: 996.
82. Razafindrazaka H, Ricaut FX, Cox M, Mormina M, Dugoujon JM, et al. (2010) Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar. Eur J Hum Genet 18: 575-581.
83. Just RS, Diegoli TM, Saunier JL, Irwin JA, Parsons TJ, (2008) Complete mitochondrial genome sequences for 265 African American and U.S. 'Hispanic' individuals. Forensic Sci Int Genet 2: 45-48.
84. Dancause KN, Chan CW, Arunotai NH, Lum JK, (2009) Origins of the Moken Sea Gypsies inferred from mitochondrial hypervariable region and whole genome sequences. J Hum Genet 54: 86-93.
85. Hartmann A, Thieme M, Nanduri LK, Stempfl T, Moehle C, et al. (2009) Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum Mutat 30: 115-122.
86. Ueno H, Nishigaki Y, Kong QP, Fuku N, Kojima S, et al. (2009) Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia. Mitochondrion 9: 385-393.
87. Zou Y, Jia X, Zhang AM, Wang WZ, Li S, et al. (2010) The MT-ND1 and MT-ND5 genes are mutational hotspots for Chinese families with clinical features of LHON but lacking the three primary mutations. Biochem Biophys Res Commun 399: 179-185.
88. Gunnarsdottir ED, Li M, Bauchet M, Finstermeier K, Stoneking M, (2011) High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res 21: 1-11.
89. Kong QP, Sun C, Wang HW, Zhao M, Wang WZ, et al. (2011) 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.
90. Wang CY, Li H, Hao XD, Liu J, Wang JX, et al. (2011) Uncovering the profile of somatic mtDNA mutations in Chinese colorectal cancer patients. PLoS One 6: e21613.
91. Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
92. 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.