Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Summerer, Monika ^a   Horst, Jürgen ^b   Erhart, Gertraud ^a   Weißensteiner, Hansi ^a,c   Schönherr, Sebastian ^a,c   Pacher, Dominic ^a,c   Forer, Lukas ^a,c   Horst, David ^d   Manhart, Angelika ^a   Horst, Basil ^e   Sanguansermsri, Torpong ^f   Kloss Brandstätter, Anita ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF MÜNSTER   (Germany)

^c UNIVERSITY OF INNSBRUCK   (Austria)

^d UNIVERSITY OF MUNICH   (Germany)

^e Och Spine at New York Presbyterian Hospitals   (United States)

^f CHIANG MAI UNIVERSITY   (Thailand)

Author keywords

Bamar; Burma; Complete mtDNA genome; Control region; Demographic history; Gene flow; Haplogroup; Karen; Migration; Population genetics; Southeast Asia

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; ASIAN; CAUCASIAN; CLASSIFICATION; CULTURAL ANTHROPOLOGY; ETHNOLOGY; GENETICS; HAPLOTYPE; HUMAN; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MYANMAR; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; SOUTHEAST ASIA;

ASIA, SOUTHEASTERN; ASIAN CONTINENTAL ANCESTRY GROUP; BASE SEQUENCE; CULTURE; DNA, MITOCHONDRIAL; EUROPEAN CONTINENTAL ANCESTRY GROUP; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, MITOCHONDRIAL; HAPLOTYPES; HUMANS; MYANMAR; PHYLOGENY;

EID: 84892924365     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-14-17     Document Type: Article

References (70)

1. Rapid evolution of animal mitochondrial DNA. Brown WM, George M Jr, Wilson AC, Proc Natl Acad Sci U S A 1979 76 1967 1971 10.1073/pnas.76.4.1967 109836 (Pubitemid 9207037)
2. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, et al. Annu Rev Ecol Syst 1987 18 489 522
3. Mitochondrial genome variation and the origin of modern humans. Ingman M, Kaessmann H, Pääbo S, Gyllensten U, Nature 2000 408 708 713 10.1038/35047064 11130070 (Pubitemid 32015984)
4. Correcting for purifying selection: an improved human mitochondrial molecular clock. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, et al. Am J Hum Genet 2009 84 740 759 10.1016/j.ajhg.2009.05.001 19500773
5. Evaluating the mitochondrial timescale of human evolution. Endicott P, Ho SY, Metspalu M, Stringer C, Trends Ecol Evol 2009 24 515 521 10.1016/j.tree.2009.04.006 19682765
6. The role of selection in the evolution of human mitochondrial genomes. Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, et al. Genetics 2006 172 373 387 16172508 (Pubitemid 43345499)
7. Natural selection shaped regional mtDNA variation in humans. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, et al. Proc Natl Acad Sci U S A 2003 100 171 176 10.1073/pnas.0136972100 12509511 (Pubitemid 36078047)
8. Large-scale mtDNA screening reveals a surprising matrilineal complexity in east asia and its implications to the peopling of the region. Kong QP, Sun C, Wang HW, Zhao MA, Wang WZ, Zhong L, et al. Mol Biol Evol 2011 28 513 522 10.1093/molbev/msq219 20713468
9. Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. Wang HW, Mitra B, Chaudhuri TK, Palanichamy MG, Kong QP, Zhang YP, J Genet Genomics 2011 38 117 122 10.1016/j.jgg.2011.02.005 21477783
10. Y-chromosome evidence for a northward migration of modern humans into eastern Asia during the last Ice Age. Su B, Xiao JH, Underhill P, Deka R, Zhang WL, Akey J, et al. Am J Hum Genet 1999 65 1718 1724 10.1086/302680 10577926 (Pubitemid 30468685)
11. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Su B, Xiao CJ, Deka R, Seielstad MT, Kangwanpong D, Xiao JH, et al. Hum Genet 2000 107 582 590 10.1007/s004390000406 11153912 (Pubitemid 32010960)
12. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Yao Y-G, Kong Q-P, Bandelt H-J, Kivisild T, Zhang Y-P, Am J Hum Genet 2002 70 635 651 10.1086/338999 11836649 (Pubitemid 34177919)
13. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, et al. Plos One 2011 6 24282 10.1371/journal.pone.0024282 21904623
14. Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans. Wen B, Xie X, Gao S, Li H, Shi H, Song X, et al. Am J Hum Genet 2004 74 856 865 10.1086/386292 15042512 (Pubitemid 38568960)
15. Farmers and their languages: the first expansions. Diamond J, Bellwood P, Science 2003 300 597 603 10.1126/science.1078208 12714734 (Pubitemid 36520577)
16. Lieberman V, Strange Parallels: Southeast Asia in Global Context, c. 800-1830. Vol. 1: Integration on the Mainland Cambridge, UK: Cambridge University Press 2003
17. Trans-Burma trade routes to China. Christian JL, Pac Aff 1940 13 173 191 10.2307/2751052
18. A mitochondrial stratigraphy for island southeast Asia. Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, et al. Am J Hum Genet 2007 80 29 43 10.1086/510412 17160892 (Pubitemid 46047648)
19. A Bayesian evaluation of human mitochondrial substitution rates. Endicott P, Ho SY, Am J Hum Genet 2008 82 895 902 10.1016/j.ajhg.2008.01.019 18371929
20. Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Peng M-S, Quang HH, Dang K-P, Trieu AV, Wang H-W, Yao Y-G, et al. Mol Biol Evol 2010 27 2417 2430 10.1093/molbev/msq131 20513740
21. Ancient voyaging and polynesian origins. Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, et al. Am J Hum Genet 2011 88 239 247 10.1016/j.ajhg.2011.01.009 21295281
22. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Gunnarsdóttir ED, Li MK, Bauchet M, Finstermeier K, Stoneking M, Genome Res 2011 21 1 11 10.1101/gr.107615.110 21147912
23. Southeast Asian diversity: first insights into the complex mtDNA structure of Laos. Bodner M, Zimmermann B, Röck A, Kloss-Brandstätter A, Horst D, Horst B, et al. BMC Evol Biol 2011 11 49 10.1186/1471-2148-11-49 21333001
24. mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. Atkinson QD, Gray RD, Drummond AJ, Mol Biol Evol 2008 25 468 474 10.1093/molbev/msm277 18093996 (Pubitemid 351231619)
25. Smith M, Ethnic groups in Burma: Development, Democracy and Human Rights Anti-Slavery International: London, UK 8 1994
26. Where there is no movement: Local resistance and the potential for solidarity. Malseed K, J Agrar Change 2008 8 489 514 10.1111/j.1471-0366.2008. 00178.x (Pubitemid 351597616)
27. Revision of the mtDNA tree and corresponding haplogroup nomenclature. van Oven M, Proc Natl Acad Sci U S A 2010 107 38 E39 10.1073/pnas.0915120107 20304802
28. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. van Oven M, Kayser M, Hum Mutat 2009 30 386 E394 10.1002/humu.20921 18853457
29. Forensic and phylogeographic characterization of mtDNA lineages from northern Thailand (Chiang Mai). Zimmermann B, Bodner M, Amory S, Fendt L, Röck AW, Horst D, et al. Int J Legal Med 2009 123 495 501 10.1007/s00414-009-0373-4 19727793
30. Mitochondrial control region sequences from a Vietnamese population sample. Irwin JA, Saunier JL, Strouss KM, Diegoli TM, Sturk KA, O'Callaghan JE, et al. Int J Legal Med 2008 122 257 259 10.1007/s00414-007-0205-3 17960413 (Pubitemid 351534092)
31. Mitochondrial DNA control region variation in a population sample from Hong Kong, China. Irwin JA, Saunier JL, Beh P, Strouss KM, Paintner CD, Parsons TJ, Forensic Sci Int Genet 2009 3 119 e125 10.1016/j.fsigen.2008.10.008 19647696
32. Evolutionary history of continental southeast asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Jinam TA, Hong LC, Phipps ME, Stoneking M, Ameen M, Edo J, et al. Mol Biol Evol 2012 29 3513 3527 10.1093/molbev/mss169 22729749
33. Updating phylogeny of mitochondrial DNA macrohaplogroup M in India: dispersal of modern human in South Asian corridor. Chandrasekar A, Kumar S, Sreenath J, Sarkar BN, Urade BP, Mallick S, et al. PLoS ONE 2009 4 7447 10.1371/journal.pone.0007447 19823670
34. Phylogeography and ethnogenesis of aboriginal Southeast Asians. Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, et al. Mol Biol Evol 2006 23 2480 2491 10.1093/molbev/msl124 16982817 (Pubitemid 44737142)
35. Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, Perkova M, et al. PLoS ONE 2010 5 15214 10.1371/journal.pone.0015214 21203537
36. Complete mitochondrial DNA analysis of eastern eurasian haplogroups rarely found in populations of northern asia and eastern europe. Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, et al. Plos One 2012 7 2 32179 10.1371/journal.pone.0032179 22363811
37. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, Fuku N, et al. Genome Res 2004 14 1832 1850 10.1101/gr.2286304 15466285 (Pubitemid 39386497)
38. Updating the east asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Kong Q-P, Bandelt H-J, Sun C, Yao Y-G, Salas A, Achilli A, et al. Hum Mol Genet 2006 15 2076 2086 10.1093/hmg/ddl130 16714301 (Pubitemid 43923397)
39. CYP2C19 genetic polymorphism in Thai, Burmese and Karen populations. Tassaneeyakul W, Mahatthanatrakul W, Niwatananun K, Na-Bangchang K, Tawalee A, Krikreangsak N, et al. Drug Metab Pharmacokinet 2006 21 286 290 10.2133/dmpk.21.286 16946555
40. Study on association between genetic polymorphisms of haem oxygenase-1, tumour necrosis factor, cadmium exposure and malaria pathogenicity and severity. Kuesap J, Hirayama K, Kikuchi M, Ruangweerayut R, Na-Bangchang K, Malaria J 2010 9 260 10.1186/1475-2875-9-260
41. Moore E, Bronze and Iron Age sites in Upper Myanmar: Chindwin, Samon and Pyu Spring: SOAS Bulletin of Burma Research, Vol.1 Nr.1 2003 ISSN 1479-8484
42. The karen people of burma: a study in anthropology and ethnology. Marshall HI, Ohio State University Bulletin 1922 26 1 329
43. Narratives and the constitution of a common identity: the karen in burma. Kuroiwa Y, Verkuyten M, Identities-Glob Stud 2008 15 391 412
44. Waiting for a righteous ruler: the karen royal imaginary in thailand and burma. Gravers M, JSoutheast Asian studies 2012 43 340 363 10.1017/ S0022463412000094
45. Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Oota H, Settheetham-Ishida W, Tiwawech D, Ishida T, Stoneking M, Nat Genet 2001 29 20 21 10.1038/ng711 11528385 (Pubitemid 32801801)
46. HLA-B*15 subtypes in Burmese population by sequence-based typing. Kongmaroeng C, Romphruk A, Ruangwerayut R, Paupairoj C, Leelayuwat C, Inoko H, et al. Tissue Antigens 2009 74 164 167 10.1111/j.1399-0039.2009.01281.x 19497038
47. Climate change and postglacial human dispersals in southeast Asia. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, et al. Mol Biol Evol 2008 25 1209 1218 10.1093/molbev/msn068 18359946
48. Major east-west division underlies Y chromosome stratification across Indonesia. Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, et al. Mol Biol Evol 2010 27 1833 1844 10.1093/molbev/msq063 20207712
49. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Kuhner MK, Bioinformatics 2006 22 768 770 10.1093/bioinformatics/ btk051 16410317
50. Generating population data for the EMPOP database-an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. Brandstätter A, Niederstätter H, Pavlic M, Grubwieser P, Parson W, Forensic Sci Int 2007 166 164 175 10.1016/j.forsciint.2006.05.006 16829006 (Pubitemid 46274122)
51. Somatic mutations throughout the entire mitochondrial genome Are associated with elevated PSA levels in prostate cancer patients. Kloss-Brandstätter A, Schäfer G, Erhart G, Hüttenhofer A, Coassin S, Seifarth C, et al. Am J Hum Genet 2010 87 802 812 10.1016/j.ajhg.2010.11.001 21129724
52. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N, Nat Genet 1999 23 147 10.1038/13779 10508508 (Pubitemid 29455385)
53. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Behar DM, Van OM, Rosset S, Metspalu M, Loogvali EL, Silva NM, et al. Am J Hum Genet 2012 90 675 684 10.1016/j.ajhg.2012.03.002 22482806
54. A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics. Salas A, Coble M, Desmyter S, Grzybowski T, Gusmao L, Hohoff C, et al. Forensic Sci Int Genet 2012 6 182 e184 10.1016/j.fsigen.2012.06.015 22840856
55. The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. Bandelt H-J, Kloss-Brandstätter A, Richards MB, Yao YG, Logan I, J Hum Genet 2013 doi:10.1038/jhg.2013.120
56. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. Weissensteiner H, Schönherr S, Specht G, Kronenberg F, Brandstätter A, BMC Bioinforma 2010 11 122 10.1186/1471-2105-11-122
57. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Kloss-Brandstätter A, Pacher D, Schönherr S, Weißensteiner H, Binna R, Specht G, et al. Hum Mutat 2011 32 25 32 10.1002/humu.21382 20960467
58. The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns. Irwin JA, Ikramov A, Saunier J, Bodner M, Amory S, Röck AW, et al. Int J Legal Med 2010 124 195 204 10.1007/s00414-009-0406-z 20140442
59. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Lee HY, Yoo J-E, Park MJ, Chung U, Shin K-J, Int J Legal Med 2006 120 5 14 10.1007/s00414-005-0005-6 16177905 (Pubitemid 41830898)
60. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Excoffier L, Lischer HE, Mol Ecol Resour 2010 10 564 567 10.1111/j.1755-0998.2010.02847.x 21565059
61. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
62. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Tamura K, Nei M, Mol Biol Evol 1993 10 512 526 8336541 (Pubitemid 23157236)
63. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
64. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Drummond AJ, Suchard MA, Xie D, Rambaut A, Mol Biol Evol 2012 29 1969 1973 10.1093/molbev/mss075 22367748
65. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Hasegawa M, Kishino H, Yano T, J Mol Evol 1985 22 160 174 10.1007/BF02101694 3934395 (Pubitemid 16227864)
66. Tracer v1.4. Rambaut A, Drummond AJ, http://beast.bio.ed.ac.uk/Tracer. 2007. Ref Type: Online Source
67. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
68. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Beerli P, Felsenstein J, Genetics 1999 152 763 773 10353916 (Pubitemid 29272726)
69. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Beerli P, Felsenstein J, Proc Natl Acad Sci U S A 2001 98 4563 4568 10.1073/pnas.081068098 11287657 (Pubitemid 32295016)
70. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Beerli P, Bioinformatics 2006 22 341 345 10.1093/bioinformatics/bti803 16317072 (Pubitemid 43205381)