Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences

International Journal of Legal Medicine

Volumn 124, Issue 1, 2010, Pages 7-12

  Nohira, C ^a   Maruyama, S ^a   Minaguchi, K ^a  

^a TOKYO DENTAL COLLEGE   (Japan)

Author keywords

Complete sequence; Control and coding region; Haplogroup; Japanese; Mitochondrial DNA polymorphism

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; ASIAN; DNA SEQUENCE; GENETICS; HAPLOTYPE; HUMAN; JAPAN; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SINGLE STRAND CONFORMATION POLYMORPHISM;

ASIAN CONTINENTAL ANCESTRY GROUP; DNA, MITOCHONDRIAL; HAPLOTYPES; HUMANS; JAPAN; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; SEQUENCE ANALYSIS, DNA;

EID: 76849094116     PISSN: 09379827     EISSN: 14371596     Source Type: Journal    
DOI: 10.1007/s00414-008-0308-5     Document Type: Article

References (32)

1. M Ingman H Kaessmann S Paabo U Gyllensten 2000 Mitochondrial genome variation and the origin of modern humans Nature 408 708 713 10.1038/35047064 1:CAS:528:DC%2BD3cXptVCrsr4%3D 11130070 (Pubitemid 32015984)
2. N Maca-Meyer AM Gonzalez JM Larruga C Flores VM Cabrera 2001 Major genomic mitochondrial lineages delineate early human expansions BMC Genet 2 13 20 10.1186/1471-2156-2-13 1:STN:280:DC%2BD38nnslGitw%3D%3D 11553319 (Pubitemid 38751013)
3. YG Yao QP Kong HJ Bandelt T Kivisild YP Zhang 2002 Phylogeographic differentiation of mitochondrial DNA in Han Chinese Am J Hum Genet 70 635 651 10.1086/338999 1:CAS:528:DC%2BD38XislChsbg%3D 11836649 (Pubitemid 34177919)
4. T Kivisild HV Tolk J Parik, et al. 2002 The emerging limbs and twigs of the East Asian mtDNA tree Mol Biol Evol 19 1737 1751 1:CAS:528: DC%2BD38XnvFSlu78%3D 12270900
5. S Maruyama K Minaguchi N Saitou 2003 Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population Int J Legal Med 117 218 225 10.1007/s00414-003-0379-2 12845447 (Pubitemid 37039761)
6. D Mishmar E Ruiz-Pesini P Golik, et al. 2003 Natural selection shaped regional mtDNA variation in humans Proc Natl Acad Sci U S A 100 171 176 10.1073/pnas.0136972100 1:CAS:528:DC%2BD3sXktlOgsQ%3D%3D 12509511 (Pubitemid 36078047)
7. M Ingman U Gyllensten 2003 Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines Genome Res 13 1600 1606 10.1101/gr.686603 1:CAS:528:DC%2BD3sXls1Krurg%3D 12840039 (Pubitemid 36874477)
8. QP Kong YG Yao C Sun HJ Bandelt CL Zhu YP Zhang 2003 Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences Am J Hum Genet 73 671 676 10.1086/377718 1:CAS:528:DC%2BD3sXnt1WqsL4%3D 12870132 (Pubitemid 37076281)
9. QP Kong YG Yao M Liu, et al. 2005 Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China Hum Genet 113 391 405 10.1007/s00439-003-1004-7
10. M Tanaka VM Cabrera AM Gonzalez, et al. 2004 Mitochondrial genome variation in eastern Asia and the peopling of Japan Genome Res 14 1832 1850 10.1101/gr.2286304 1:CAS:528:DC%2BD2cXotl2hurg%3D 15466285
11. K Thangaraj G Chaubey T Kivisild AG Reddy VK Singh AA Rasalkar L Singh 2005 Reconstructing the origin of Andaman Islanders Science 308 5724 996 10.1126/science.1109987 1:CAS:528:DC%2BD2MXkt1eqtb8%3D 15890876 (Pubitemid 40664404)
12. M Derenko B Malyarchuk T Grzybowski, et al. 2007 Phylogeographic analysis of mitochondrial DNA in northern Asian populations Am J Hum Genet 81 1025 1041 10.1086/522933 1:CAS:528:DC%2BD2sXht1KmsLzJ 17924343 (Pubitemid 47580254)
13. QP Kong HJ Bandelt C Sun, et al. 2006 Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations Hum Mol Genet 15 2076 2786 10.1093/hmg/ddl130 1:CAS:528:DC%2BD28XmtFKgurk%3D 16714301 (Pubitemid 43923397)
14. SD Lee CH Shin KB Kim YS Lee JB Lee 1997 Sequence variation of mitochondrial DNA control region in Koreans Forensic Sci Int 87 99 116 10.1016/S0379-0738(97)02114-2 1:CAS:528:DyaK2sXlt1Wls7Y%3D 9237373 (Pubitemid 27277726)
15. H Pfeiffer R Steighner R Fisher H Mornstad CL Yoon MM Holland 1998 Mitochondrial DNA extraction and typing from isolated dentin-experimental evaluation in a Korean population Int J Legal Med 111 309 313 10.1007/s004140050177 1:STN:280:DyaK1M%2FktFClsQ%3D%3D 9826090 (Pubitemid 28477805)
16. LC Tsai CY Lin JCI Lee JG Chang A Linacre W Goodwin 2000 Sequence polymorphism of mitochondrial D-loop DNA in the Taiwanese Han population Forensic Sci Int 119 239 247 10.1016/S0379-0738(00)00439-4
17. YG Yao YP Zhang 2002 Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal J Hum Genet 47 311 318 10.1007/s100380200042 1:CAS:528:DC%2BD38XltVWisrY%3D 12111379 (Pubitemid 34717618)
18. K Imaizumi TJ Parsons M Yoshino MM Holland 2002 A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals Int J Legal Med 116 68 73 10.1007/s004140100211 1:STN:280: DC%2BD38zhtl2gsg%3D%3D 12056523 (Pubitemid 36056578)
19. H Koyama M Iwasa Y Maeno, et al. 2002 Mitochondrial sequence haplotype in the Japanese population Forensic Sci Int 125 93 96 10.1016/S0379-0738(01)00611- 9 1:CAS:528:DC%2BD38XhtlSkt7s%3D 11852209 (Pubitemid 34145281)
20. YG Yao QP Kong XY Man HJ Bandelt YP Zhang 2003 Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA Mol Biol Evol 20 214 219 10.1093/molbev/msg026 1:CAS:528:DC%2BD3sXhsVOitbc%3D 12598688 (Pubitemid 36237379)
21. YG Yao QP Kong CY Wang CL Zhu YP Zhang 2004 Different matrilineal contributions to genetic structure of ethnic groups in the Silk Road region in China Mol Biol Evol 21 2265 2280 10.1093/molbev/msh238 1:CAS:528: DC%2BD2cXhtVSisLbJ 15317881 (Pubitemid 39488897)
22. L Rao MY Wu WB Liang L Zhang 2003 Sequence polymorphisms of the mitochondrial DNA control region in 105 Chinese Han population J Forensic Sci 48 891 895 1:CAS:528:DC%2BD3sXmtVWrtrc%3D 12877316
23. HY Lee JE Yoo MJ Park U Chung KJ Shin 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 10.1007/s00414-005-0005-6 16177905 (Pubitemid 41830898)
24. HJ Jin KD Kwak SB Hong DJ Shin MS Han C Tyler-Smith W Kim 2006 Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database Forensic Sci Int 158 125 130 10.1016/j.forsciint.2005.03.026 1:CAS:528:DC%2BD28XisF2itbo%3D 15990264
25. M Asari K Umetsu N Adachi J Azumi K Shimizu H Shiono 2007 Utility of haplogroup determination for forensic mtDNA analysis in the Japanese population Leg Med 9 237 240 10.1016/j.legalmed.2007.01.007 1:CAS:528:DC%2BD2sXotlSgsLo%3D (Pubitemid 47089051)
26. T Mabuchi R Susukida A Kido M Oya 2007 Typing the 1.1 kb control region of human mitochondrial DNA in Japanese individuals J Forensic Sci 52 355 363 10.1111/j.1556-4029.2006.00366.x 1:CAS:528:DC%2BD2sXkvFSgtrg%3D 17316232 (Pubitemid 46280530)
27. JA Irwin JL Saunier KM Strouss, et al. 2008 Mitochondrial control region sequences from a Vietnamese population sample Int J Legal Med 122 257 259 10.1007/s00414-007-0205-3 17960413
28. C Turchi L Buscemi C Previderè, et al. 2008 Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing Int J Legal Med 122 199 204 10.1007/s00414-007-0207-1 17952451
29. S Horai K Murayama K Hayasaka, et al. 1996 mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan Am J Hum Genet 59 579 590 1:CAS:528:DyaK28Xls1arsbo%3D 8751859
30. K Umetsu M Tanaka I Yuasa, et al. 2001 Multiplex amplified product-length polymorphism analysis for rapid detection of human mitochondrial DNA variations Electrophoresis 22 3533 3538 10.1002/1522-2683(200109)22:16<3533::AID- ELPS3533>3.0.CO;2-S 1:CAS:528:DC%2BD3MXnsFOmsb0%3D 11669538 (Pubitemid 32970667)
31. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585 595 1:CAS:528: DyaK3cXhslentA%3D%3D 2513255
32. RM Andrews I Kubacka PF Chinnery RN Lightowlers DM Turnbull N Howell 1999 Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat Genet 23 147 10.1038/13779 1:CAS:528:DyaK1MXmtlOhtLY%3D 10508508 (Pubitemid 29455385)