Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences

Original Article

Abstract

We investigated control and coding region polymorphisms in mitochondrial DNA (mtDNA) in 100 unrelated individuals from a Japanese population and determined the basal phylogenetic haplogroup lineages in all samples under updated information. Many of the basal phylogenetic haplogroup lineages assigned on East Asian mtDNA haplogroups corresponded to those previously established. However, new haplogroup lineages such as M7a2a, M7a2b, M7a2*, M7c1b, M11b2*, G2b*, D4c1b1a, D4g2b, A4*, A9, N9b*, B4d1, B4d2, and F1e were identified and established by complete sequencing. Although sequence comparison of the 1.15-kb control region identified 84 mitochondrial haplotypes, examination of coding region polymorphisms increased the total number of haplotypes to 91. Determination of the basal haplogroup lineages increased the discrimination power of mtDNA polymorphisms for personal identification and their usefulness in determining geographic origin in forensic casework in Japanese and other East Asian populations.

Keywords

Mitochondrial DNA polymorphism Control and coding region Haplogroup Complete sequence Japanese 

Supplementary material

414_2008_308_MOESM1_ESM.ppt (88 kb)
Fig. S1Geographic location and the number (in parenthesis) of the present Japanese samples. Abbreviations for prefectures are HO; Hokkaido, AM; Aomori, AT; Akita, YGA; Yamagata, MG; Miyagi, FS; Fukushima, TG; Tochigi, IR; Ibaragi, NG; Niigata, GM; Gunma, ST; Saitama, TK; Tokyo, CB; Chiba, KN; Kanagawa, NN; Nagano, YN; Yamanashi, SO; Shizuoka, AC; Aichi, TY; Toyama, IK; Ishikawa, WK; Wakayama, HG; Hyougo, OY; Okayama, HS; Hiroshima, SN; Shimane, EH; Ehime, FO; Fukuoka, OI; Ohita, NS; Nagasaki, and KGO; Kagoshima. (PPT 89 kb)
414_2008_308_MOESM2_ESM.xls (48 kb)
Table S1PCR primers, annealing temperature, and conditions for sequencing and SSCP analysis. (XLS 49 kb)
414_2008_308_MOESM3_ESM.xls (218 kb)
Table S3Variable nucleotide positions in 100 Japanese samples compared to reference sequences. (XLS 222 KB)

References

  1. 1.
    Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713CrossRefPubMedGoogle Scholar
  2. 2.
    Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM (2001) Major genomic mitochondrial lineages delineate early human expansions. BMC Genet 2:13–20CrossRefPubMedGoogle Scholar
  3. 3.
    Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635–651CrossRefPubMedGoogle Scholar
  4. 4.
    Kivisild T, Tolk HV, Parik J et al (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19:1737–1751PubMedGoogle Scholar
  5. 5.
    Maruyama S, Minaguchi K, Saitou N (2003) Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population. Int J Legal Med 117:218–225CrossRefPubMedGoogle Scholar
  6. 6.
    Mishmar D, Ruiz-Pesini E, Golik P et al (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A 100:171–176CrossRefPubMedGoogle Scholar
  7. 7.
    Ingman M, Gyllensten U (2003) Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res 13:1600–1606CrossRefPubMedGoogle Scholar
  8. 8.
    Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP (2003) Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. Am J Hum Genet 73:671–676CrossRefPubMedGoogle Scholar
  9. 9.
    Kong QP, Yao YG, Liu M et al (2005) Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China. Hum Genet 113:391–405CrossRefGoogle Scholar
  10. 10.
    Tanaka M, Cabrera VM, Gonzalez AM et al (2004) Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 14:1832–1850CrossRefPubMedGoogle Scholar
  11. 11.
    Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L (2005) Reconstructing the origin of Andaman Islanders. Science 308(5724):996CrossRefPubMedGoogle Scholar
  12. 12.
    Derenko M, Malyarchuk B, Grzybowski T et al (2007) Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 81:1025–1041CrossRefPubMedGoogle Scholar
  13. 13.
    Kong QP, Bandelt HJ, Sun C et al (2006) Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15:2076–2786CrossRefPubMedGoogle Scholar
  14. 14.
    Lee SD, Shin CH, Kim KB, Lee YS, Lee JB (1997) Sequence variation of mitochondrial DNA control region in Koreans. Forensic Sci Int 87:99–116CrossRefPubMedGoogle Scholar
  15. 15.
    Pfeiffer H, Steighner R, Fisher R, Mornstad H, Yoon CL, Holland MM (1998) Mitochondrial DNA extraction and typing from isolated dentin-experimental evaluation in a Korean population. Int J Legal Med 111:309–313CrossRefPubMedGoogle Scholar
  16. 16.
    Tsai LC, Lin CY, Lee JCI, Chang JG, Linacre A, Goodwin W (2000) Sequence polymorphism of mitochondrial D-loop DNA in the Taiwanese Han population. Forensic Sci Int 119:239–247CrossRefGoogle Scholar
  17. 17.
    Yao YG, Zhang YP (2002) Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal. J Hum Genet 47:311–318CrossRefPubMedGoogle Scholar
  18. 18.
    Imaizumi K, Parsons TJ, Yoshino M, Holland MM (2002) A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals. Int J Legal Med 116:68–73CrossRefPubMedGoogle Scholar
  19. 19.
    Koyama H, Iwasa M, Maeno Y et al (2002) Mitochondrial sequence haplotype in the Japanese population. Forensic Sci Int 125:93–96CrossRefPubMedGoogle Scholar
  20. 20.
    Yao YG, Kong QP, Man XY, Bandelt HJ, Zhang YP (2003) Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA. Mol Biol Evol 20:214–219CrossRefPubMedGoogle Scholar
  21. 21.
    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 21:2265–2280CrossRefPubMedGoogle Scholar
  22. 22.
    Rao L, Wu MY, Liang WB, Zhang L (2003) Sequence polymorphisms of the mitochondrial DNA control region in 105 Chinese Han population. J Forensic Sci 48:891–895PubMedGoogle Scholar
  23. 23.
    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 120:5–14CrossRefPubMedGoogle Scholar
  24. 24.
    Jin HJ, Kwak KD, Hong SB, Shin DJ, Han MS, Tyler-Smith C, Kim W (2006) Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database. Forensic Sci Int 158:125–130CrossRefPubMedGoogle Scholar
  25. 25.
    Asari M, Umetsu K, Adachi N, Azumi J, Shimizu K, Shiono H (2007) Utility of haplogroup determination for forensic mtDNA analysis in the Japanese population. Leg Med 9:237–240CrossRefGoogle Scholar
  26. 26.
    Mabuchi T, Susukida R, Kido A, Oya M (2007) Typing the 1.1 kb control region of human mitochondrial DNA in Japanese individuals. J Forensic Sci 52:355–363CrossRefPubMedGoogle Scholar
  27. 27.
    Irwin JA, Saunier JL, Strouss KM et al (2008) Mitochondrial control region sequences from a Vietnamese population sample. Int J Legal Med 122:257–259CrossRefPubMedGoogle Scholar
  28. 28.
    Turchi C, Buscemi L, Previderè C et al (2008) Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing. Int J Legal Med 122:199–204CrossRefPubMedGoogle Scholar
  29. 29.
    Horai S, Murayama K, Hayasaka K et al (1996) mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan. Am J Hum Genet 59:579–590PubMedGoogle Scholar
  30. 30.
    Umetsu K, Tanaka M, Yuasa I et al (2001) Multiplex amplified product-length polymorphism analysis for rapid detection of human mitochondrial DNA variations. Electrophoresis 22:3533–3538CrossRefPubMedGoogle Scholar
  31. 31.
    Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  32. 32.
    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 23:147CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of Forensic OdontologyTokyo Dental CollegeChiba CityJapan

Personalised recommendations