Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences

  • C. Nohira
  • S. Maruyama
  • K. MinaguchiEmail author
Original Article


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.


Mitochondrial DNA polymorphism Control and coding region Haplogroup Complete sequence Japanese 



We thank Associate Professor Jeremy Williams, Laboratory of International Dental Information, Tokyo Dental College, for editing the manuscript. This research was partially supported by the Ministry of Education, Science, Sports and Culture, Grant-in-Aid for Scientific Research (B) (14370701) and Exploratory Research (16659171).

Supplementary material

414_2008_308_MOESM1_ESM.ppt (88 kb)
Fig. S1 Geographic 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 S1 PCR primers, annealing temperature, and conditions for sequencing and SSCP analysis. (XLS 49 kb)
414_2008_308_MOESM3_ESM.xls (218 kb)
Table S3 Variable nucleotide positions in 100 Japanese samples compared to reference sequences. (XLS 222 KB)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of Forensic OdontologyTokyo Dental CollegeChiba CityJapan

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