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.

An unknown skeletonized body was identified by DNA analysis and dental information. The body had already been cremated when a candidate for the unknown body was proposed. Therefore, for DNA analysis we used teeth that had been kept for a long time after use for serological examination. We also used a chest X-ray photograph of the candidate and photographs of dentition, as well as dental X-ray photographs taken when the unknown body was found. Because DNA obtained from teeth was highly degraded, we amplified three PCR fragments to determine the 766 bp mitochondrial DNA (mtDNA) sequence including HV1 and HV2. Polymorphism of the ABO locus was also analyzed using small PCR fragments. Although the isolated DNA was contaminated, probably with DNA from a different individual, DNA polymorphisms of mtDNA and the ABO locus could be analyzed. We discuss the reliability of our conclusions from the point of view of the necessity of constructing an accurate mtDNA database. Although a dentist who had treated the teeth of the unknown body could not be found, a chest X-ray photograph for medical diagnosis was very useful in comparing dental characteristics, as it included an image of the frontal part of the lower jaw and upper teeth.