The detailed examination of the human ancient mitochondrial DNA using the Ion PGM™ System

Abstract

An archaeological site that has three cemeteries was found in northeastern part of Japan. A total of 45 human skeletons were excavated from the site and dated to about early 18th to mid-19th centuries based on the archaeological evidences. In the previous study, three skeletons were excluded from the results because the partial mtDNA sequences of these samples were identical to those of the two researchers who were in charge of skeletal reconstruction. In this study, the whole mtDNA sequences of these three skeletons and the two researchers were amplified by the Precision ID mtDNA Whole Genome Panel kit, followed by the massively parallel sequencing using the Ion PGM™ System (Thermo Fisher Scientific). The three skeleton samples had the same whole mtDNA sequences with 38 mutations as compared to the rCRS, being assigned to haplogroup D4a1c. These results suggested that the three skeletons might belong to the same maternal line. Meanwhile, the two researchers were typed as “D4a1*” and “D4a1b”. Although analyses of the hyper variable regions I–III and the conventional partial sequencing of mtDNA could not discriminate skeletons from the researchers, the mtDNA whole genome sequencing made it possible. Thus the whole mtDNA sequencing using the Ion PGM system is highly effective to shed light on the matrilineal relationship of the ancient human skeletons.