Analysis of Mitochondrial DNA from Minatogawa 1 Human Remains Reveals Genetic Relationships among People of the Japanese Archipelago from the Past to the Present

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Ancient DNA research, in which DNA is extracted from ancient human bones and teeth excavated from archeological sites and their sequences are determined, is a very powerful tool for understanding the origin of past human populations and their connections with present-day human populations. The Japanese archipelago has a lot of acidic soil made of volcanic ash, which makes it difficult for the DNA remaining in ancient human bones to be preserved. Therefore, it has been generally considered difficult to conduct ancient DNA research using ancient human bones and teeth excavated from the Japanese archipelago. In addition, although archeological evidence has shown that humans were present in the Japanese archipelago during the Paleolithic period, only a limited number of human remains from the Paleolithic have been excavated. Various studies have suggested that the present-day Japanese archipelago population is a mixture of the Jomon period population and the immigrant population that brought rice culture from the continent at the beginning of the Yayoi period (Kazuro Hanihara’s “Dual Structure Hypothesis of the Japanese”). However, due to the lack of paleolithic DNA research, it has been difficult to distinguish among the Paleolithic, Jomon, and subsequent groups. However, because of the lack of paleolithic DNA research, it is unclear whether there is a genetic link between the populations that existed in the Japanese archipelago during the Paleolithic, the Jomon, and subsequent populations.

In this study, they extracted DNA from the Paleolithic human remains of Minatogawa 1 excavated from the Minatogawa fissure site, followed by next-generation sequencing. In addition, they determined the complete mtDNA sequence from the human remains of the Jomon period sites of Iyai rock-shelter, Higashimyou, Todoroki Shell midden, Kasori Shell midden, Ubayama Shell midden, and Mabunin hantabaru, and from the Yayoi period sites of Doigahama and Hanaura . In addition, they analyzed the mtDNA of about 2,000 people from the present-day Japanese archipelago, together with ancient DNA from the Funadomari and Ikawazu shell midden sites of the Jomon period, which had already been published in a paper.

The phylogenetic relationship of the mtDNAs showed a close relation between mtDNAs of the Jomon and Yayoi period human bones and the mtDNAs of the present-day Japanese archipelago population, supporting Hanihara’s dual structure hypothesis(figure 1 and figure2). This suggests that the mtDNA of the Minatogawa 1 human remains is not the direct ancestor of the Jomon, Yayoi, and present-day populations. In contrast, the mtDNA of Minatogawa 1 was found to be an ancestral form of haplogroup M. Haplogroup M is a haplogroup of mtDNA widely distributed in Asia and is also found in many populations in the present-day Japanese archipelago, indicating that the mtDNA of the Minatogawa 1 human remains is not the direct ancestor of the present-day Japanese archipelago population, but is included in or very close to the ancestral group of the present-day Japanese archipelago population. These results suggest that there is genetic continuity in the mtDNA of human populations in the Japanese archipelago from the Paleolithic to the present. They also estimated the change in effective population size in the past based on the mtDNA information of approximately 2,000 people in the present-day Japanese archipelago population. As a result, an increase in effective population size was observed 45,000-35,000 years ago, 15,000-12,000 years ago, and 3,000 years ago. In particular, the increase in effective population size 3,000 years ago was remarkable, suggesting the influence of rice paddy farming introduced from the continent and the continental influx that continued after the Yayoi period.