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June 16, 2021
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June 16, 2021

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

Dr. Fuzuki Mizuno
A group of researchers led by Dr. Fuzuki Mizuno, Department of Legal Medicine, Toho University Faculty of Medicine, have analyzed the mitochondrial DNA (mtDNA) of archeological remains excavated from the Paleolithic, Jomon, and Yayoi periods, as well as the mitochondrial DNA of more than 2,000 people from the Japanese archipelago. They found that the mitochondrial DNA (hereinafter referred to as mtDNA) of more than 2,000 people in the Japanese archipelago has been clearly analyzed. As a result, the genetic relationship of the Japanese archipelago population from the past to the present, which had never been clarified before, was revealed for the first time. In addition, they estimated the population of the Japanese archipelago since the first appearance of humans approximately 40,000 years ago, and published these results in a paper.

These achievements were published in the journal Scientific Reports (open access) on June 13, 2021 under the title “Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences”.
Dr. Fuzuki Mizuno
A group of researchers led by Dr. Fuzuki Mizuno, Department of Legal Medicine, Toho University Faculty of Medicine, have analyzed the mitochondrial DNA (mtDNA) of archeological remains excavated from the Paleolithic, Jomon, and Yayoi periods, as well as the mitochondrial DNA of more than 2,000 people from the Japanese archipelago. They found that the mitochondrial DNA (hereinafter referred to as mtDNA) of more than 2,000 people in the Japanese archipelago has been clearly analyzed. As a result, the genetic relationship of the Japanese archipelago population from the past to the present, which had never been clarified before, was revealed for the first time. In addition, they estimated the population of the Japanese archipelago since the first appearance of humans approximately 40,000 years ago, and published these results in a paper. These achievements were published in the journal Scientific Reports (open access) on June 13, 2021 under the title “Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences”.
Key Points
They clarified the mitochondrial phylogeny and genetic diversity of the Japanese archipelago population in the Paleolithic, Jomon, and Yayoi periods. Furthermore, simulations using the complete mtDNA sequence of a present-day Japanese population of more than 2,000 people revealed that large increases in the effective population size occurred multiple times in the past. In the Japanese archipelago, they determined the complete mtDNA sequence of Paleolithic human bones for the first time. This is the first time that the complete mtDNA sequence of Paleolithic human remains has been determined in the Japanese archipelago. The position of Paleolithic humans in the formation of the Japanese archipelago will be clarified by further nuclear DNA analysis of the Minatogawa I human remains.
Outline
In this study, they succeeded in determining the complete mtDNA sequence of the Minatogawa 1 human remains from the Minatogawa fissure site, one of the few Paleolithic sites in the Japanese archipelago. By combining the newly determined mtDNA of Jomon and Yayoi period human bones with the mtDNA of approximately 2,000 present-day Japanese archipelago population, it was determined that 1) the Minatogawa 1 human bone is not a direct ancestor of the Jomon, Yayoi, or present-day populations, but 2) the mtDNA of the Minatogawa 1 human bone is included in or very close to the ancestral group of the present-day Japanese archipelago population. As a result, the Japanese archipelago is now known to have a large number of ancestors, thereby suggesting is the genetic continuity in the human population in the Japanese archipelago from the Paleolithic to the present.

 

Bayesian phylogenetic tree of complete mitogenome sequences of 18 ancient and 171 present-day individuals in the Japanese Archipelago. Coloured arrows show the positions of ancient individuals; red, yellow, and purple for Palaeolithic, Jomon, and Yayoi, respectively. The tree was rooted with mitogenome haplogroup L0a (accession number: EF184601.1). The estimated haplogroups for newly determined ancient samples are Minato1:M, Iyai1:N9b, Iyai4:N9b3, Iyai8:N9b, Higa002:N9a2a, Higa006:M7a1a, Higa020:M80’D, Todo5:M7a1a, Kaso6:M7a, Uba2:N9b, MB-TB27:M7a1a, DH-S01:D4b2b1, DH-A:D4b2b1, HN-SJ001:B4b1a1a and HN-SJ002:D4b2a1, respectively

Content
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.

(スマホで崩れるようなら使用する。)

Dr. Taro Toho, Professor, Department of Environmental Science

Key Pointsテキスト

Figure 2: Multi Dimensional Scaling (MDS) plot of whole coding sequences of mitogenome of 1 Palaeolithic (red), 13 Jomon (yellow), 4 Yayoi (purple), and 2,062 present-day (grey) individuals in the Japanese Archipelago. For present-day Japanese, assigned haplogroups were shown.

Authors 

  • Fuzuki Mizuno (Assistant Professor, Department of Legal Medicine, Toho University Faculty of Medicine)
  • Jun Gojobori (Lecturer, Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies)
  • Masahiko Kumagai (Senior Researcher, Advanced Analysis Center, National Agriculture and Food Research Organization)
  • Yasuhiro Taniguchi (Professor, Department of Archaeology, Faculty of Letters, Kokugakuin University)
  • Osamu Kondo (Associate Professor, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)
  • Masami Matsushita (Manager, The Organization of Anthropological Research)
  • Takayuki Matsushita (Director, The Organization of Anthropological Research)
  • Fumihiko Matsuda (Professor, Graduate School of Medicine, Kyoto University)
  • Koichiro Higasa (Professor, Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University)
  • Michiko Hayashi (Department of Legal Medicine, Toho University Faculty of Medicine)
  • Li Wang (Professor, School of Medicine, Hangzhou Normal University, Hangzhou)
  • Kunihiko Kurosaki (Professor, Department of Legal Medicine, Toho University Faculty of Medicine)
  • Shintaroh Ueda (Professor Emeritus, The University of Tokyo; Visiting Professor, Toho University Faculty of Medicine)
DOI number: 10.1038/s41598-021-91357-2

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