〇Naoki OSADA (Hokkaido University), Takao SATO (Keio University), Hitomi HONGO (The Graduate University for Advanced Studies), Yohey TERAI (The Graduate University for Advanced Studies)

１．Objectives and Directions of the Study

The title of Group C02's research project is "Study on the Anthropogenic Environmental Formation (Fauna) by Prehistoric Humans". Since the arrival of prehistoric humans to the Japanese archipelago, our ancestors have adapted to their environment by modifying the surrounding environment through collaboration between genome science and zooarchaeology. One of these environmental changes has been a shift in the relationship between humans and animals. Some important animals have become domesticated and have had a strong influence on the social structure. Animals that are hunted are also one of the important foundations of human livelihoods. There are many other animals that are parasitic on human life and expand their habitats. This year, we conducted genome analysis and ancient genome analysis on many of these animals. The following is a summary of the major results for each animal species.

1） House mouse（Mus musculus）

The original habitat of the house mouse is thought to have been around India, and it spread throughout the world as humans migrated and traded. three major subspecies are known, but the wild Japanese house mouse is known to be an interspecific hybrid of 90% musculus from the north and 10% castaneus from the south. Japanese wild house mice are known to be an interspecific hybrid of 90% musculus from the north and 10% castaneus from the south. We analyzed the whole genomes of 170 mice from all over the world to clarify the mixing patterns of subspecies genomes in the Japanese archipelago and southern China. In the Japanese archipelago, the subspecies castaneus has been thought to be distributed in the Hokkaido and Tohoku regions and the subspecies musculus in the southern regions, but our analysis showed that the genetic component of the subspecies castaneus is higher in individuals from the Sea of Japan. In addition, we found that the genome of subspecies castaneus is significantly more abundant in genes related to immunity and pheromone receptors in individuals from the Japanese archipelago. This is thought to be due to the spread of genomes of southern origin in the Japanese archipelago by selection for some reason. The results were published in the following paper.

  • K. Fujiwara, S. Kubo, T. Endo, T. Takada, T. Shiroishi, H. Suzuki, N. Osada (2024) Inference of selective force on house mouse genomes during secondary contact in East Asia. Genome Research, 34(3), pp. 366-375.
    https://doi.org/10.1101/gr.278828.123

2）Muskrat（Suncus murinus）

The muskrat is phylogenetically quite different from the house mouse, and is a member of the mole family. In the Japanese archipelago, it is widely distributed in the Okinawa Islands. We performed whole genome analysis of individuals from Okinawa and Southeast Asia, and showed that: 1) individuals in Okinawa were not naturally distributed but introduced from Southeast Asia; 2) the introduction occurred not once but repeatedly; and 3) the species was not introduced from Southeast Asia but was introduced from the islands of Okinawa. The results of this study showed that The analysis of the mitochondrial genome showed that the first arrival was estimated to have occurred about 3,000 years ago. The results were published in the following paper.

  • S.D. Ohdachi, K. Fujiwara, C. Shekhar, T.N. Son, H. Suzuki, N. Osada (2024) Phylogenetics and Population Genetics of the Asian House Shrew, Suncus murinus-S. montanus Species Complex, Inferred From Whole-Genome and Mitochondrial DNA Sequences, with Special Reference to the Ryukyu Archipelago, Japan. Zoological Science, 41, pp. 216-229.
    https://doi.org/10.2108/zs230030

3）Japanese wolf and dog（Canis lupus）

The Japanese wolf is an extinct species in the Japanese archipelago. The research group C02 has been analyzing ancient genomes of Japanese wolves and dogs from various angles, and a major milestone has been reached with the publication of a new paper. Through the high-depth genome analysis of nine Japanese wolves and eleven Japanese dogs, the group found that: 1) the Japanese wolf is a monophyletic and genetically distinct group from other wolves; 2) the Japanese wolf is the most genetically related wolf to dogs; 3) Canines on the east side of the Eurasian continent contain the genome of the ancestor of the Japanese wolf. These results support the East Asian origin of the Canis lupus, and provide a breakthrough in the study of the origin of domestication of the canine, for which no direct ancestor has been found so far. We also conducted mitochondrial analysis of Jomon-era canines. The research results were published in the following paper.

  • J. Gojobori, N. Arakawa, X. Xiaokaiti, Y. Matsumoto, S. Matsumura, H. Hongo, N. Ishiguro, Y.  Terai (2024) Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs. Nature Communications, 15 (1680).
    https://doi.org/10.1038/s41467-024-46124-y
  • X. Xiaokaiti, T. Sato, K. Kasai, K. Machida, K. Yamazaki, N. Yamaji, H. Kikuchi, J. Gojobori, H. Hongo, Y. Terai, T. Gakuhari. (2024) The history of ancient Japanese dogs revealed by mitogenomes. Anthropological Science, 132, pp. 1-11.
    https://doi.org/10.1537/ase.230617