1. Ishii Y.*, S. Kanamori, R. Deguchi, M. Kawata, S. Maruyama*, T. Yoshida, R. Kamikawa* (2025) Positive selection of a starch synthesis gene and phenotypic differentiation of starch accumulation in symbiotic and free-living coral symbiont dinoflagellate species. Genome Biology and Evolution. evaf133

2. Gyaltshen† Y, Y. Ishii†, S. Charvet, E. Goetz, S. Maruyama, E. Kim (2024) Molecular diversity of green-colored microbial mats from hot springs of northern Japan. Extremophiles. Jun 5:e0033423. †These authors contributed equally to the study.

3. Sakamoto F., S. Kanamori, L. M. Díaz, A. Cádiz, Y. Ishii, K. Yamaguchi, S. Shigenobu, T. Nakayama, T. Makino, M. Kawata (2024) Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards. Ecology and Evolution 14(3):e11117

4. Wakamiya T., T. Kamioka, Y. Ishii, J. Takahashi, T. Maeda, M. Kawata (2023) Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica. Ecology and Evolution 13(10):e10573

5. Ishii Y., H. Ishii, T. Kuroha, R. Yokoyama, R. Deguchi, K. Nishitani, J. Minagawa, M. Kawata, S. Takahashi, S. Maruyama (2023) Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga. eLife 12:e80628

6. Thoma, V, S. Sakai, K. Nagata, Y. Ishii, S. Maruyama, A. Abe, S. Kondo, M. Kawata, S. Hamada, R. Deguchi, H. Tanimoto (2023) On the origin of appetite: GLWamide in jellyfish represents an ancestral satiety neuropeptide. Proc. Natl. Acad. Sci. U.S.A. 120 (15) e2221493120

7. Mihirogi, Y., M. Kaneda, D. Yamagishi, Y. Ishii, S. Maruyama, S. Nakamura, N. Shimoyama, C. Oohori, M. Hatta (2023) Establishment of a new model sea anemone for comparative studies on cnidarian-algal symbiosis. Zoological Science 40(3):235-245

8. Yoshida, N., SI. Morinaga, T. Wakamiya, Y. Ishii, S. Kubota, K. Hikosaka (2022) Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient. Journal of Plant Research 136(2):183-199

9. Ishii, Y.*, M. Hatta, R, Deguchi, M, Kawata, S. Maruyama* (2022) Gene expression alterations from reversible to irreversible stages during coral metamorphosis. Zoological Letters 8, 4

10. Kawamoto, M., Y. Ishii, M. Kawata (2021) Genetic basis of orange spot formation in the guppy (Poecilia reticulata). BMC Ecology and Evolution 21: 211

11. Kanamori, S., A. Cadiz, L. Diaz, Y. Ishii, T. Nakayama and M. Kawata (2021) Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas, and currently thrive in urban areas. Ecology and Evolution 11:1719‒ 1728.

12. Faktorová, D., ... Y. Ishii, ... T. Mock, A. Z. Worden, J. Lukeš [113 authors] (2020) Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17:481‒494

13. Sato, D. X., Y. Ishii, T. Nagai, K. Ohashi, M. Kawata (2019) Human-specific mutations in VMAT1 confer functional changes and multi-directional evolution in the regulation of monoamine circuits. BMC Evolutionary Biology 19:220

14. Ishii Y., S. Maruyama, H. Takahashi, Y. Aihara, T. Yamaguchi, K. Yamaguchi, S. Shigenobu, M. Kawata, N. Ueno, J. Minagawa (2019) Global shifts in gene expression profiles accompanied with environmental changes in cnidarian-dinoflagellate endosymbiosis. G3: Genes, Genomes, Genetics 9: 2337-2347

15. Ishii Y., S. Maruyama, K. Fujimura-Kamada, N. Kutsuna, S. Takahashi, M. Kawata, J. Minagawa (2018) Isolation of uracil auxotroph mutants of coral symbiont alga for symbiosis studies. Scientific Reports Vol. 8: 3237

†: equally contributed

*: corresponding author

1. 石井悠. 褐虫藻は共生していることをどう感じているのか. BSJ-Review, (公社)日本植物学会, Vol. 13:3, 2022

2. 石井悠，丸山真一朗. サンゴ共生藻と環境との対話、宿主との対話. 光合成研究, 光合成学会, Vol. 30(1), pp35-45, 2020

3. 石井悠，丸山真一朗. サンゴ共生藻における形質転換技術開発の現状と展望. BSJ-Review, (公社)日本植物学会, Vol. 8, pp160-168, 2017