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森の木

Original Articles in peer-reviewed journals

* is the corresponding author(s)

  1. *Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja, C. M., Marzal, J. C. S., Cooney, C. R., Feulner, P. G. D., Domingos, F. M. C. B., North, H. L., Yamaguchi, R., Butlin, R. K., Wolf, J. B. W., Coughlan, J., Heidbreder, P., Hernández-Gutiérrez, R., Barnard-Kubow, K. B., Peede, D., Rancilhac, L., Salvador, R. B., Thompson, K. A., Stacy, E. A., Moyle, L. C., Garlovsky, M. D., Maulana, A., Kantelinen, A., Cacho, N. I., Schneemann, H., Domínguez, M., Dopman, E. B., Lohse, K., Rometsch, S. J., Comeault, A. A., Merrill, R. M., Scordato, E. S.C., Singhal, S., Pärssinen, V., Lackey, A. C. R., Kumar, S., Meier, J. I., Barton, N., Fraïsse, C., Ravinet, M., Kulmuni, J. 2024. Toward the integration of speciation research. Evolutionary Journal of the Linnean Society 3: kzae001
     

  2. Sunagawa, J., Park, H., Kim, K. S., Komorizono, R., Choi, S., Ramirez Torres, L., Woo, J., Jeong, Y. D., Hart, W.S., Thompson, R.N., Aihara, K., *Iwami, S., and *Yamaguchi, R. 2023. Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution. Nature Communications 14: 7395.
    Top 25 Nature Communications COVID-19 Articles of 2023
     

  3. *Kumakura, D., Yamaguchi, R., Hara, A., and Nakaoka, S. 2023. Disentangling the growth curve of microbial culture. Journal of Theoretical Biology 111597.
     

  4. Sunagawa, J., Komorizono, R., Park, H., Hart, W.S., Thompson, R.N., Makino, A., Tomonaga, K., *Iwami, S., and *Yamaguchi, R. 2023. Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection. PLOS Computational Biology 19: e1011173.
     

  5. *Kyogoku, D., and Yamaguchi, R. 2023. Males and females contribute differently to the evolution of habitat segregation driven by hybridization. Journal of Evolutionary Biology 2023;00:1–14.
     

  6. *Yamaguchi, R. Wiley B., and Otto, S.P. 2022. The phoenix hypothesis of speciation. Proc. Roy. Soc. B 289: 20221186
     

  7. *Yamaguchi, R. 2022. Intermediate dispersal hypothesis of species diversity: new insights. Ecological Research 37, 301-315. (Award paper: the seventh Suzuki Award at the 66th Annual Meeting of the Ecological Society of Japan)
     

  8. *Sunagawa, J., Yamaguchi, R., and Nakaoka, S. 2022. Evolving Neural Networks through Bio-inspired Parent Selection in Dynamic Environments. BioSystems 218, 104686.
     

  9. *Matsubayashi, K. W., and Yamaguchi, R. 2022. Adaptive and non‐adaptive causes of radiation: Is adaptation a harsh mistress of diversity? Population Ecology 64, 93–94.
     

  10. *MacPherson, A., Wang, S., Yamaguchi, R., Rieseberg, L.H., and Otto, S.P. 2022. Parental population range expansion before secondary contact promotes heterosis. The American Naturalist 200, E1-E15.
     

  11. *Yamaguchi, R. and Matsubayashi, K.W. 2022. Reply to Kagawa’s comment: Quantifying mixture modes of evolutionary radiations. Population Ecology 64, 127–129.
     

  12. *Matsubayashi, K.W. and Yamaguchi, R. 2022. The speciation view: Disentangling multiple causes of adaptive and nonadaptive radiation in terms of speciation. Population Ecology 64, 95–107.
    Top cited article 2022-2023
     

  13. *Yamaguchi, R., Iwasa, Y., and  Tachiki Y. 2021. Recurrent speciation rates on islands decline with species number. Proc. Roy. Soc. B  288: 20210255.
     

  14. *Yamaguchi, R. and Otto, S.P. 2020. Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change. Evolution 74: 1603-1619.
    Top cited article 2020-2021
     

  15. Lee, JH, Yamaguchi, R., Yokomizo, H., and * Nakamaru, M. 2020. Preservation of the value of rice paddy fields: Investigating how to prevent farmers from abandoning the fields by means of evolutionary game theory. Journal of Theoretical Biology 110247.
     

  16. *Nakahara, T., Horita, J., Booton, R.D., and  Yamaguchi, R. 2020. Extra molting, cannibalism and pupal diapause under unfavorable growth conditions in Atrophaneura alcinous (Lepidoptera: Papilionidae). Entomological Science 23: 57-65.
     

  17. *Yamaguchi, R., Yamanaka, T. and Liebhold, A.M. 2019. Consequences of hybridization during invasion on establishment success. Theoretical Ecology 1-9.
     

  18. *Booton, R., Yamaguchi, R., and Iwasa, Y. 2019. A population model for diapausing multivoltine insects under asymmetric cannibalism. Population Ecology 61: 35-44.
     

  19. *Yamaguchi, R., Suefuji, S., Odagiri K., Peggie D., and Yata O. 2018. A color pattern difference in the fifth instar larva of two subspecies of Faunis menado Hewitson (Lepidoptera, Nymphalidae). Lepidoptera Science 69: 67-73.
     

  20. *Booton, RD, Yamaguchi, R., Marshall, J.A.R., Childs, D.Z., and Iwasa, Y. 2018. Interactions between immunotoxicants and parasite stress: implications for host health. Journal of Theoretical Biology 445: 120-127.
     

  21. *Yamaguchi, R. and Iwasa, Y. 2017. A tipping point in parapatric speciation. Journal of Theoretical Biology 421: 81-92.
     

  22. *Yamaguchi, R. and Iwasa, Y. 2017. Parapatric speciation in three islands: dynamics of Geographic configuration of allele sharing. Royal Society Open Science 4: 160819.
     

  23. *Yamaguchi, R. , Suefuji, S., Odagiri K., and Yata O. 2016. The endemic Sulawesi amathusiine Faunis menado Hewitson (Lepidoptera, Nymphalidae) is divisible into two morphospecies. Lepidoptera Science 67: 12-21.
     

  24. *Yamaguchi, R. and Iwasa, Y. 2016. Smallness of the number of incompatibility loci can facilitate parapatric speciation. Journal of Theoretical Biology 405: 36-45.
     

  25. Yamaguchi, R. and *Iwasa, Y. 2015. Reproductive interference can promote recurrent parapatric speciation. Population Ecology 57: 343-346.
     

  26. *Yamaguchi, R. and Iwasa, Y. 2013. Reproductive character displacement by the evolution of female mate choice. Evolutionary Ecology Research 15: 25-41.
     

  27. *Yamaguchi, R. and Iwasa, Y. 2013. First passage time to allopatric speciation. Interface Focus 3: 20130026.

Review and commentary (in Japanese)

  1. *Ryo Yamaguchi. 2023.  Butterfly Species Diversity: Distribution of Endemic Species in Malay Archipelago. Insects and nature. 58: 31-34.
     

  2. *Ryo Yamaguchi. 2022.  Reproductive isolation and speciation in butterflies. Insects and nature. 57: 28-32.
     

  3. *Ryo Yamaguchi. 2021. The endemic butterfly fauna of Sulawesi. Insects and nature. 56: 13-17.
     

  4. *Ryo Yamaguchi, Kei Matsubayashi. 2019. Species boundary: approaching Speciation from Evolutionary Ecology and Molecular Genetics. Journal of the Ecological Society of Japan. 69: 145-149.
     

  5. *Ryo Yamaguchi. 2019. Speciation Dynamics and Mathematical Models: exploring factors promoting reproductive isolation. Journal of the Ecological Society of Japan. 69: 151-169.
     

  6. *Ryo Yamaguchi, Vane-Wright, RI 2017. Butterflies and diversification in the Sulawesi region: Complex subspecies composition of Faunis menado. Insects and nature. 52: 9-14.
     

  7. *Junnosuke Hotta, Toru Nakahara, Ryo Yamaguchi. 2016. Dormancy induction of Chinese windmill Byasa alcinous. Insects and nature. 51: 21-23.
     

  8. *Ryo Yamaguchi. 2015. Biogeography of Sulawesi amathusiine. Insects and nature. 50: 4-8.
     

  9. *Ryo Yamaguchi, Seiichi Suefuji, Kenichi Odagiri. 2013. Taxonomic review of Faunis menado. Insects and nature. 48: 28-31.
     

  10. *Ryo Yamaguchi. 2012. Butterfly fauna survey in south-central Sulawesi. Insects and nature. 47: 25-29.

Books (in Japanese)

  1. Ryo Yamaguchi. 2024. How do new species arise? ―In search of the origins of biodiversity― Kyoritsu Shuppan. 176pp.
     

  2. Grant, PR and Grant BR (Original), Yoh Iwasa (Translated), Ryo Yamaguchi (Translated). 2017. How and Why species multiply: Darwin's Finches in Galapagos. Kyoritsu Shuppan. 223pp.

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