Apr. 2025, 文部科学省, 令和7年度科学技術分野の文部科学大臣表彰 若手科学者賞　　　　　　　　　　　　　　　
山口 諒

Aug. 2024, 日本進化学会, 第24回日本進化学会研究奨励賞　　　　　　　　　　　　　　　
山口 諒

Oct. 2023, 個体群生態学会, 第16回個体群生態学会奨励賞　　　　　　　　　　　　　　　
山口 諒

Sep. 2022, Japanese Society for Mathematical Biology, The 17th JSMB Early Career Award　　　　　　　　　　　　　　　
Ryo Yamaguchi

Mar. 2019, The Ecological Society of Japan, The 7th Young Scholar Award of the Ecological Society of Japan (ESJ Suzuki Award)　　　　　　　　　　　　　　　
Ryo Yamaguchi

Inferring the strength of directional selection on armor plates in Lake Washington stickleback while accounting for migration and drift
Yo Y Yamasaki, Ryo Yamaguchi, Atsushi J Nagano, Bo-Jyun Chen, Naomi Musto, Sophie Archambeault, Catherine L Peichel, Jennifer A Schulien, Tessa J Code, David A Beauchamp, Jun Kitano
Evolution, 16 Dec. 2025, [Peer-reviewed], [International Magazine]
English, Scientific journal, Contemporary evolution allows us to investigate how natural selection drives phenotypic and genotypic evolution in nature. Recent advances in molecular genetics have identified causative genes underlying adaptive traits, enabling estimation of selection coefficients at these loci. However, estimating selection is challenging when populations receive migrants from genetically and phenotypically distinct populations. With genome-wide data now allowing estimation of migration rates and effective population sizes, these demographic parameters can be integrated into models for measuring selection. In Lake Washington, USA, the frequency of the completely plated morph of the threespine stickleback (Gasterosteus aculeatus) increased from 1957 to 2005, plausibly due to increased trout predation pressure caused by enhanced water clarity. Here, we estimated the selection coefficient at a major locus responsible for the plate morph using historical data, taking migration and genetic drift into consideration. Model-based predictions of present allele frequencies were tested with samples collected in 2022. Consistent with directional selection, the completely plated morphs and the underlying allele have increased since 2005, but to higher frequencies than predicted, suggesting a recent increase in selection. Thus, integrating molecular genetics, population genomics, and simulations enables the estimation of selection strength while considering migration and drift, to reveal directional selection in nature.

Speciation Through the Lens of Population Dynamics: A Theoretical Primer on How Small and Large Populations Diverge
Ryo Yamaguchi, Hidaka Kubo, Tokuya Ogawa, Hayate Omura
Population Ecology, Wiley, 09 Oct. 2025, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal, ABSTRACT

Speciation—the process by which new species arise—is fundamentally influenced by population‐level factors, such as population size and demographic dynamics. Here, we review how population size and its dynamics shape speciation mechanisms and the generation of biodiversity across evolutionary scales. Small populations can undergo rapid genetic changes via drift and founder events, potentially promoting speciation, whereas large populations harbor greater genetic diversity and adaptive potential, influencing divergence in different ways. We examine how genetic drift and gene flow interact to facilitate or impede speciation under various scenarios and how extinction risk during adaptation affects the development of reproductive isolation. Finally, we explore how speciation rates and the persistence of populations/species over time are related in theoretical models. We highlight insights from mathematical models—especially those explicitly incorporating population size—and identify open questions for future research.

The genomics of discrete polymorphisms maintained by disruptive selection
Jun Kitano, Kotaro Kagawa, Takashi Tsuchimatsu, Ryo Yamaguchi, Masato Yamamichi
Trends in Ecology & Evolution, Elsevier BV, Sep. 2025, [Peer-reviewed]
Scientific journal

Modeling alternative strategies of male emergence timing
Hidaka Kubo, Shinji Nakaoka, Ryo Yamaguchi
Journal of Theoretical Biology, 612, 112214, Elsevier BV, Sep. 2025, [Peer-reviewed], [Last author]
Scientific journal

Why Do Some Lineages Radiate While Others Do Not? Perspectives for Future Research on Adaptive Radiations.
Rishi De-Kayne, Rowan Schley, Julia M I Barth, Luke C Campillo, Catalina Chaparro-Pedraza, Jahnavi Joshi, Walter Salzburger, Bert Van Bocxlaer, Darko D Cotoras, Carmelo Fruciano, Anthony J Geneva, Rosemary Gillespie, Joseph Heras, Stephan Koblmüller, Blake Matthews, Renske E Onstein, Ole Seehausen, Pooja Singh, Erik I Svensson, David Salazar-Valenzuela, Maarten P M Vanhove, Guinevere O U Wogan, Ryo Yamaguchi, Anne D Yoder, José Cerca
Cold Spring Harbor perspectives in biology, 01 May 2024, [Peer-reviewed], [International Magazine]
English, Scientific journal, Understanding the processes that drive phenotypic diversification and underpin speciation is key to elucidating how biodiversity has evolved. Although these processes have been studied across a wide array of clades, adaptive radiations (ARs), which are systems with multiple closely related species and broad phenotypic diversity, have been particularly fruitful for teasing apart the factors that drive and constrain diversification. As such, ARs have become popular candidate study systems for determining the extent to which ecological features, including aspects of organisms and the environment, and inter- and intraspecific interactions, led to evolutionary diversification. Despite substantial past empirical and theoretical work, understanding mechanistically how ARs evolve remains a major challenge. Here, we highlight a number of understudied components of the environment and of lineages themselves, which may help further our understanding of speciation and AR. We also outline some substantial remaining challenges to achieving a detailed understanding of adaptation, speciation, and the role of ecology in these processes. These major challenges include identifying factors that have a causative impact in promoting or constraining ARs, gaining a more holistic understanding of features of organisms and their environment that interact resulting in adaptation and speciation, and understanding whether the role of these organismal and environmental features varies throughout the radiation process. We conclude by providing perspectives on how future investigations into the AR process can overcome these challenges, allowing us to glean mechanistic insights into adaptation and speciation.

Toward the integration of speciation research
Sean Stankowski, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan Rolland, Carole M Smadja, J Carolina Segami Marzal, Christopher R Cooney, Philine G D Feulner, Fabricius Maia Chaves Bicalho Domingos, Henry L North, Ryo Yamaguchi, Roger K Butlin, Jochen B W Wolf, Jenn Coughlan, Patrick Heidbreder, Rebeca Hernández-Gutiérrez, Karen B Barnard-Kubow, David Peede, Loïs Rancilhac, Rodrigo Brincalepe Salvador, Ken A Thompson, Elizabeth A Stacy, Leonie C Moyle, Martin D Garlovsky, Arif Maulana, Annina Kantelinen, N Ivalú Cacho, Hilde Schneemann, Marisol Domínguez, Erik B Dopman, Konrad Lohse, Sina J Rometsch, Aaron A Comeault, Richard M Merrill, Elizabeth S C Scordato, Sonal Singhal, Varpu Pärssinen, Alycia C R Lackey, Sanghamitra Kumar, Joana I Meier, Nicholas Barton, Christelle Fraïsse, Mark Ravinet, Jonna Kulmuni
Evolutionary Journal of the Linnean Society, 3, 1, 24, Oxford University Press (OUP), 16 Feb. 2024, [Peer-reviewed]
English, Scientific journal, Abstract

Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.

Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution
Junya Sunagawa, Hyeongki Park, Kwang Su Kim, Ryo Komorizono, Sooyoun Choi, Lucia Ramirez Torres, Joohyeon Woo, Yong Dam Jeong, William S. Hart, Robin N. Thompson, Kazuyuki Aihara, Shingo Iwami, Ryo Yamaguchi
Nature Communications, 14, 1, Springer Science and Business Media LLC, 21 Nov. 2023, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal, Abstract

During the COVID-19 pandemic, human behavior change as a result of nonpharmaceutical interventions such as isolation may have induced directional selection for viral evolution. By combining previously published empirical clinical data analysis and multi-level mathematical modeling, we find that the SARS-CoV-2 variants selected for as the virus evolved from the pre-Alpha to the Delta variant had earlier and higher peak in viral load dynamics but a shorter duration of infection. Selection for increased transmissibility shapes the viral load dynamics, and the isolation measure is likely to be a driver of these evolutionary transitions. In addition, we show that a decreased incubation period and an increased proportion of asymptomatic infection are also positively selected for as SARS-CoV-2 mutated to adapt to human behavior (i.e., Omicron variants). The quantitative information and predictions we present here can guide future responses in the potential arms race between pandemic interventions and viral evolution.

Disentangling the growth curve of microbial culture
Daiki Kumakura, Ryo Yamaguchi, Akane Hara, Shinji Nakaoka
Journal of Theoretical Biology, 573, 111597, 111597, Elsevier BV, Aug. 2023, [Peer-reviewed]
Scientific journal

Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection
Junya Sunagawa, Ryo Komorizono, Hyeongki Park, William S. Har, Robin, N. Thompson, Akiko Makino, Keizo Tomonaga, Shingo Iwami, Ryo Yamaguchi
PLOS Computational Biology, 19, 5, e1011173, e1011173, Public Library of Science (PLoS), 30 May 2023, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal, Viruses evolve in infected host populations, and host population dynamics affect viral evolution. RNA viruses with a short duration of infection and a high peak viral load, such as SARS-CoV-2, are maintained in human populations. By contrast, RNA viruses characterized by a long infection duration and a low peak viral load (e.g., borna disease virus) can be maintained in nonhuman populations, and the process of the evolution of persistent viruses has rarely been explored. Here, using a multi-level modeling approach including both individual-level virus infection dynamics and population-scale transmission, we consider virus evolution based on the host environment, specifically, the effect of the contact history of infected hosts. We found that, with a highly dense contact history, viruses with a high virus production rate but low accuracy are likely to be optimal, resulting in a short infectious period with a high peak viral load. In contrast, with a low-density contact history, viral evolution is toward low virus production but high accuracy, resulting in long infection durations with low peak viral load. Our study sheds light on the origin of persistent viruses and why acute viral infections but not persistent virus infection tends to prevail in human society., 40241668

Males and females contribute differently to the evolution of habitat segregation driven by hybridization
Daisuke Kyogoku, Ryo Yamaguchi
Journal of Evolutionary Biology, Wiley, 31 Jan. 2023, [Peer-reviewed], [Last author]
Scientific journal

The phoenix hypothesis of speciation
Ryo Yamaguchi, Bryn Wiley, Sarah P Otto
Proceedings of the Royal Society B, 289, 1987, 20221186, 20221186, 30 Nov. 2022, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, Genetic divergence among allopatric populations builds reproductive isolation over time. This process is accelerated when populations face a changing environment that allows large-effect mutational differences to accumulate, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher's geometric model with explicit population dynamics to explore the genetic changes that occur in the face of environmental changes. Because evolutionary rescue leads to the fixation of mutations whose phenotypic effects are larger on average compared with populations not at risk of extinction, these mutations are thus more likely to lead to reproductive isolation. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. With only a small number of potential rescue mutations, however, mutations that fixed in different populations were more likely to be identical, with such parallel changes reducing isolation. Consequently, reproductive isolation builds fastest in populations subject to an intermediate extinction risk, given a limited number of mutations available for adaptation.

Evolving neural networks through bio-inspired parent selection in dynamic environments
Junya Sunagawa, Ryo Yamaguchi, Shinji Nakaoka
Biosystems, 218, 104686, 104686, Elsevier BV, Aug. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Environmental variability often degrades the performance of algorithms designed to capture the global convergence of a given search space. Several approaches have been developed to challenge environmental uncertainty by incorporating biologically inspired notions, focusing on crossover, mutation, and selection. This study proposes a bio-inspired approach called NEAT-HD, which focuses on parent selection based on genetic similarity. The originality of the proposed approach rests on its use of a sigmoid function to accelerate species formation and contribute to population diversity. Experiments on two classic control tasks were performed to demonstrate the performance of the proposed method. The results show that NEAT-HD can dynamically adapt to its environment by forming hybrid individuals originating from genetically distinct parents. Additionally, an increase in diversity within the population was observed due to the formation of hybrids and novel individuals, which has never been observed before. Comparing two tasks, the characteristics of NEAT-HD were improved by appropriately setting the algorithm to include the distribution of genetic distance within the population. Our key finding is the inherent potential of newly formed individuals for robustness against dynamic environments.

Intermediate dispersal hypothesis of species diversity: New insights
Ryo Yamaguchi
Ecological Research, Wiley, 08 Apr. 2022, [Peer-reviewed], [Lead author, Corresponding author]
Scientific journal

Adaptive and non‐adaptive causes of radiation: Is adaptation a harsh mistress of diversity?
Kei W. Matsubayashi, Ryo Yamaguchi
Population Ecology, 64, 2, 93, 94, Wiley, Apr. 2022, [Peer-reviewed], [Last author]
Scientific journal

Reply to Kagawa's comment: Quantifying mixture modes of evolutionary radiations
Ryo Yamaguchi, Kei W. Matsubayashi
POPULATION ECOLOGY, Mar. 2022, [Peer-reviewed], [Lead author, Corresponding author]
English

Parental Population Range Expansion Before Secondary Contact Promotes Heterosis
Ailene MacPherson, Silu Wang, Ryo Yamaguchi, Loren Rieseberg, Sarah Otto
The American Naturalist, University of Chicago Press, 23 Feb. 2022, [Peer-reviewed]
Scientific journal

The speciation view: Disentangling multiple causes of adaptive and nonadaptive radiation in terms of speciation
Kei W. Matsubayashi, Ryo Yamaguchi
POPULATION ECOLOGY, Dec. 2021, [Peer-reviewed]
English

Recurrent speciation rates on islands decline with species number.
Ryo Yamaguchi, Yoh Iwasa, Yuuya Tachiki
Proceedings of the Royal Society B, 288, 1949, 20210255, 20210255, 28 Apr. 2021, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal, In an archipelagic system, species diversity is maintained and determined by the balance among speciation, extinction and migration. As the number of species increases, the average population size of each species decreases, and the extinction likelihood of any given species grows. By contrast, the role of reduced population size in geographic speciation has received comparatively less research attention. Here, to study the rate of recurrent speciation, we adopted a simple multi-species two-island model and considered symmetric interspecific competition on each island. As the number of species increases on an island, the competition intensifies, and the size of the resident population decreases. By contrast, the number of migrants is likely to exhibit a weaker than proportional relationship with the size of the source population due to rare oceanic dispersal. If this is the case, as the number of species on the recipient island increases, the impact of migration strengthens and decelerates the occurrence of further speciation events. According to our analyses, the number of species can be stabilized at a finite level, even in the absence of extinction.

Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change
Ryo Yamaguchi, Sarah P. Otto
EVOLUTION, 74, 8, 1603, 1619, Aug. 2020, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Preservation of the value of rice paddy fields: Investigating how to prevent farmers from abandoning the fields by means of evolutionary game theory
Joung Hun Lee, Ryo Yamaguchi, Hiroyuki Yokomizo, Mayuko Nakamaru
JOURNAL OF THEORETICAL BIOLOGY, 495, 110247, 110247, Jun. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal

Extra molting, cannibalism and pupal diapause under unfavorable growth conditions in Atrophaneura alcinous (Lepidoptera: Papilionidae)
Toru Nakahara, Junnosuke Horita, Ross D. Booton, Ryo Yamaguchi
ENTOMOLOGICAL SCIENCE, 23, 1, 57, 65, Mar. 2020, [Peer-reviewed], [Last author]
English, Scientific journal

種分化ダイナミクスと数理モデル －生殖隔離進化の促進要因を探る－　　　　　　　　　　　　　　　
山口 諒
日本生態学会誌, 69, 3, 151, 169, Dec. 2019, [Peer-reviewed], [Lead author, Corresponding author]
Japanese, Scientific journal

種の境界：進化学と生態学、分子遺伝学から種分化に迫る －序論と趣旨説明－　　　　　　　　　　　　　　　
山口 諒, 松林 圭
日本生態学会誌, 69, 3, 145, 149, Dec. 2019, [Peer-reviewed], [Lead author, Corresponding author]
Japanese, Scientific journal

Consequences of hybridization during invasion on establishment success
Ryo Yamaguchi, Takehiko Yamanaka, Andrew M. Liebhold
THEORETICAL ECOLOGY, 12, 2, 197, 205, Jun. 2019, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

A population model for diapausing multivoltine insects under asymmetric cannibalism
Ross Booton, Ryo Yamaguchi, Yoh Iwasa
POPULATION ECOLOGY, 61, 1, 35, 44, Jan. 2019, [Peer-reviewed]
English, Scientific journal

A color pattern difference in the fifth instar larva of two subspecies of Faunis menado Hewitson (Lepidoptera, Nymphalidae)　　　　　　　　　　　　　　　
Ryo Yamaguchi, Seiichi Suefuji, Ken-Ichi Odagiri, Djunijanti Peggie, Osamu Yata
Lepidoptera Science, 69, 2, 67, 73, Oct. 2018, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

Interactions between immunotoxicants and parasite stress: Implications for host health.
Ross D Booton, Ryo Yamaguchi, James A R Marshall, Dylan Z Childs, Yoh Iwasa
Journal of theoretical biology, 445, 120, 127, 14 May 2018, [Peer-reviewed], [International Magazine]
English, Scientific journal, Many organisms face a wide variety of biotic and abiotic stressors which reduce individual survival, interacting to further reduce fitness. Here we studied the effects of two such interacting stressors: immunotoxicant exposure and parasite infection. We model the dynamics of a within-host infection and the associated immune response of an individual. We consider both the indirect sub-lethal effects on immunosuppression and the direct effects on health and mortality of individuals exposed to toxicants. We demonstrate that sub-lethal exposure to toxicants can promote infection through the suppression of the immune system. This happens through the depletion of the immune response which causes rapid proliferation in parasite load. We predict that the within-host parasite density is maximised by an intermediate toxicant exposure, rather than continuing to increase with toxicant exposure. In addition, high toxicant exposure can alter cellular regulation and cause the breakdown of normal healthy tissue, from which we infer higher mortality risk of the host. We classify this breakdown into three phases of increasing toxicant stress, and demonstrate the range of conditions under which toxicant exposure causes failure at the within-host level. These phases are determined by the relationship between the immunity status, overall cellular health and the level of toxicant exposure. We discuss the implications of our model in the context of individual bee health. Our model provides an assessment of how pesticide stress and infection interact to cause the breakdown of the within-host dynamics of individual bees.

A tipping point in parapatric speciation
Ryo Yamaguchi, Yoh Iwasa
JOURNAL OF THEORETICAL BIOLOGY, 421, 81, 92, May 2017, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing
Ryo Yamaguchi, Yoh Iwasa
ROYAL SOCIETY OPEN SCIENCE, 4, 2, 160819, 160819, Feb. 2017, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Smallness of the number of incompatibility loci can facilitate parapatric speciation
Ryo Yamaguchi, Yoh Iwasa
JOURNAL OF THEORETICAL BIOLOGY, 405, 36, 45, Sep. 2016, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

The endemic Sulawesi amathusiine Faunis menado Hewitson (Lepidoptera, Nymphalidae) is divisible into two morphospecies
R Yamaguchi, S Suefuji, K Odagiri, O Yata
Lepidoptera science, 67, 1, 12, 21, THE LEPIDOPTEROLOGICAL SOCIETY OF JAPAN, May 2016, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal,

Faunis menado (Nymphalidae, Satyrinae, Amathusiini), a butterfly endemic to Sulawesi, is separated into two morphotypes, one distributed in the north, the other in the south of the island. Morphological differences between their male and female genitalia and wing markings are as great as those seen between some other Faunis species. The ranges of the two morphospecies overlap, and some evidence suggests that they segregate locally as the result of differential responses to solar radiation intensity, and to altitude.

Reproductive interference can promote recurrent speciation
Ryo Yamaguchi, Yoh Iwasa
POPULATION ECOLOGY, 57, 2, 343, 346, Apr. 2015, [Peer-reviewed], [Lead author]
English, Scientific journal

First passage time to allopatric speciation
Ryo Yamaguchi, Yoh Iwasa
INTERFACE FOCUS, 3, 6, 20130026, 20130026, Dec. 2013, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
English, Scientific journal

Reproductive character displacement by the evolution of female mate choice
Ryo Yamaguchi, Yoh Iwasa
EVOLUTIONARY ECOLOGY RESEARCH, 15, 1, 25, 41, Jan. 2013, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal

生態学と集団遺伝学のあいだで探す種の起源　　　　　　　　　　　　　　　
山口 諒, 進化学会ニュース, Mar. 2025, [Invited], [Lead author]

個体群生態学会奨励賞受賞記　　　　　　　　　　　　　　　
山口 諒, 個体群生態学会会報, 81, 16, 18, Aug. 2024, [Invited], [Lead author]

海外で種分化の数理モデルを見つめ直す　　　　　　　　　　　　　　　
山口 諒, 進化学会ニュース, 24, 2, 5, 8, Jul. 2023, [Invited], [Lead author]

固有種数でみる東南アジア島嶼部のチョウ類多様性—Butterfly species diversity : Distribution of endemic species in Malay Archipelago
山口 諒, 昆虫と自然 / 昆虫と自然編集委員会 編, 58, 4, 31, 34, Apr. 2023, [Lead author, Corresponding author]
ニューサイエンス社, Japanese

数理モデルで解き明かす種多様性の起源　　　　　　　　　　　　　　　
山口 諒, 日本数理生物学会ニュースレター, 99, 29, 33, Mar. 2023, [Invited], [Lead author]

チョウの生殖隔離と種分化—Reproductive isolation and speciation in butterflies
山口 諒, 昆虫と自然 / 昆虫と自然編集委員会 編, 57, 8, 30, 34, Jul. 2022, [Lead author, Corresponding author]
ニューサイエンス社, Japanese

スラウェシの固有な蝶相—The endemic butterfly fauna of Sulawesi—特集 東南アジアの蝶学
山口 諒, 昆虫と自然 / 昆虫と自然編集委員会 編, 56, 4, 巻頭2p,13, 17, Apr. 2021, [Invited], [Lead author, Corresponding author]
ニューサイエンス社, Japanese

形質のモジュール性が適応度地形における進化に及ぼす影響—第15回生物数学の理論とその応用 : 次世代の数理科学への展開
山口 諒, 数理解析研究所講究録, 2165, 59, 63, Jul. 2020, [Lead author, Corresponding author]
京都大学数理解析研究所, Japanese

Speciation despite gene flow when genetic incompatibility accumulates continuously (Theory of Biomathematics and Its Applications XI)
Yamaguchi Ryo, Iwasa Yoh, RIMS Kokyuroku, 1937, 56, 63, Apr. 2015, [Lead author, Corresponding author]
Kyoto University, Japanese

スラウェシの生物地理とワモンチョウ族
山口 諒, 昆虫と自然, 50(4), 4, 8, 2015, [Lead author, Corresponding author]

メスの配偶者選択による生殖的形質置換 (第9回生物数学の理論とその応用)
山口 諒, 巌佐 庸, 数理解析研究所講究録, 1853, 116, 123, Oct. 2013, [Lead author, Corresponding author]
京都大学, Japanese

スラウェシ島中南部におけるチョウ相調査—Butterfly fauna of South-Central Sulawesi, Indonesia
山口 諒, 昆虫と自然 / 昆虫と自然編集委員会 編, 47, 3, 25, 29, Mar. 2012, [Lead author, Corresponding author]
ニューサイエンス社, Japanese

理論生物学事典　　　　　　　　　　　　　　　
巌佐庸, 大槻久, 佐竹暁子, 望月敦史
朝倉書店, Nov. 2025, 9784254172034, [Contributor]

種分化の生物学 : 生物多様性を生み出す進化のしくみ
種生物学会, 阪口翔太, 村中智明, 川北篤
文一総合出版, Sep. 2025, 9784829962138, viii, 287p, Japanese, [Contributor]

How do new species arise?　　　　　　　　　　　　　　　
Ryo Yamaguchi
Kyoritsu Shuppan, Mar. 2024, 9784320009424, [Single work]

How and why species multiply
Ryo Yamaguchi, Yoh Iwasa
Kyoritsu Shuppan Co., Ltd., Jan. 2017, 9784320057845, xxv, 223p, 図版 [32] p, Japanese

新種はいかにして誕生するか：種分化の数理モデル　　　　　　　　　　　　　　　
山口諒
ゲーム理論ワークショップ2026, 06 Mar. 2026
[Invited]

生殖隔離の進化速度と個体群動態　　　　　　　　　　　　　　　
第72回日本生態学会大会自由集会, 17 Mar. 2025
[Invited]

Speciation Through the Lens of Population Dynamics　　　　　　　　　　　　　　　
Yamaguchi, R
Speciation - Gordon Research Conference, 06 Mar. 2025
[Invited]

進化実験における急速な適応と予測制御に向けた挑戦　　　　　　　　　　　　　　　
山口諒
第47回日本分子生物学会年会, 28 Nov. 2024, Invited oral presentation
[Invited]

進化動態の理論的探究と未来予測に向けた探索　　　　　　　　　　　　　　　
山口諒
未踏探索の数理情報技術：第四回WS, 13 Nov. 2024, Invited oral presentation
[Invited]

Exploring virus evolution and adaptation through genetic algorithms on fitness landscapes　　　　　　　　　　　　　　　
Yamaguchi, R
KSMB-SMB conference, Jul. 2024
[Invited]

ダイナミックな進化過程の数理解析: 環境適応から種分化まで　　　　　　　　　　　　　　　
山口諒
第1回生物の基礎探求会, Mar. 2024
[Invited]

The phoenix hypothesis of speciation: reproductive isolation among populations experiencing extinction risk　　　　　　　　　　　　　　　
Yamaguchi, R
Symposium “Genomics of adaptation and speciation” at The 3rd AsiaEvo Conference, Dec. 2023
[Invited]

種分化サイクルにおける個体群動態−種多様性創出の理解に向けて−　　　　　　　　　　　　　　　
山口諒
第39回個体群生態学会⼤会, Oct. 2023
[Invited]

Integrating speciation over spatial temporal scales　　　　　　　　　　　　　　　
Yamaguchi, R.
Integration Of Speciation Research (IOS) workshop, Mar. 2023
[Invited]

Macroevolutionary patterns of diversification and implications for species persistence　　　　　　　　　　　　　　　
Yamaguchi, R.
Gordon Research Seminar (Speciation 2023), Jan. 2023
[Invited]

数理モデルで解き明かす種多様性の起源　　　　　　　　　　　　　　　
山口諒
第32回⽇本数理⽣物学会⼤会, Sep. 2022
[Invited]

Dynamics of speciation rate in an island biogeography framework　　　　　　　　　　　　　　　
Yamaguchi, R
第69回日本生態学会大会, Mar. 2022
[Invited]

群集生態学の中立モデルによるHTLV-1感染クローンの多型進化パターン検出　　　　　　　　　　　　　　　
山口諒, 立木佑弥
第28回日本数理生物学会年会, Sep. 2020
[Invited]

種間相互作用による地理的分断プロセスの理論と実証　　　　　　　　　　　　　　　
山口諒
第67回日本生態学会大会, Mar. 2020
[Invited]

ウイルスの集団遺伝学的動態と群集生態学の中立モデル　　　　　　　　　　　　　　　
山口諒, 立木佑弥
第27回日本数理生物学会年会, Sep. 2019
[Invited]

Fisher’s geometric model on the likelihood of speciation under different adaptation scenarios　　　　　　　　　　　　　　　
Yamaguchi, R.
Gordon Research Seminar (Speciation 2019), Mar. 2019
[Invited]

種の境界と生物多様性の隠れたパターン　　　　　　　　　　　　　　　
山口諒
第66回日本生態学会大会, Mar. 2019
[Invited]

環境適応シナリオの違いと種分化可能性　　　　　　　　　　　　　　　
山口諒
第15回RIMS ⽣物数学の理論とその応⽤―次世代の数理科学への展開―, Sep. 2018
[Invited]

都市化と人為的な遺伝子流動: デング熱媒介蚊の集団文化予測　　　　　　　　　　　　　　　
山口諒
第65回日本生態学会大会, Mar. 2018
[Invited]

Gene flow by human-mediated dispersal: population structure of Aedes aegypti in the Philippines　　　　　　　　　　　　　　　
Yamaguchi, R.,Tachiki Y.,Minakawa N.,Iwami S.
IWOMB, 2018
[Invited]

都市化に伴う遺伝子流動: デング熱媒介蚊の集団構造予測　　　　　　　　　　　　　　　
山口諒, 立木佑弥, 布野孝明, 皆川昇, 岩見真吾
第27回日本数理生物学会年会, Oct. 2017
[Invited]

Mathematical modeling of an evolutionary radiation and its patterns caused by non-adaptive processes　　　　　　　　　　　　　　　
山口諒
第33回個体群生態学会大会, Oct. 2017
[Invited]

メナドヒメワモンの分類学的再検討とスラウェシの生物地理　　　　　　　　　　　　　　　
山口諒
日本鱗翅学会九州支部例会, Mar. 2017
[Invited]

An increase in gene flow by urbanization: predictions on population structure of Aedes aegypti　　　　　　　　　　　　　　　
Yamaguchi, R.,Tachiki Y.,Minakawa N.,Iwami S.
ISEM, 2017
[Invited]

連続的な変化がもたらす種の分かれ目　　　　　　　　　　　　　　　
山口諒
第63回日本生態学会大会, Mar. 2016
[Invited]

Reproductive character displacement by the evolution of female mate choice　　　　　　　　　　　　　　　
Yamaguchi, R.
第31回個体群生態学会, Oct. 2015
[Invited]

メナドヒメワモンFaunis menadoに見るスラウェシのチョウ相　　　　　　　　　　　　　　　
山口諒
日本鱗翅学会第61回大会, Oct. 2014
[Invited]

生命科学の最前線　　　　　　　　　　　　　　　
北海道大学
2026 - Present

生物系の数理科学　　　　　　　　　　　　　　　
北海道大学
2025 - Present

生命情報科学演習　　　　　　　　　　　　　　　
北海道大学
2023 - Present

一般教育演習（SDGsと生命科学）　　　　　　　　　　　　　　　
北海道大学
2021 - Present

統合生物科学特論Ⅰ　　　　　　　　　　　　　　　
九州大学 大学院システム生命科学府
Jun. 2025 - Dec. 2025

実験生物科学　　　　　　　　　　　　　　　
北海道大学
2020 - 2023

異なる標高帯への適応に伴って生じる種分化の検証
科学研究費助成事業
Apr. 2026 - Mar. 2030
松林 圭, 山口 諒
日本学術振興会, 基盤研究(C), Coinvestigator, 26K09437

種分化サイクルの時間動態：待ち時間分布フレームワークの実装と実証
科学研究費助成事業
Apr. 2026 - Mar. 2029
山口 諒
日本学術振興会, 国際共同研究加速基金(国際共同研究強化), Principal investigator, 25KK0069

An Integrated Theory of Speciation Cycles and Species Diversity through the Lens of Ecology　　　　　　　　　　　　　　　
科学研究費助成事業
Apr. 2024 - Mar. 2028
Ryo Yamaguchi, Daisuke Aoki
日本学術振興会, 基盤研究(B), Principal investigator, 24K02092

Prediction on infectious disease control driven SARS-CoV-2 evolution for living with COVID-19
Grants-in-Aid for Scientific Research
Apr. 2023 - Mar. 2026
Shingo Iwami, Koji Noshita, Ryo Yamaguchi
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Nagoya University, Coinvestigator, 23H03497

Establishment of eco-evolutionary experiment controlled by Real-Time AI
ACT-X
Oct. 2022 - Mar. 2025
Ryo Yamaguchi
Japan Science and Technology Agency (JST), Principal investigator, JPMJAX22AK

生殖隔離における種間非対称性の進化生態学的起源
科学研究費助成事業 若手研究
01 Apr. 2021 - 31 Mar. 2024
山口 諒
交配前隔離の非対称性は広範な分類群の近縁種間でごく一般的に観察される。このパターンを進化的帰結として捉え、その原因となるメカニズムを解明するため、野外オオヨモギハムシ集団のゲノム解析および数理モデルによる理論解析を実施した。
まずゲノム解析では、特定集団の全ゲノムシーケンスによるリファレンスゲノムを作成したうえで、交配前隔離に非対称性のある集団間ペアの遺伝的多型情報をRAD-seqデータより得た。過去の集団サイズ遷移を推定した結果、一部の集団で個体数の著しい減少を経験していたことが判明した。またそれらの集団は、同類交配の強度を測定する実験において、メスが自種のオスと同様に他種のオスを受け入れてしまう傾向にある集団であることが明らかとなった。現在は、交配前隔離に非対称性のある3集団の各組み合わせについて、感覚器である触角を含む頭部および前脚のRNA-seqが完了しており、今後は隔離メカニズムの推定に向けた発現変動遺伝子解析を行う予定である。
続いて、性淘汰の量的遺伝モデルの枠組みを拡張し、集団サイズを考慮した同類交配進化モデルを構築した。ここで集団サイズの影響は、遺伝的分散と交配成功率の２つに影響を与えると仮定した。単純化した解析では、ランナウェイ型の形質分化による種分化の条件を導出することができた。一方で、この導出された条件では遺伝的分散（共分散）に強く依存することも判明した。今後は先のゲノム解析によって推定されたシナリオを再現する、集団サイズ依存的な条件の探索を目標として解析を展開する。
日本学術振興会, 若手研究, 北海道大学, 21K15160

Relative importance of ecological speciation versus mutation- order speciation using a fitness landscape model
人材育成事業 海外特別研究員
Apr. 2020 - Mar. 2022
Ryo Yamaguchi
日本学術振興会, University of British Columbia, Principal investigator

Biotic interactions can cause allopatry and subsequent speciation: theoretical and empirical approaches
Grants-in-Aid for Scientific Research
01 Apr. 2018 - 31 Mar. 2021
Yamaguchi Ryo
We propose that the geographic isolation of populations can occur not due to physical factors such as tectonic or climatic changes but due to biological interactions represented by hybrid zones. We named this novel process of geographic isolation by interacting closely related species "Biotic Population Subdivision (BPS)." We used natural populations of a species complex of a flightless leaf beetle to test our hypothesis. Using this species complex as an example, we analyzed the repetition of the origination of isolated populations and subsequent speciation in the continuous space using molecular phylogenetic analysis, mating experiments, and mathematical modeling. We showed that interactions in the hybrid zone are one of the factors that drive recurrent speciation.
Japan Society for the Promotion of Science, Grant-in-Aid for Early-Career Scientists, 首都大学東京, 18K14793

ゲノムデータと種分化モデルの統合： 新種形成を促進する形質の特定へ
科学研究費助成事業 特別研究員奨励費
26 Apr. 2017 - 31 Mar. 2020
山口 諒
進化実験と種分化をつなぐ研究課題では、適応度地形理論を用い、生態的種分化と突然変異順位種分化が相対的にどれだけ生殖隔離に貢献するかを様々な環境シナリオで検証した。その結果、環境変化速度が速い状況や、より長期間の適応プロセスを経た集団間において、交雑個体の適応度が低下しやすいことを明らかにした。本課題について国内外での学会発表を行ったほか、現在論文を投稿済み（査読中）である。
また、もうひとつの研究課題として、系統情報を考慮した適応形質の遺伝的基盤を探る研究を進めている。系統的な制約のもとである形質が進化してきた事実に着目し、祖先復元によって配列の進化確率を計算することで、より効率的な候補遺伝子領域または塩基置換の探索手法開発を行っている。現在、配列進化と形質進化を結ぶ確率過程シミュレーションが完成し、パラメータ依存性を検証している段階である。次年度、ショウジョウバエ野生種の配列・形質データを伴う具体的な解析を行い、適応形質の遺伝学に関する議論を行う。
日本学術振興会, 特別研究員奨励費, 首都大学東京, 17J01380

種分化プロセスと種多様性創出速度の理論的研究
科学研究費助成事業 特別研究員奨励費
25 Apr. 2014 - 31 Mar. 2017
山口 諒
平成28年度は、申請時の年次計画に基づき、研究内容[1]局所的な分布パターン: 近縁種における繁殖干渉とその進化的帰結の検証について、メナドヒメワモンの分類学的再検討を行った。大英自然史博物館を訪問し、1850年以降の本種標本全ての外部形態を調査した。その結果、前年度に出版した論文に加え、あらたに1新種を発見したほか、種間の棲み分けが森林の照度と標高に大きく依存していることが明らかとなった。また、交雑個体と思われる標本も発見されており、種分化後の二次的接触と形質置換の可能性が示唆された。これらの内容は共同研究として、現在論文原稿を執筆中である。
研究内容[2]: 大域的な分布パターン: 種形成メカニズムとその分布予測について、集団間で遺伝子流動がある場合に種分化が起こるスピードを定式化する研究を継続して行った。メタ集団間での種多様性創出速度予測のため、これまでの2集団から3集団以上へのモデルの拡張を行った。この内容は「Speciation in Three Islands: Dynamics of Geographic Configuration of Allele Sharing」としてRoyal Society Open Scienceに掲載された。さらに、近年実証研究で支持されている連続的かつ段階的な不和合性蓄積様式による種分化モデルを構築し、他の島への移入個体は在来個体との間には中程度の不和合性が存在するとした。結果として、突然変異による不和合性の蓄積は連続的であっても、移入の効果が急速に薄れる、「種分化への復帰不能点」の存在を提唱した。この種分化メカニズムに関する理論研究は、論文「A tipping point in parapatric speciation」として、Journal of Theoretical Biologyに受理された。
日本学術振興会, 特別研究員奨励費, 九州大学, 14J02775

行動変容でコロナウイルス進化？ コロナ株解析、名古屋大
25 Nov. 2023
中部経済新聞
（3面）, 42931270, [Paper]

コロナウイルス感染対策、ウイルス進化引き起こしたか 名大・北大など研究
24 Nov. 2023
朝日新聞 夕刊
（10面）, 42931270, [Paper]

コロナウイルス感染力、人の行動変容で変化？名古屋大など
24 Nov. 2023
日本経済新聞
（26面）, 42931270, [Paper]

行動変容でウイルス進化か 3密回避に対抗、感染力高める 名大チーム、コロナ株解析
24 Nov. 2023
岐阜新聞
（20面）, 42931270, [Paper]

3密回避や隔離がコロナを「進化」させた？ウイルス増・ピーク早く　　　　　　　　　　　　　　　
22 Nov. 2023
朝日新聞デジタル
[Internet]

Wie Verhalten das Coronavirus veränderte　　　　　　　　　　　　　　　
22 Nov. 2023
science.orf.at
[Internet]

変異株ウイルス量増 感染者排出ピーク時
22 Nov. 2023
毎日新聞
（20面）, 42931270, [Paper]

新型コロナ、変異でウイルス排出量5倍に ピークも1.5倍早まる　　　　　　　　　　　　　　　
21 Nov. 2023
毎日新聞デジタル
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
共同通信社
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
西日本新聞me
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
河北新報ONLINE
[Internet]

行行動変容でウイルス進化か 名大チーム、コロナ株解析 ３密回避に対抗、感染力高める　　　　　　　　　　　　　　　
21 Nov. 2023
岐阜新聞Web
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
福井新聞ONLINE
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
沖縄タイムス＋プラス
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
佐賀新聞
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
高知新聞Plus
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
新潟日報デジタルプラス
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
北日本新聞webunプラス
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
埼玉新聞
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
神戸新聞NEXT
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
大分合同新聞Gate
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
北國新聞デジタル
[Internet]

行動変容でコロナウイルス進化？名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
北海道新聞
[Internet]

新型コロナ、変異でウイルス排出量5倍に ピークも1.5倍早まる　　　　　　　　　　　　　　　
21 Nov. 2023
Yahoo!ニュース
[Internet]

行動変容でコロナウイルス進化？ 名古屋大、感染者のデータ解析　　　　　　　　　　　　　　　
21 Nov. 2023
東京新聞 TOKYO Web
[Internet]

Human behavior may drive the evolution of new coronavirus strains　　　　　　　　　　　　　　　
21 Nov. 2023
News Medical
[Internet]

COVID's Evolution May Have Been Driven by Human Behavior, Say Biologists　　　　　　　　　　　　　　　
21 Nov. 2023
Newsweek
[Internet]

How Lockdowns Shaped the Virus: AI Uncovers COVID-19’s Evolutionary Secrets　　　　　　　　　　　　　　　
Nov. 2023
SciTechDaily
[Internet]