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Last Updated :2024/10/16

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Master

Affiliation (Master)

  • Faculty of Advanced Life Science　Functional Life Sciences　Functional Cell Science

Affiliation (Master)

  • Faculty of Advanced Life Science　Functional Life Sciences　Functional Cell Science

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Profile and Settings

Degree

  • Ph.D.（2017/03 Kyushu University）

Profile and Settings

  • Name (Japanese)

    Yamaguchi

  • Name (Kana)

    Ryo

  • Name

    O-7909-2018, 202001016048785093

Alternate Names

Achievement

Research Interests

  • Population dynamics   Species diversity   Genetic drift   Reproductive isolation   Extinction   Adaptation   Evolution experiment   Speciation   Mathematical model   

Research Areas

  • Life sciences / Evolutionary biology
  • Life sciences / Biodiversity and systematics
  • Life sciences / Ecology and environmental science

Research Experience

  • 2020/04 - Today Hokkaido University Faculty of Advanced Life Science Division of Functional Life Sciences Assistant Professor
  • 2022/02 - 2024/01 The University of British Columbia
  • 2017/04 - 2020/03 Tokyo Metropolitan University
  • 2014/04 - 2017/03 Kyushu University Graduate School of Systems Life Sciences

Education

  • 2012/04 - 2017/03  Kyushu University  Graduate School of Systems Life Sciences
  • 2008/04 - 2012/03  Kyushu University  Department of Biological Sciences, Faculty of Sciences

Awards

  • 2024/08 日本進化学会 第24回日本進化学会研究奨励賞
     
    受賞者: 山口 諒
  • 2023/10 個体群生態学会 第16回個体群生態学会奨励賞
     
    受賞者: 山口 諒
  • 2022/09 Japanese Society for Mathematical Biology The 17th JSMB Early Career Award
     
    受賞者: Ryo Yamaguchi
  • 2019/03 The Ecological Society of Japan The 7th Young Scholar Award of the Ecological Society of Japan (ESJ Suzuki Award)
     
    受賞者: Ryo Yamaguchi

Published Papers

  • 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 2024/05/01 [Refereed]
     
    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.
  • 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 2024/02/16 [Refereed][Not invited]
     
    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.
  • 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) 2023/11/21 [Refereed][Not invited]
     
    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.
  • Daiki Kumakura, Ryo Yamaguchi, Akane Hara, Shinji Nakaoka
    Journal of Theoretical Biology 573 111597 - 111597 0022-5193 2023/08 [Refereed][Not invited]
  • 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 2023/05/30 [Refereed][Not invited]
     
    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.
  • Daisuke Kyogoku, Ryo Yamaguchi
    Journal of Evolutionary Biology 1010-061X 2023/01/31 [Refereed][Not invited]
  • Ryo Yamaguchi, Bryn Wiley, Sarah P Otto
    Proceedings of the Royal Society B 289 (1987) 20221186 - 20221186 2022/11/30 [Refereed][Not invited]
     
    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.
  • Junya Sunagawa, Ryo Yamaguchi, Shinji Nakaoka
    Biosystems 218 104686 - 104686 0303-2647 2022/08 [Refereed][Not invited]
     
    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.
  • Ryo Yamaguchi
    Ecological Research 0912-3814 2022/04/08 [Refereed][Not invited]
  • Kei W. Matsubayashi, Ryo Yamaguchi
    Population Ecology 64 (2) 93 - 94 1438-3896 2022/04 [Refereed][Not invited]
  • Ryo Yamaguchi, Kei W. Matsubayashi
    POPULATION ECOLOGY 1438-3896 2022/03 [Refereed]
  • Ailene MacPherson, Silu Wang, Ryo Yamaguchi, Loren Rieseberg, Sarah Otto
    The American Naturalist 0003-0147 2022/02/23 [Refereed][Not invited]
  • Kei W. Matsubayashi, Ryo Yamaguchi
    POPULATION ECOLOGY 1438-3896 2021/12 [Refereed]
     
    Biological diversification often includes burst of lineage splitting. Such "radiation" has been known to act as evolutionary arenas with the potential to generate unique phylogenetic clusters and further novel groups. Although these radiations when accompanied by ecological diversification, so-called "adaptive radiation" have persisted as a central premise in evolutionary biology, the ecological and genetic mechanism of such rapid diversification has remained unclear. There are several critical definitions for the pattern of adaptive radiation, and those provide delimitation of adaptive and nonadaptive radiation. That being said, only a few studies have provided any clear demarcations in our understanding of the adaptive and nonadaptive causes of radiation from the mechanism of speciation. Here, we review the current consensus for the causes of adaptive radiation, especially along with the recent theoretical synthesis of "ecological speciation." Further, we suggest the signature of adaptive and nonadaptive radiation in the earliest stages of diversification from the viewpoint of speciation. These criteria from the speciation view are useful to find the cases with the signatures of adaptive/nonadaptive radiation.
  • Ryo Yamaguchi, Yoh Iwasa, Yuuya Tachiki
    Proceedings of the Royal Society B 288 (1949) 20210255 - 20210255 2021/04/28 [Refereed]
     
    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.
  • Ryo Yamaguchi, Sarah P. Otto
    EVOLUTION 74 (8) 1603 - 1619 0014-3820 2020/08 [Refereed][Not invited]
     
    The formation of new species via the accumulation of incompatible genetic changes is thought to result either from ecologically based divergent natural selection or the order by which mutations happen to arise, leading to different evolutionary trajectories even under similar selection pressures. There is growing evidence in support of both ecological speciation and mutation-order speciation, but how different environmental scenarios affect the rate of species formation remains underexplored. We use a simple model of optimizing selection on multiple traits ("Fisher's geometric model") to determine the conditions that generate genetic incompatibilities in a changing environment. We find that incompatibilities are likely to accumulate in isolated populations adapting to different environments, consistent with ecological speciation. Incompatibilities also arise when isolated populations face a similar novel environment; these cases of mutation-order speciation are particularly likely when the environment changes rapidly and favors the accumulation of large-effect mutations. In addition, we find that homoploid hybrid speciation is likely to occur either when new environments arise in between the parental environments or when parental populations have accumulated large-effect mutations following a period of rapid adaptation. Our results indicate that periods of rapid environmental change are particularly conducive to speciation, especially mutation-order or hybrid speciation.
  • Joung Hun Lee, Ryo Yamaguchi, Hiroyuki Yokomizo, Mayuko Nakamaru
    JOURNAL OF THEORETICAL BIOLOGY 495 110247 - 110247 0022-5193 2020/06 [Refereed][Not invited]
     
    The evolution of group cooperation is still an evolutionary puzzle and has been studied from the perspective of not only evolutionary ecology but also social sciences. Some socio-ecological problems are caused by collapse of group cooperation. By applying theoretical studies about the evolution of cooperation, we can elucidate what causes the problems and find solutions. One of the appropriate examples is maintaining rice paddy field landscapes, which are a grand spectacle in Asia, and some are UNESCO world heritage sites. These magnificent landscapes and the associated biodiversity are at risk of abandonment for social and financial reasons. Rice paddy fields can be preserved not only by regular cultivation, which requires farmers to invest effort in cultivation, but also by the maintenance of common facilities such as irrigation canals.To investigate how this landscape might be preserved, we developed an agent-based model in which each farmer makes two types of efforts: an effort for land cultivation and an effort for collective action such as common facility maintenance. Additionally, we consider the side effects of rice production such as field deterioration from abandonment and water use competition. These factors determine the utility of each player who imitates the level of efforts necessary to invest in land cultivation and common facility maintenance of one with higher utility. This decision-making of each player can be described by the evolutionary game theory.We find that maintenance effort promotes cultivation effort, but not vice versa, even though we usually consider that each farmer's cultivation effort makes rice field landscape sustainable. We also find that if players and their near neighbors are responsible for maintaining their common facilities together, they continue to maintain them and cultivate, but if all players are responsible for maintaining all facilities in the whole farmland, players are likely to quit facility maintenance and stop cultivation. Competition for water use among all players, however, promotes cultivation more than competition among neighbors only. Therefore, rice paddy field landscapes can be sustainable if neighbors, but not the whole players, are responsible for maintaining their common facilities and cooperate together, and if the water usage of all players, but not neighbors, influences the productivity of each rice field. (C) 2020 Elsevier Ltd. All rights reserved.
  • Toru Nakahara, Junnosuke Horita, Ross D. Booton, Ryo Yamaguchi
    ENTOMOLOGICAL SCIENCE 23 (1) 57 - 65 1343-8786 2020/03 [Refereed][Not invited]
     
    Atrophaneura alcinous adopt multiple strategies such as extra molting, cannibalism and pupal diapause under unfavorable growth conditions. The conditions under which these strategies are adopted have been separately verified, but their relationship has often been overlooked. We examined which strategy A. alcinous adopted and the relative advantages of strategies using four experimental groups under different food quantity and individual density conditions. Our results indicated that A. alcinous often extra-molted, prolonged the larval period, and larval and pupal weights were lighter under food shortage. Cannibalism and disease often occurred under the high density and food shortage condition. We also showed that individuals cannibalized during the prepupal or pupal period were less likely to extra molt before they were killed. Extra molting tended to occur more frequently in females than in males under a shortage of food. In addition, we showed that, when food was insufficient, A. alcinous might initiate pupal diapause under low densities, but not under high densities. These results suggest that A. alcinous prolongs the larval period by engaging in extra molting during times of unfavorable food conditions. This strategy might decrease the risk of cannibalization because surrounding larvae who could potentially cannibalize others pupate before larvae who prolong the larval period pupate. Our results also suggest that diapausing pupae under a shortage of food can only survive when there are few surrounding conspecifics, due to a lower cannibalization risk. In conclusion, there is a complex interaction between extra molting, cannibalism and pupal diapause strategies.
  • 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 2019/12 [Refereed][Not invited]
  • 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 2019/12 [Refereed][Not invited]
  • Ryo Yamaguchi, Takehiko Yamanaka, Andrew M. Liebhold
    THEORETICAL ECOLOGY 12 (2) 197 - 205 1874-1738 2019/06 [Refereed][Not invited]
     
    Initial colonization by non-native species sometimes occurs in regions already occupied by closely related species, and subsequent hybridization is often inevitable. However, there are several different ways that such hybridization might affect the successful establishment of the non-native species, but many of these remain insufficiently explored. Although there is growing evidence in support of improved local adaptation by genetic rescue, we demonstrate here another way that closely related species can facilitate invasions in which hybridization assists the invading species to overcome Allee effects arising from mate-finding failure. We explore this phenomenon using a simple mathematical model of two closely related diploid insect species, native and non-native, exhibiting differences in mate searching efficacy, relative strength of competition, and mate preference. We find that when the carrying capacity in the invading species is higher than in the native species, invasion success is facilitated. Invasion is also facilitated under parameterization for high hybrid fitness and severe competition between natives and hybrids. In light of these results, we discuss general patterns of how invasion success is affected by the manner in which native, non-native, and hybrids interact with each other and note situations where such conditions might occur in nature.
  • Ross Booton, Ryo Yamaguchi, Yoh Iwasa
    POPULATION ECOLOGY 61 (1) 35 - 44 1438-3896 2019/01 [Refereed][Not invited]
     
    Pupa-eating cannibalism occurs naturally in several insect species. Byasa alcinous is a multivoltine species of Red-bodied Swallowtail butterfly found in East Asia, which diapauses as pupa over the winter and whose larvae cannibalize eggs and pupae. We investigate the effects on population dynamics of increasing the asymmetric cannibalistic attack rate of a general insect species in different environmental conditions. We do this by theoretically formulating a generalized system of univoltine and bivoltine larvae over two generations in the spring and summer months. We predict that a lack of resources over the summer can force the population to become entirely univoltine, unless the second-generation bivoltine larvae increase their cannibalistic attack rate, and consume the diapausing pupae from the first generation. The model shows that under extreme environmental conditions, the persistence of univoltine larvae is favoured when faced with the threat of extinction. The model also predicts the conditions for the coexistence of both univoltine and bivoltine larvae, and the degree to which they can both coexist, which decreases as the resource in the second generation increases. This work provides the grounding for future theoretical and experimental consideration of the role of cannibalism in determining insect voltinism.
  • 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 2018/10 [Refereed][Not invited]
  • Ross D Booton, Ryo Yamaguchi, James A R Marshall, Dylan Z Childs, Yoh Iwasa
    Journal of theoretical biology 445 120 - 127 2018/05/14 [Refereed][Not invited]
     
    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.
  • Ryo Yamaguchi, Yoh Iwasa
    JOURNAL OF THEORETICAL BIOLOGY 421 81 - 92 0022-5193 2017/05 [Refereed][Not invited]
     
    More than two loci are involved in reproductive isolation in most cases of putative recent speciation. We study the speciation between two geographically isolated populations connected by infrequent migration, in which incompatibility is controlled by quantitative loci. Incompatibility genetic distance is defined as the fraction of compatibility controlling loci that are different between individuals. Speciation is established when genetic distance reaches a threshold level in spite of occasional migration and subsequent hybridization that reduce genetic distance. With stochastic analysis, we investigate how the time to speciation depends on the manner in which the magnitude of incompatibility increases with genetic distance. Results are: (1) The time to speciation is short if the migration rate is smaller than the mutation rate, or if intermediate levels of genetic distance cause mild incompatibility, making migrants less effective in reducing genetic distance. (2) Genetic distance may fluctuate around a positive quasi-equilibrium level for a long time, and suddenly show a quick passage to speciation when it goes beyond a "tipping point." Notably a gradual increase in incompatibility can result in a sudden and rapid formation of a new species. (3) Speciation becomes very slow if incompatibility is effective for individuals differing at only one locus. These findings provide testable predictions on reproductive traits controlled by specific incompatibility accumulation forms that facilitate the speciation process. (C) 2017 Elsevier Ltd. All rights reserved.
  • Ryo Yamaguchi, Yoh Iwasa
    ROYAL SOCIETY OPEN SCIENCE 4 (2) 160819 - 160819 2054-5703 2017/02 [Refereed][Not invited]
     
    We studied the time to speciation by geographical isolation for a species living on three islands connected by rare migration. We assumed that incompatibility was controlled by a number of quantitative loci and that individuals differing in loci by more than a threshold did not mix genetically with each other. For each locus, we defined the geographical configuration (GC), which specifies islands with common alleles, and traced the stochastic transitions between different GCs. From these results, we calculated the changes in genetic distances. As a single migration event provides an opportunity for transitions in multiple loci, the GCs of different loci are correlated, which can be evaluated by constructing the stochastic differential equations of the number of loci with different GCs. Our model showed that the low number of incompatibility loci facilitates parapatric speciation and that migrants arriving as a group shorten the waiting time to speciation compared with the same number of migrants arriving individually. We also discuss how speciation rate changes with geographical structure.
  • Ryo Yamaguchi, Yoh Iwasa
    JOURNAL OF THEORETICAL BIOLOGY 405 36 - 45 0022-5193 2016/09 [Refereed][Not invited]
     
    We studied the time to speciation by geographic isolation for a species living on two islands connected by infrequent migration. Assumptions were that incompatibility was controlled by a finite number of quantitative loci, and individuals differing in loci of more than some threshold fraction do not mix genetically with each other. We also assumed sexual haploid species, each population being nearly monomorphic, and free recombination between loci for within-population processes. The genetic distance (defined as the fraction of loci differing between populations) followed stochastic processes, which were analyzed by means of stochastic differential equations, diffusion equations, and individual-based simulations. The distance increases by the accumulation of novel mutations but decreases by migration and hybridization. It may converge to a quasi-equilibrium around which it fluctuates thereafter. If the threshold fraction of speciation is controlled, the smallness of the number of incompatibility loci enhanced the magnitude of fluctuation around the quasi-equilibrium and shortened the time to speciation considerably. Novel species were created by mutation accumulation and repeated infrequent migration, and the rate of species creation was the fastest for an intermediate rate of migration. A smaller number of loci increased the optimal migration rate and the species creation rate. (C) 2015 Published by Elsevier Ltd.
  • R Yamaguchi, S Suefuji, K Odagiri, O Yata
    Lepidoptera science 日本鱗翅学会 67 (1) 12 - 21 0024-0974 2016/05 [Refereed][Not invited]
     

    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.

  • Ryo Yamaguchi, Yoh Iwasa
    POPULATION ECOLOGY 57 (2) 343 - 346 1438-3896 2015/04 [Refereed][Not invited]
     
    Many consequences of reproductive interference have important implications in biodiversity conservation policy. After briefly summarizing our comments on the articles in this special feature, we focus on the role of reproductive interference in speciation due to geographic isolation with only infrequent migration between islands (or island-like habitats). As two isolated populations accumulate incompatible genes, they became genetically distinct. When a rare migration occurs from one island to the other, reproductive interference greatly affects its outcome. A paper in this special feature showed that either the migrant or resident population becomes extinct, presumably due to reproductive interference. However, we also found cases in which the migrant and resident populations evolved quickly to avoid mixing, either by character displacement or spatial segregation within the island. To improve our understanding of the dynamics of species diversity, theoretical modeling and empirical studies of reproductive interference immediately after invasion are important targets for future studies.
  • Ryo Yamaguchi, Yoh Iwasa
    INTERFACE FOCUS 3 (6) 20130026 - 20130026 2042-8898 2013/12 [Refereed][Not invited]
     
    Allopatric speciation is a mechanism to evolve reproductive isolation; it is caused by the accumulation of genetic differences between populations while they are geographically isolated. Here, we studied a simple stochastic model for the time until speciation caused by geographical isolation in fragmented populations that experience recurrent but infrequent migration between subpopulations. We assumed that mating incompatibility is controlled by a number of loci that behave as neutral characters in the accumulation of novel mutations within each population. Genetic distance between populations was defined as the number of incompatibility-controlling loci that differ between them. Genetic distance increases through the separate accumulation of mutations in different populations, but decreases after a successful migration event followed by genetic mixing between migrants and residents. We calculated the time to allopatric speciation, which occurs when the genetic distance exceeds a specified threshold. If the number of invasive individuals relative to the resident population is not very large, diffusion approximation provides an accurate prediction. There is an intermediate optimal rate of migration that maximizes the rate of species creation by recurrent invasion and diversification. We also examined cases that involved more than two populations.
  • Ryo Yamaguchi, Yoh Iwasa
    EVOLUTIONARY ECOLOGY RESEARCH 15 (1) 25 - 41 1522-0613 2013/01 [Refereed][Not invited]
     
    Background: Interspecific mating often results in the loss of female reproductive success and can lead to the extinction of a species. In such situations, females evolve a stronger mate preference to avoid heterospecific mating, which promotes pre-mating barriers between species.Questions: What is the magnitude of reproductive character displacement and how large is the damage done by reproductive interference? What is the effect of female mate preference on reproductive character displacement? Can the character displacement prevent extinction of the species?Key assumptions: There are two closely related species whose individuals can mate but whose hybrids are inviable. One, the resident, lives in an isolated area where it is common. Individuals of the other, the invader, regularly migrate to the isolated area. Resident females accept mates based on a male ornament or other secondary sexual trait. Both female preference and the male trait are determined by sex-limited autosomal loci.Methods: Build mathematical models for male and female fitnesses. Analyse the evolution of male and female traits. Deduce the amount of character displacement caused by resident females evolving to prefer males that do not resemble invaders. Deduce the evolutionary change of resident male traits. Determine the effect on character displacement of varying the fitness cost of interspecific mating to the females. Calculate numerically the course of the evolutionary transition as well as the time required to complete it. Study the chance that the invasion will cause the extinction of the resident species.Conclusions: Both the resident male trait and the resident female preference evolve away from the male trait of the invader. The evolutionary shift in the male trait is largest at an intermediate intensity of female mate choice. Equilibrium in male and female traits is maintained by the balance between natural and sexual selection, and the male trait value most preferred by females is more exaggerated than the actual male trait. Sexual dimorphism may evolve if female morphology (as opposed to female preference) remains at the viability optimum. The risk of extinction of the resident species strongly depends on the speed of extinction relative to the time it takes for the adaptation to evolve.

MISC

Books etc

  • How do new species arise?
    Ryo Yamaguchi (Single work)
    Kyoritsu Shuppan 2024/03 (ISBN: 9784320009424)
  • Ryo Yamaguchi, Yoh Iwasa 
    Kyoritsu Shuppan Co., Ltd. 2017/01 (ISBN: 9784320057845) xxv, 223p, 図版 [32] p

Presentations

  • Exploring virus evolution and adaptation through genetic algorithms on fitness landscapes  [Invited]
    Yamaguchi, R
    KSMB-SMB conference  2024/07
  • 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  [Invited]
    山口諒
    第1回生物の基礎探求会  2024/03
  • The phoenix hypothesis of speciation: reproductive isolation among populations experiencing extinction risk  [Invited]
    Yamaguchi, R
    Symposium “Genomics of adaptation and speciation” at The 3rd AsiaEvo Conference  2023/12
  • 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−  [Invited]
    山口諒
    第39回個体群生態学会⼤会  2023/10
  • Integrating speciation over spatial temporal scales  [Invited]
    Yamaguchi, R.
    Integration Of Speciation Research (IOS) workshop  2023/03
  • Macroevolutionary patterns of diversification and implications for species persistence  [Invited]
    Yamaguchi, R.
    Gordon Research Seminar (Speciation 2023)  2023/01
  • 数理モデルで解き明かす種多様性の起源  [Invited]
    山口諒
    第32回⽇本数理⽣物学会⼤会  2022/09
  • Dynamics of speciation rate in an island biogeography framework  [Invited]
    Yamaguchi, R
    第69回日本生態学会大会  2022/03
  • 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  [Invited]
    山口諒, 立木佑弥
    第28回日本数理生物学会年会  2020/09
  • 種間相互作用による地理的分断プロセスの理論と実証  [Invited]
    山口諒
    第67回日本生態学会大会  2020/03
  • 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  [Invited]
    山口諒, 立木佑弥
    第27回日本数理生物学会年会  2019/09
  • Fisher’s geometric model on the likelihood of speciation under different adaptation scenarios  [Invited]
    Yamaguchi, R.
    Gordon Research Seminar (Speciation 2019)  2019/03
  • 種の境界と生物多様性の隠れたパターン  [Invited]
    山口諒
    第66回日本生態学会大会  2019/03
  • 環境適応シナリオの違いと種分化可能性  [Invited]
    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―  2018/09
  • 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  [Invited]
    山口諒
    第65回日本生態学会大会  2018/03
  • Gene flow by human-mediated dispersal: population structure of Aedes aegypti in the Philippines  [Invited]
    Yamaguchi, R.,Tachiki Y.,Minakawa N.,Iwami S.
    IWOMB  2018
  • 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  [Invited]
    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  2017/10
  • Mathematical modeling of an evolutionary radiation and its patterns caused by non-adaptive processes  [Invited]
    山口諒
    第33回個体群生態学会大会  2017/10
  • 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  [Invited]
    山口諒
    日本鱗翅学会九州支部例会  2017/03
  • An increase in gene flow by urbanization: predictions on population structure of Aedes aegypti  [Invited]
    Yamaguchi, R.,Tachiki Y.,Minakawa N.,Iwami S.
    ISEM  2017
  • 連続的な変化がもたらす種の分かれ目  [Invited]
    山口諒
    第63回日本生態学会大会  2016/03
  • Reproductive character displacement by the evolution of female mate choice  [Invited]
    Yamaguchi, R.
    第31回個体群生態学会  2015/10
  • メナドヒメワモンFaunis menadoに見るスラウェシのチョウ相  [Invited]
    山口諒
    日本鱗翅学会第61回大会  2014/10

Association Memberships

  • Society for the Study of Evolution   日本進化学会   日本数理生物学会   個体群生態学会   日本生態学会   

Research Projects

  • An Integrated Theory of Speciation Cycles and Species Diversity through the Lens of Ecology
    日本学術振興会：科学研究費助成事業
    Date (from‐to) : 2024/04 -2028/03 
    Author : Ryo Yamaguchi, Daisuke Aoki
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2023/04 -2026/03 
    Author : Shingo Iwami, Koji Noshita, Ryo Yamaguchi
  • Japan Science and Technology Agency (JST)：ACT-X
    Date (from‐to) : 2022/10 -2025/03 
    Author : Ryo Yamaguchi
  • 日本学術振興会：科学研究費助成事業 若手研究
    Date (from‐to) : 2021/04 -2024/03 
    Author : 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：人材育成事業 海外特別研究員
    Date (from‐to) : 2020/04 -2022/03 
    Author : Ryo Yamaguchi
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2018/04 -2021/03 
    Author : 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.
  • 日本学術振興会：科学研究費助成事業 特別研究員奨励費
    Date (from‐to) : 2017/04 -2020/03 
    Author : 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：科学研究費助成事業 特別研究員奨励費
    Date (from‐to) : 2014/04 -2017/03 
    Author : 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。

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