Biology subjects

Yamamichi, M.

Publications and source records attributed to Yamamichi, M..

14 recordsLinked to original sources

bioRxiv2026

Rapid trait adaptation has contrasting effects on different dimensions of stability under environmental change

Environmental change alters species growth rates and, through species interactions, can produce complex effects on community functioning and composition. Because functional traits mediate both environmental responses and competition, rapid trait adaptation may modify these effects, but its consequences in multispecies communities remain unclear. We used a trait-based model of competitive communities to test how adaptation affects the mean and diversity of species growth responses to environmental change, and how this influences functional and compositional resistance (how unaffected the community is by the environmental change) and resilience (how well it recovers after it has acclimated to the altered environment). Adaptation altered response variance more strongly than the mean by changing the balance between environmental optimisation and competition-driven trait divergence. As a result, adaptation strongly increased compositional stability, but had less clear effects on abundance. Adaptation also generated a trade-off between resistance and resilience: faster adaptation improved resistance but reduced resilience as communities were displaced less by the environmental change and thus recovered less. Overall, adaptation can be stabilising, but higher adaptation rates do not necessarily produce greater stability across all stability components.

ecology↗

bioRxiv2026

Response diversity can stabilize or destabilize community dynamics depending on the number of insensitive species

Investigating the factors that stabilize biological communities is a central topic in ecology. Response diversity, defined as variation in species responses to environmental change, has been proposed as a key mechanism underlying the biodiversity-ecosystem functional stability (BEFS) relationship, whereby greater species diversity enhances ecological stability. Previous studies have shown that response diversity promotes ecological stability by generating asynchronous population fluctuations and the resulting compensatory dynamics. Although several metrics have been proposed to quantify response diversity, they do not explicitly consider the presence of insensitive species whose performance is unaffected by current environmental conditions. To examine how insensitive species influence response diversity, species persistence, and ecological stability, we conducted numerical simulations of a generalized Lotka-Volterra model under environmental forcing. We first confirmed that increasing variation among sensitive species increased the response diversity index and stabilized community dynamics. We then examined a scenario in which response diversity depended solely on the proportion of sensitive and insensitive species, assuming that all sensitive species responded identically to environmental change. Under this assumption, the response diversity index was maximized when sensitive and insensitive species occurred in equal proportions, whereas increasing the number of sensitive species monotonically destabilized community dynamics. Consequently, the relationship between response diversity and community stability depended on how response diversity was generated, such that higher response diversity could even be associated with lower community stability. These findings demonstrate that overlooking environmentally insensitive species can obscure the mechanisms linking response diversity and ecological stability. More broadly, our results reveal that response diversity comprises at least two distinct biological components--species sensitivity and response variation among sensitive species--that can have contrasting consequences for community stability. We therefore highlight the need to quantify sensitive species empirically and to develop response diversity metrics that distinguish these components. Author SummaryUnderstanding why some communities remain stable despite environmental change is a longstanding goal in ecology. Response diversity, which refers to differences in how species respond to environmental change, has been proposed as a key mechanism explaining why greater biodiversity (species richness) can promote ecological stability. Because species respond differently to changing environments, declines in some species can be compensated by increases in others, helping to stabilize community dynamics. However, previous studies have rarely considered species that are insensitive to current environmental changes. Using a mathematical model, we show that response diversity can arise from two distinct biological components--the number of sensitive species and variation in their responses--and that these components can have contrasting effects on ecological stability. When response diversity reflects variation among sensitive species, greater response diversity stabilizes community dynamics, as expected. In contrast, when response diversity changes only because of the proportions of sensitive and insensitive species, higher response diversity can be associated with lower community stability. Our findings highlight the importance of quantifying the number of sensitive species and developing response diversity metrics that distinguish species sensitivity from variation in responses among sensitive species.

ecology↗

bioRxiv2026

Complexity-multistability relationships: How does species diversity shape the number of alternative stable states?

Ecologists have long investigated how community complexity affects ecological stability, yet how community complexity influences multistability, defined as the presence of alternative stable states, remains poorly understood. We developed a novel framework integrating stochastic community assembly with stability landscape analysis to quantify multistability from species interaction matrices. Using this framework, we systematically explored how species interaction properties shape the relationship between species diversity (species pool size) and the number of alternative stable states. Mean interaction strength was the primary determinant: competitive interactions amplified the positive relationship between species diversity and the number of alternative stable states. In competitive communities, a greater number of alternative stable states was associated with lower community uncertainty, a measure of the long-term unpredictability of community assembly dynamics. These results highlight the importance of characterizing the entire stability landscape. Our framework provides a general approach for understanding and quantifying multistability in complex ecological communities.

ecology↗

bioRxiv2025

Applying invasion criterion to cultural evolution

Cultural diversity is a fundamental aspect of human life and a driver of innovation; however, the underlying mechanisms remain poorly understood. While previous studies focused on how innovation generates cultural diversity, we investigated whether ecological theory, specifically the invasion criterion for understanding species coexistence in community ecology, could predict the maintenance of cultural diversity under various social learning biases. Using mathematical and individual-based models, we showed that the invasion criterion reliably predicts the duration of coexistence in the stochastic dynamics of multiple cultural traits under content-, conformity-, and anticonformity-biased social learning as well as under unbiased learning. The invasion criterion predicted moderate cultural coexistence under two types of model-biased social learning: prestige and success biases. In contrast, similarity-biased social learning, where people tend to learn from those with the same "tag" traits (e.g., gender, language), breaks the predictive power of the invasion criterion because the cultural traits were associated with the tag traits. Our results demonstrate that ecological theory offers valuable tools for understanding cultural evolution, but modifications are required to account for dynamic learning environments. Our model also showed that increasing the number of cultural models can prolong cultural coexistence under certain biases, with implications for fostering innovation and preserving culture. These findings bridge the ecological and cultural evolutionary theories and offer a unified framework for studying diversity maintenance across biological and cultural domains. Significance statementCultural diversity benefits societal innovation and environmental adaptation, but how it is maintained remains unclear. This study applies the invasion criterion, an ecological concept, to predict how long different cultural traits coexist in a population. Simulations and mathematical analyses indicated that this ecological concept is appropriate for many types of social learning but fails for learning from similar individuals. Our mathematical analysis also showed that increasing the number of role models can support or hinder cultural diversity depending on the learning strategy. This work bridges biology and culture and offers new insights into how diversity persists.

evolutionary biology↗

bioRxiv2025

Quantifying a trait-mediated indirect effect of an environmental stressor on population dynamics

Trait-mediated indirect interactions have been intensively studied to understand ecological dynamics in biological communities. Yet, little is known about the relative importance of trait-mediated indirect effects of environmental stressors on population dynamics. How does an environmental stressor indirectly affect the population dynamics of a focal species by altering the traits of interacting species and the strength of interspecific interactions? Here, we quantified the direct and trait-mediated indirect effects of an environmental stressor by combining rotifer-alga experiments and Bayesian parameter estimation of a dynamic model. These days, human activities salinize freshwater lakes globally, thereby increasing the death rates and decreasing birth rates of plankton species. Salinity stress is also known to induce cell clumping in certain phytoplankton species. As larger clumps work as a defense trait against gape-limited predation by zooplankton, the salinity stress can affect zooplankton not only directly but also indirectly through phytoplankton trait changes. We first show that a green alga, Chlamydomonas sphaeroides, formed larger clumps than the two model species of green algae (Chlamydomonas reinhardtii and Chlorella vulgaris) under a moderate salinity stress (0.06M NaCl). Then, by tracking the clump size distributions of Chlamydomonas sphaeroides, we confirmed that small clumps are more vulnerable to predation by rotifers, Brachionus calyciflorus, as previous studies demonstrated. Finally, we co-cultured the green algae and rotifers for a week with and without salinity stress and fitted the Lotka-Volterra predator-prey model. We first estimated how salinity stress increased the rotifer mortality rate using Chlorella vulgaris, which seldom showed clump formation. Then, by using Chlamydomonas sphaeroides, we estimated how salinity stress increased the mortality rate and decreased the attack rate due to clump formation. We found that salinity stress increased the rotifer mortality rate by more than seventeen-fold, and decreased the attack rate on Chlamydomonas sphaeroides to approximately half of that without salinity stress. These results indicate that salinity stress can weaken the predator-prey interaction, and thus salinization can harm freshwater zooplankton species through increasing the mortality rates and decreasing the attack rates. This will be an important step for a quantitative understanding of how environmental stressors can affect community dynamics via trait modifications.

ecology↗

bioRxiv2024

The double-edged effect of environmental fluctuations on evolutionary rescue

Recent studies revealed that contemporary evolution can be rapid enough to prevent population extinction in deteriorating environments through "evolutionary rescue". Researchers have investigated how evolutionary rescue is affected by various factors such as initial population sizes, the amount of genetic variation, and the speed of environmental changes, but few studies focused on environmental fluctuations. As the ongoing global changes are influencing the mean and variance of many environmental variables, it is crucial to explore how environmental fluctuations affect evolutionary rescue for understanding eco-evolutionary dynamics in the wild. Here we show that increasing the amplitude of environmental fluctuations around long-term deteriorating trends has negative and positive effects on evolutionary rescue by analyzing a mathematical model and conducting laboratory experiments on the green alga Chlorella vulgaris under increasing salinity. Increasing the amplitude of environmental fluctuations produces an episode of a huge environmental change, thereby increasing the adaptation lag between the optimal trait value and the population trait mean, which eventually causes population extinction in model simulations. On the other hand, large environmental fluctuations can increase trait variance within a population, potentially promoting adaptive evolution. Indeed, we observed that algal strains that experienced large environmental fluctuations could grow in a harsh environment whereas strains that experienced smaller or no environmental fluctuations could not. These results suggest that we will be able to promote or prohibit evolutionary rescue in nature by carefully considering the double-edged effect of environmental fluctuations on evolutionary rescue.

evolutionary biology↗

bioRxiv2024

A single episode of sexual reproduction can prevent population extinction under multiple stressors

Recent studies have shown that organisms can adapt to changing environments through rapid contemporary evolution. Although intraspecific genetic variation is necessary for rapid evolution to occur, little is known how genetic variation has been produced and maintained before rapid evolution. Here we show that a single episode of sexual reproduction can produce a large amount of intraspecific trait variation that allows population growth in degraded environments by laboratory experiments of a green alga, Closterium peracerosum-strigosum-littorale complex. We observed population dynamics of the alga under multiple stressors and confirmed that high salinity and low pH decreased population growth rates. By comparing parental and their hybrid F1 populations, we observed larger variation in population growth rates of F1 populations (i.e., transgressive segregation) when pH was low. Interestingly, even when parental populations had negative growth rates, some F1 populations showed positive growth rates in severe environmental conditions due to the large variation in population growth. By utilizing the recently obtained genomic information of the alga, we found greater enrichment of genes with copy number variations in terms related to pH stress than those to salt stress in a gene ontology (GO) enrichment analysis. Our results suggest that recombination and variation in the number of gene copies might produce large genetic variation in the F1 generation. This will be an important step toward a better understanding of evolutionary rescue, where rapid evolution prevents population extinction in changing environments.

evolutionary biology↗

bioRxiv2023

Facilitative interaction networks in experimental microbial community dynamics

Understanding potential roles of facilitative interactions between species is one of the major challenges in ecology and microbiology. However, we still have limited knowledge of entangled webs of facilitative interactions in ecosystems. By compiling whole-genome shotgun metagenomic data of an experimental microbial community, we tested the hypothesis that architecture of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.

ecology↗

bioRxiv2023

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we show that community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was explained by the magnitude of gene-repertoire overlaps among bacterial species. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

microbiology↗

bioRxiv2022

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics

Microbiome dynamics are both crucial indicators and drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. We here integrate theoretical and empirical bases for anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We then confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the energy landscape analysis of statistical physics or that of a stability index of nonlinear mechanics. These results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems.

ecology↗

bioRxiv2021

How does the magnitude of genetic variation affect eco-evolutionary dynamics in character displacement?

AO_SCPLOWBSTRACTC_SCPLOWWhile previous studies on character displacement tended to focus on trait divergence and convergence as a result of long-term evolution, recent studies suggest that character displacement can be a special case of evolutionary rescue, where rapid evolution prevents population extinction by weakening negative interspecific interactions. When the magnitude of genetic variation is small, however, the speed of trait divergence can be slow and populations may go extinct before the completion of character displacement. Here we analyzed a simple model to examine how the magnitude of genetic variation affects evolutionary rescue via ecological and reproductive character displacement that weakens resource competition and reproductive interference, respectively. We found that the large additive genetic variance is more important for preventing extinction in reproductive character displacement than in ecological character displacement. This is because reproductive interference produces a locally stable coexistence equilibrium with positive frequency-dependence (i.e., minority disadvantage) whereas ecological character displacement results in a globally stable coexistence equilibrium. Furthermore, population extinction becomes less likely when ecological and reproductive character displacement occur simultaneously due to positive covariance between ecological and reproductive traits. Our results suggest that while reproductive character displacement may be rarer than ecological character displacement, it is more likely to occur when there exists positive trait covariance, such as the case of a magic trait in reinforcement of speciation processes.

ecology↗

bioRxiv2020

Rapid evolution promotes fluctuation-dependent species coexistence

AO_SCPLOWBSTRACTC_SCPLOWRecent studies have demonstrated that rapid contemporary evolution can play a significant role in regulating population dynamics on ecological timescales. Here we identify a previously unrecognized mode by which rapid evolution can promote species coexistence via temporal fluctuations and a trade-off between competitive ability and the speed of adaptive evolution. We show that this interaction between rapid evolution and temporal fluctuations not only increases the range of coexistence conditions under a gleaner-opportunist trade-off (i.e., low minimum resource requirement [R*] vs. high maximum growth rate), but also yields stable coexistence in the absence of a classical gleaner-opportunist trade-off. Given the propensity for both oscillatory dynamics and divergent rates of adaptation (including rapid evolution and phenotypic plasticity) in the real world, we argue that this expansion of fluctuation-dependent coexistence theory provides an important overlooked solution to the so-called paradox of the plankton.

ecology↗

bioRxiv2019

Antagonistic coevolution between multiple quantitative traits: matching interactions can be subsets of difference interactions

AO_SCPLOWBSTRACTC_SCPLOWCoevolution is one of the major drivers of complex dynamics in population ecology. Historically, antagonistic coevolution in victim-exploiter systems has been a topic of special interest, and involves traits with various genetic architectures (e.g., the number of genes involved) and effects on interactions. For example, exploiters may need to have traits that \"match\" those of victims for successful exploitation (i.e., a matching interaction), or traits that exceed those of victims (i.e., a difference interaction). Different models exist which are appropriate for different types of traits, including Mendelian (discrete) and quantitative (continuous) traits. For models with multiple Mendelian traits, recent studies have shown that antagonistic coevolutionary patterns that appear as matching interactions can arise due to multiple difference interactions with costs of having large trait values. Here we generalize their findings to quantitative traits and show, analogously, that the multidimensional difference interactions with costs sometimes behave qualitatively the same as matching interactions. While previous studies in quantitative genetics have used the dichotomy between matching and difference frameworks to explore coevolutionary dynamics, we suggest that exploring multidimensional trait space is important to examine the generality of results obtained from one-dimensional traits.

evolutionary biology↗

bioRxiv2017

When rarity has costs: coexistence under positive frequency-dependence and environmental stochasticity

Stable coexistence relies on negative frequency-dependence, in which rarer species invading a patch benefit from a lack of conspecific competition experienced by residents. In nature, however, rarity can have costs, resulting in positive frequency-dependence (PFD) particularly when species are rare. Many processes can cause positive frequency-dependence, including a lack of mates, mutualist interactions, and reproductive interference from heterospecifics. When species become rare in the community, positive frequency-dependence creates vulnerability to extinction, if frequencies drop below certain thresholds. For example, environmental fluctuations can drive species to low frequencies where they are then vulnerable to PFD. Here, we analyze deterministic and stochastic mathematical models of two species interacting through both PFD and resource competition in a Chessonian framework. Reproductive success of individuals in these models is reduced by a product of two terms: the reduction in fecundity due to PFD, and the reduction in fecundity due to competition. Consistent with classical coexistence theory, the effect of competition on individual reproductive success exhibits negative frequency-dependence when individuals experience greater intraspecific competition than interspecific competition i.e., niche overlap is less than one. In the absence of environmental fluctuations, our analysis reveals that (1) a synergistic effect of PFD and niche overlap that hastens exclusion, (2) trade-offs between susceptibility to PFD and maximal fecundity can mediate coexistence, and (3) coexistence, when it occurs, requires that neither species is initially rare. Analysis of the stochastic model highlights that environmental fluctuations, unless perfectly correlated, coupled with PFD ultimately drive one species extinct. Over any given time frame, this extinction risk decreases with the correlation of the demographic responses of the two species to the environmental fluctuations, and increases with the temporal autocorrelation of these fluctuations. For species with overlapping generations, these trends in extinction risk persist despite the strength of the storage effect decreasing with correlated demographic responses and increasing with temporal autocorrelations. These results highlight how the presence of PFD may alter the outcomes predicted by modern coexistence mechanisms.

ecology↗