Biology subjects

Shibasaki, S.

Publications and source records attributed to Shibasaki, S..

12 recordsLinked to original sources

bioRxiv2026

Comparison of evolutionary rescue via biological and cultural evolution

Rapid evolution allows populations to persist in environments where they would otherwise go extinct. This phenomenon, known as evolutionary rescue, is typically studied in the framework of biological evolution, yet adaptive traits can also arise and spread through cultural evolution. The present study developed a stochastic eco-evolutionary model to compare rescue probabilities through biological and cultural evolution. Transmission bias governed the rescue probability under cultural evolution by setting how readily a rare adaptive trait was copied. Conformity bias suppressed population persistence because a rare trait was the least likely to be copied. Content bias toward the adaptive trait enabled evolutionary rescue when social learning was rapid, but it typically yielded a lower rescue probability than biological evolution. Only anticonformity bias, together with a high social learning rate, exceeded the rescue probability of biological evolution by enabling the adaptive trait to be established more rapidly. These results demonstrate that transmission bias alters the demographic consequences of cultural evolution and highlight the importance of transmission processes in evolutionary rescue theory. Understanding how adaptive behaviours are socially transmitted may also improve predictions of animal population persistence and inform conservation efforts in rapidly changing environments.

evolutionary biology↗

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↗

bioRxiv2023

Food web complexity modulates environmental impacts on food chain length

Food chain length (FCL), a crucial aspect of biodiversity, has long been debated for its determinants. Previous studies proposed resource availability, disturbance, and ecosystem size as environmental drivers. However, studies using stable isotope approaches have shown inconsistent results, indicating missing links between environmental drivers and FCL. Here, we hypothesized that species richness and motifs (i.e., 3-species subgraphs) modulated environmental effects on FCL. Combining empirical food webs with our N -species food web model, we found that FCL disproportionately changed at low species richness with saturation at high species richness. This functional response was essential to the interdependent effects of disturbance and ecosystem size in our model. Disturbance more strongly regulated FCL in smaller ecosystems, where species richness was low. Similarly, increasing ecosystem size enhanced FCL under strong, but not weak, disturbance regimes. Our study suggests that internal food web structure should deepen our understanding of how FCL changes over environments.

ecology↗

bioRxiv2022

PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer

BackgroundFluoropyrimidine-based adjuvant chemotherapy is globally recommended for postoperative stage III colon cancer and high-risk stage II patients. However, adjuvant chemotherapy is often associated with severe adverse events and is not highly effective in preventing recurrence. Therefore, a recurrence-prevention biomarker of adjuvant chemotherapy for colorectal cancer is necessary for providing such treatments to appropriate patients. Autophagy (including mitophagy) is activated under chemotherapy-induced stress and contributes to chemotherapy resistance. Expression of autophagy-related genes and their single-nucleotide polymorphisms are reported to be effective predictors of chemotherapy response in some cancers. Our goal was to evaluate the relationship between the single-nucleotide variants of autophagy-related genes and recurrence rates to identify the recurrence-prevention biomarkers of adjuvant chemotherapy in colorectal cancer. MethodsWe analyzed surgical or biopsy specimens from 84 patients who underwent radical surgery followed by fluoropyrimidine-based adjuvant chemotherapy at Saitama Medical University International Medical Center between January and December 2016. Using targeted enrichment sequencing, we identified single-nucleotide variants and insertions/deletions in 50 genes, including autophagy-related genes, and examined their association with colorectal cancer patient relapse rates. ResultsWe detected 560 single-nucleotide variants or insertions/deletions in the target region. The results of Fishers exact test indicated that the recurrence rate of colorectal cancer after adjuvant chemotherapy was significantly lower in patients with the single- nucleotide variants (c.1018G>A [p < 0.005] or c.1562A>C [p < 0.01]) of the mitophagy-related gene PTEN-induced kinase 1. ConclusionsThe two single-nucleotide variants of this mitophagy-related gene may be biomarkers of non-recurrence in colorectal cancer patients who received postoperative adjuvant chemotherapy.

cancer biology↗

bioRxiv2020

Microbial species interactions determine community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

ecology↗

bioRxiv2019

Controlling evolutionary dynamics to optimize microbial bioremediation

Some microbes have a fascinating ability to degrade compounds that are toxic for humans in a process called bioremediation. Although these traits help microbes survive the toxins, carrying them can be costly if the benefit of detoxification is shared by all surrounding microbes, whether they detoxify or not. Detoxification can thereby be seen as a public goods game, where non-degrading mutants can sweep through the population and collapse bioremediation. Here, we constructed an evolutionary game theoretical model to optimize bioremediation in a chemostat initially containing "cooperating" (detoxifying) microbes. We consider two types of mutants: "cheaters" that do not detoxify, and mutants that become resistant to the toxin through private mechanisms that do not benefit others. By manipulating the concentration and flow rate of a toxin into the chemostat, we identified conditions where cooperators can exclude cheaters that differ in their private resistance. However, eventually, cheaters are bound to invade. To overcome this inevitable outcome and maximize detoxification efficiency, cooperators can be periodically reinoculated into the population. Our study investigates the outcome of an evolutionary game combining both public and private goods and demonstrates how environmental parameters can be used to control evolutionary dynamics in practical applications.

evolutionary biology↗

bioRxiv2018

The evolutionary game theory of interspecific mutualism in multi-species communities

Mutualistic interspecific interactions, including Mullerian mimicry and division of labor, are common in nature. In contrast to antagonistic interactions, where faster evolution is favored, mutualism can favor slower evolution under some conditions. This is called the Red King effect. After Bergstrom and Lachmann (2003) proposed Red King effect, it has been investigated in two species models. However, biological examples suggest that the mutualisms can include three or more species. Here, I modeled the evolutionary dynamics of mutualism in communities where there exist two or more species, and all species mutually interact with one another. Regardless of the number of species in the community, it is possible to derive conditions for the stable equilibria. Although there exist nonlinear relationship between the evolutionary rates and the evolutionary fate of each species in the multi-species communities, the model suggests that it is possible to predict whether the faster evolution is favored or disfavored for the relatively fast species; on the other hand, it is difficult to predict the evolutionary fate of relatively slow species because the evolutionary dynamics of the slow species is affected by the evolutionary fate of the fast species.

evolutionary biology↗

bioRxiv2018

Cyclic dominance emerges from the evolution of two cooperative behaviors in the social amoeba

Evolution of cooperation has been one of the most important problems in sociobiology, and many researchers have revealed mechanisms that can facilitate the evolution of cooperation. However, most studies deal only with one cooperative behaviour, even though some organisms perform two or more cooperative behaviours. The social amoeba Dictyostelium discoideum performs two cooperative behaviours in starvation: fruiting body formation and macrocyst formation. Here, we constructed a model that couples these two behaviours, and we found that the two behaviours are maintained due to the emergence of cyclic dominance, although cooperation cannot evolve if only either of the two behaviours is performed. The common chemoattractant cyclic AMP is used in both fruiting body formation and macrocyst formation, providing a biological context for this coupling. Cyclic dominance emerges regardless of the existence of mating types or spatial structure in the model. In addition, cooperation can re-emerge in the population even after it goes extinct. These results indicate that the two cooperative behaviours of the social amoeba are maintained due to the common chemical signal that underlies both fruiting body formation and macrocyst formation. We demonstrate the importance of coupling multiple games when the underlying behaviours are associated with one another.

evolutionary biology↗