Journal of Theoretical Biology最新文献

{"title":"Bounded environmental stochasticity generates secondary Allee thresholds","authors":"Sebastian J. Schreiber","doi":"10.1016/j.jtbi.2025.112228","DOIUrl":"10.1016/j.jtbi.2025.112228","url":null,"abstract":"<div><div>A population exhibits an Allee effect when there is a critical density below which it goes extinct and above which it persists. Classical models with environmental stochasticity predict inevitable extinction, stemming from the assumption that environmental variation is normally distributed with rare but arbitrary large effect sizes. However, environmental fluctuations are bounded and often not normally distributed. To address this reality, I analyze piecewise deterministic Markov models (PDMPs) of populations experiencing Allee effects, where environmental dynamics are governed by a finite-state Markov chain. These models predict that populations can persist through the emergence of two threshold densities. Below the lower threshold, populations deterministically go extinct; above the higher threshold, they deterministically persist. At intermediate densities, populations experience stochastic bistability: with positive, complementary probabilities, they either go extinct or persist. Persistence becomes impossible when the carrying capacity in one environment falls below the Allee threshold in another. Such mismatch occurs only when the environmental state affects per-capita growth rates non-monotonically, as when environments supporting higher carrying capacities also produce higher predation levels or greater mate limitation. This work demonstrates that incorporating realistic bounded environmental fluctuations substantially alters predictions about population persistence, with important implications for conservation and management.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"614 ","pages":"Article 112228"},"PeriodicalIF":2.0,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fitness landscapes of simple regulatory genetic interactions show pervasive heterozygote advantage and support stable polymorphism","authors":"Adam H. Porter ,&nbsp;Norman A. Johnson ,&nbsp;Alexander Y. Tulchinsky","doi":"10.1016/j.jtbi.2025.112233","DOIUrl":"10.1016/j.jtbi.2025.112233","url":null,"abstract":"<div><div>Although the regulation of gene expression is a fundamental link between genotype, phenotype, and fitness, little is known about how natural selection drives its evolution. To address this gap, we used a biophysical (thermodynamic) model of molecular interactions between allelic variants of transcription factors (TFs) and their <em>cis</em>-regulatory binding sites. We generated diploid genotype-phenotype maps for gene expression. We then applied a Gaussian fitness function to these maps, where the environment determines optimal expression level. The corresponding genotype-fitness landscapes are characterized by high ridges of heterozygote superiority. Heterozygote advantage occurs whenever the environmentally determined phenotypic optimum lies between the phenotypes of the two homozygotes.</div><div>To determine whether this superiority could lead to stable polymorphism, for each of 201 optimal expression levels we determined frequency-fitness landscapes (allele frequency vs. fitness) for all allelic combinations; maximized their population mean fitnesses; identified combinations with globally maximal mean fitness; and found their equilibrium allele frequencies. Globally stable polymorphisms occurred whenever the phenotypic optimum laid between the phenotypes of the best two homozygotes. Stable polymorphisms occupied 49–75% of the range of optimal expression levels, depending on biophysical and fitness parameters. Virtually all included TF polymorphism, with binding site co-polymorphisms across 33–55% of the range. Neutral polymorphisms were also widely distributed. Neither molecular complexity of the TF-<em>cis</em> interaction nor pleiotropic constraint had qualitative effects on polymorphism. However, genetic load was negatively correlated with molecular complexity, suggesting that reducing genetic load may be an important mechanism for increasing the complexity of regulatory genetic interactions.</div><div>While this analysis assumes environmental homogeneity, the results suggest that this phenomenon may enhance the role of environmental heterogeneity in maintaining regulatory polymorphism. Selection favors the maintenance of polymorphism not just because different homozygotes have higher fitness in different environments, but also because heterozygote advantage can act as a ‘storage effect’ by promoting regulatory polymorphism during the transitions between environmental states.</div><div>We use the model to make predictions about future evolutionary trajectories in a well-documented case of regulatory heterozygote advantage involving flower color in an Alpine orchid. More empirical research on the extent and maintenance of regulatory polymorphism within populations is needed.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"614 ","pages":"Article 112233"},"PeriodicalIF":2.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging short- and long-distance dispersal in individual animal movement","authors":"Danish A. Ahmed ,&nbsp;Sergei V. Petrovskii ,&nbsp;Joseph D. Bailey ,&nbsp;Michael B. Bonsall ,&nbsp;Phillip J. Haubrock","doi":"10.1016/j.jtbi.2025.112227","DOIUrl":"10.1016/j.jtbi.2025.112227","url":null,"abstract":"<div><div>Random walks (RW) provide a useful modelling framework for the movement of animals at an individual level. If the RW is uncorrelated and unbiased such that the direction of movement is completely random, the dispersal is characterised by the statistical properties of the probability distribution of step lengths, or the dispersal kernel. Whether an individual exhibits short- or long-distance dispersal can be distinguished by the rate of asymptotic decay in the end-tail of the distribution of step-lengths. If the decay is exponential or faster, referred to as a thin-tail, then the step length variance is finite – as occurs in Brownian motion. On the other hand, inverse power-law step length distributions have a heavy end-tail with slower decay, resulting in an infinite step length variance, which is the hallmark of a Lévy walk. In theoretical studies of individual animal movement, various approaches have been employed to connect these dispersal mechanisms, yet they are often ad hoc. We provide a more robust method by ensuring that the survival probability, that is the probability of occurrence of steps longer than a certain threshold is the same for both distributions. Furthermore, the dispersal kernels are then standardised by adjusting the probability to minimise disparities between these distributions. By assuming the same survival probability for movement paths with commonly used thin- and heavy-tailed step length distributions, we form a relationship between the short- and long-distance dispersal of animals in different spatial dimensions. We also demonstrate how our findings can be applied in different ecological contexts, to relate dispersal kernels within theoretical models for boundary effects and spatio-temporal population dynamics. Moreover, we show that the relationship between these dispersal kernels can drastically affect the outcomes across various ecological scenarios.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"614 ","pages":"Article 112227"},"PeriodicalIF":2.0,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The consequence of uneven walking transitory modulation strategies: A simulation-based approach","authors":"Seyed-Saleh Hosseini-Yazdi ,&nbsp;John EA Bertram","doi":"10.1016/j.jtbi.2025.112234","DOIUrl":"10.1016/j.jtbi.2025.112234","url":null,"abstract":"<div><div>Human gait control involves regulating multiple parameters, particularly when navigating uneven terrain. Terrain perturbations can introduce substantial challenges. While the regulation of total step mechanical work across multiple steps has been studied, other observed measures of gait adjustment remain less explored. Using an analytical model, we examined the center of mass (COM) mechanical work and step frequency cost to evaluate the mechanistic implications of transitory step adjustment strategies reported in the literature. Since COM work represents most walking energetics, mechanical analysis shows a specific threshold for which the cost of going atop a perturbation and extending the step length are equal. The same could be observed when the total cost (work and frequency) is examined. Thus, beyond the point of equilibrium, the strategy with less metabolic cost must be favorable. As this evaluation is based on a Just-in-Time walking strategy, extended lookahead horizon on less complicated terrains may change the preference. Our simulations reveal that transient step length reduction with nominal push-off has less collisional dissipation and, as such, elevated walking momentum post step transition. This strategy can compensate for lost momentum atop terrain perturbations yet, it is costlier than push-off regulation. Hence, it might instead be for foothold selection. An extended step may also be utilized when momentum reduction is needed. Additionally, simulations showed that effective leg length adjustment can not only alter the step length but may also limit COM elevation changes. It in turn limits the work against gravity or perhaps limb loading due to elevated collisions. Therefore, step length adjustments, achieved either by adopting different gait strategies or by controlling the effective leg length, are noted as possible complementary approaches to modulating the magnitude of the push-off and preparation to vault atop a perturbation. We also evaluated the anticipatory control traits of older adults, who are more vulnerable to falls on uneven terrain. Older adults demonstrated a transitory speed decrease before encountering perturbation. This might be an indication that older adults require extra time to select a secure foothold. Even without penalty for the lost time of deceleration, to achieve the average speed after a terrain perturbation encounter, we observe materially increased total mechanical work when the walker slows down just before a perturbation. This added cost likely contributes to the higher mechanical work observed in older adults when walking. Elevated mechanical work demand may contribute to fall incidents in older adults when they are not able to perform adequately.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"614 ","pages":"Article 112234"},"PeriodicalIF":2.0,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time-delay enhanced SIR model for COVID-19 waves in Mexico: Parameter estimation using evolutionary algorithms","authors":"Anahí Flores-Pérez ,&nbsp;Marcos A. González-Olvera ,&nbsp;Gustavo Chávez-Peña ,&nbsp;Ana G. Gallardo-Hernández ,&nbsp;Lizeth Torres","doi":"10.1016/j.jtbi.2025.112229","DOIUrl":"10.1016/j.jtbi.2025.112229","url":null,"abstract":"<div><div>In this work, we analyze the progression of COVID-19 across six distinct epidemic waves in Mexico using a time-delay SIR model, focusing specifically on whether the inclusion of incubation and recovery delays into the classical SIR framework enhances the model’s ability to capture the complex dynamics observed in epidemic data. To achieve robust and reliable estimation of both model parameters and time delays despite the inherent uncertainties present in pandemic data, we employ Particle Swarm Optimization (PSO) and Genetic Algorithms (GA). The performance of these optimization methods is assessed by examining their effectiveness in accurately reconstructing parameters across varying data with noise and uncertainties. Our findings indicate that both PSO and GA yield robust parameter and time-delay estimations even under scenarios where data have uncertainties, highlighting the critical role that time delays play in realistically modeling epidemic dynamics. The obtained results provide valuable insights into COVID-19 transmission patterns in Mexico and demonstrate the practical advantages of evolutionary algorithms for epidemic model calibration.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"613 ","pages":"Article 112229"},"PeriodicalIF":2.0,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144745913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the onset of multicellular invasive behavior in hierarchical lineage: The role of inhibitory feedback and local fluctuations","authors":"Josué Manik Nava-Sedeño ,&nbsp;Abraham Martínez ,&nbsp;Haralampos Hatzikirou","doi":"10.1016/j.jtbi.2025.112220","DOIUrl":"10.1016/j.jtbi.2025.112220","url":null,"abstract":"<div><div>The emergence of multicellular invasive behavior is a key characteristic of various biological processes, including wound healing, development, and tissue regeneration. In this study, we develop a lattice-gas cellular automaton (LGCA) model to explore the role of inhibitory feedback in the invasive behavior of a hierarchical lineage composed of stem cells and differentiated cells. We consider both non-spatial and spatial stochastic models to investigate how spatial interactions influence invasion dynamics. Our findings suggest that inhibitory feedback from differentiated cells significantly impacts the invasive potential of stem cells. In addition, local fluctuations induce unstable fronts that move with relatively low speed. Finally, we explore the implications of our work for understanding the regulation of multicellular dynamics in various pathophysiological contexts.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"613 ","pages":"Article 112220"},"PeriodicalIF":2.0,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stability and reactivity of food webs with trophic interactions","authors":"Xiaoting Liu ,&nbsp;Maoxing Liu ,&nbsp;Donghua Zhao ,&nbsp;Yongzheng Sun","doi":"10.1016/j.jtbi.2025.112216","DOIUrl":"10.1016/j.jtbi.2025.112216","url":null,"abstract":"<div><div>Ecosystems are increasingly vulnerable to species extinctions and functional disruptions driven by climate change and anthropogenic pressures. Although significant progress has been made in understanding the stability and reactivity of ecosystems, the influence of functionally distinct species groups remains underexplored. Here, we develop a food web model that incorporates producers, consumers, decomposers, and detritus, effectively capturing key characteristics of real food webs. By simulating ecologically realistic perturbations-including species loss, interaction loss, and changes in interaction strength-we examine how trophic structure shapes the stability and reactivity of food webs. We demonstrate that stability and reactivity are not determined solely by species richness or network connectivity, but are critically influenced by the functional roles of species. Shifts in interaction strength can trigger phase transitions in food webs. Our results reveal that, compared to other taxa, variations in the interaction strength of consumer taxa pose a greater threat to the overall state of food webs, increasing the likelihood of reactive or unstable dynamics. Finally, we propose that enhancing self-regulation and managing species abundances can promote ecosystem resilience and mitigate large-scale species loss under persistent disturbances. This work offers a functional perspective on ecosystem stability and reactivity, and provides new insights for the conservation and restoration of food webs.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"613 ","pages":"Article 112216"},"PeriodicalIF":2.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How population control of pests is modulated by density dependence: The perspective of genetic biocontrol","authors":"Cole D. Butler,&nbsp;Alun L. Lloyd","doi":"10.1016/j.jtbi.2025.112215","DOIUrl":"10.1016/j.jtbi.2025.112215","url":null,"abstract":"<div><div>Managing pest species relies critically on mechanisms that regulate population dynamics, particularly those factors that change with population size. These density-dependent factors can help or hinder control efforts and are especially relevant considering recent advances in genetic techniques that allow for precise manipulation of the timing and sex-specificity of population suppression. Despite this importance, density dependence is often poorly characterized owing to limited data and an incomplete understanding of organism development. To address this issue, we construct and analyze a mathematical model of a pest population with a general control under a wide range of density dependence scenarios. Using this model, we investigate how control performance is affected by the strength of density dependence. By modifying the timing and sex-specificity of the control, we tailor our analysis to simulate different pest control strategies, including conventional and genetic biocontrol methods. We pay particular attention to the latter, using case studies to explore specific examples with an extended version of the baseline model that includes genetic dynamics. Finally, we clarify past work on mechanistic models with flawed derivations that do not exhibit overcompensatory density dependence. We find substantial differences in control performance for differing strengths of density dependence, with populations exhibiting strong density dependence being most resilient to suppression. However, these results change with the size and timing of the control load, as well as the target sex. Interestingly, we also find that the strength of density dependence affects population invasion by certain genetic biocontrol strategies. While the model is parameterized using the life history traits of the yellow fever mosquito, <em>Aedes aegypti</em>, the principles developed here apply to many pest species. We conclude by discussing the implications of density dependence timing and strength for suppression of pest populations.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"614 ","pages":"Article 112215"},"PeriodicalIF":2.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Infections are not alike: The effects of covariation between individual susceptibility and transmissibility on epidemic dynamics","authors":"Jeremy D. Harris ,&nbsp;Esther Gallmeier ,&nbsp;Jonathan Dushoff ,&nbsp;Stephen J. Beckett ,&nbsp;Joshua S. Weitz","doi":"10.1016/j.jtbi.2025.112211","DOIUrl":"10.1016/j.jtbi.2025.112211","url":null,"abstract":"<div><div>Individual-level variation in susceptibility to infection and transmissibility of infection can affect population-level dynamics in epidemic outbreaks. Prior work has incorporated independent variation in susceptibility or transmissibility of individuals into epidemic compartmental models. Here, we develop and assess a mathematical framework that includes covariation in susceptibility and transmissibility. We show that uncorrelated variation in susceptibility and transmissibility leads to an effective transmissibility distribution that has a constant coefficient of variation such that the epidemic dynamics match those with variation in susceptibility alone, providing a baseline for comparison across different correlation structures. Increasing the correlation between susceptibility and transmissibility increases both the speed and strength of the outbreak – and is indicative of outbreaks which might be strongly structured by contact rate variation. In contrast, negative correlations between susceptibility and transmissibility lead to overall weaker outbreaks – with the caveat that the strength of effective transmission increases over time. In either case, correlations can shift the transmissibility distribution, thereby modifying the speed of the epidemic as the susceptible population is depleted. Overall, this work demonstrates how (often unaccounted) covariation in susceptibility and transmission can shape the course of outbreaks and final outbreak sizes.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"613 ","pages":"Article 112211"},"PeriodicalIF":2.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “An optimal network that promotes the spread of an advantageous variant in an SIR epidemic”. [J. Theor. Biol. 605 (2025) 112095]","authors":"Samuel Lopez ,&nbsp;Natalia L. Komarova","doi":"10.1016/j.jtbi.2025.112217","DOIUrl":"10.1016/j.jtbi.2025.112217","url":null,"abstract":"","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"613 ","pages":"Article 112217"},"PeriodicalIF":1.9,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}