Theoretical Population Biology最新文献_第2页

Effect of competition on emergent phases and phase transitions in competitive systems 竞争对竞争系统中涌现阶段和相变的影响。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.12.003

Shikun Wang , Yuanshi Wang , Hong Wu

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The impact of simultaneous infections on phage-host ecology 同时感染对噬菌体-宿主生态的影响。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.12.002

Jaye Sudweeks , Christoph Hauert

{"title":"The impact of simultaneous infections on phage-host ecology","authors":"Jaye Sudweeks , Christoph Hauert","doi":"10.1016/j.tpb.2024.12.002","DOIUrl":"10.1016/j.tpb.2024.12.002","url":null,"abstract":"<div><div>Phages use bacterial host resources to replicate, intrinsically linking phage and host survival. To understand phage dynamics, it is essential to understand phage-host ecology. A key step in this ecology is infection of bacterial hosts. Previous work has explored single and multiple, sequential infections. Here we focus on the theory of simultaneous infections, where multiple phages simultaneously attach to and infect one bacterial host cell. Simultaneous infections are a relevant infection dynamic to consider, especially at high phage densities when many phages attach to a single host cell in a short time window. For high bacterial growth rates, simultaneous infection can result in bi-stability: depending on initial conditions phages go extinct or co-exist with hosts, either at stable densities or through periodic oscillations of a stable limit cycle. This bears important consequences for phage applications such as phage therapy: phages can <em>persist</em> even though they cannot <em>invade</em>. Consequently, through spikes in phage densities it is possible to infect a bacterial population even when the phage basic reproductive number is less than one. In the regime of stable limit cycles, if timed right, only small densities of phage may be necessary.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"161 ","pages":"Pages 42-49"},"PeriodicalIF":1.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142899634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Selection for altruistic defense in structured populations 结构化种群中利他主义防御的选择。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.11.001

Felix Jordan , Martin Hutzenthaler , Dirk Metzler

{"title":"Selection for altruistic defense in structured populations","authors":"Felix Jordan , Martin Hutzenthaler , Dirk Metzler","doi":"10.1016/j.tpb.2024.11.001","DOIUrl":"10.1016/j.tpb.2024.11.001","url":null,"abstract":"<div><div>We model natural selection for or against an anti-parasite (or anti-predator) defense allele in a host (or prey) population that is structured into many demes. The defense behavior has a fitness cost for the actor compared to non defenders (“cheaters”) in the same deme and locally reduces parasite growth rates. Hutzenthaler et al. (2022) have analytically derived a criterion for fixation or extinction of defenders in the limit of large populations, many demes, weak selection and slow migration. Here, we use both individual-based and diffusion-based simulation approaches to analyze related models. We find that the criterion still leads to accurate predictions for settings with finitely many demes and with various migration patterns.</div><div>A key mechanism of providing a benefit of the defense trait is genetic drift due to randomness of reproduction and death events leading to between-deme differences in defense allele frequencies and host population sizes. We discuss an inclusive-fitness interpretation of this mechanism and present <em>in-silico</em> evidence that under these conditions a defense trait can be altruistic and still spread in a structured population.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"161 ","pages":"Pages 13-24"},"PeriodicalIF":1.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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社论。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2025-02-01 DOI: 10.1016/j.tpb.2024.12.001

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Species coexistence as an emergent effect of interacting mechanisms 物种共存是相互作用机制的一种涌现效应。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2025-01-14 DOI: 10.1016/j.tpb.2024.12.005

Thomas Seidelmann, Sanaz Mostaghim

{"title":"Species coexistence as an emergent effect of interacting mechanisms","authors":"Thomas Seidelmann, Sanaz Mostaghim","doi":"10.1016/j.tpb.2024.12.005","DOIUrl":"10.1016/j.tpb.2024.12.005","url":null,"abstract":"<div><div>Although extensively studied, the maintenance of biodiversity remains a highly debated and investigated topic of contemporary research in ecology. Several studies have quantified the contributions of various coexistence mechanisms to biodiversity. However, often stochastic individual-level interactions are abstracted away, or mechanisms are studied in isolation. The intertwined nature and reciprocal influences between mechanisms, as they arise from individual-level interactions, are therefore rarely considered. We propose a novel mechanistic simulation model grounded in neutral theory to capture and quantify emergent effects arising from such mechanism interactions. Three coexistence mechanisms are supported: storage effect, intransitivity, and resource partitioning. We show that basic neutral dynamics and related models of isolated mechanisms can be replicated. Beyond that, we observe difficult to predict, yet significant emergent effects for mechanism combinations. In some cases, coexistence times could be extended more than tenfold compared to the individual mechanisms’ performances. Our findings suggest that studies of individual coexistence mechanisms might be insufficient and indeed misleading for quantifying their overall impact on biodiversity. The particular combination of mechanisms and their interactions appear to be of vital importance.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"162 ","pages":"Pages 13-21"},"PeriodicalIF":1.2,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143014957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Catching a wave: On the suitability of traveling-wave solutions in epidemiological modeling 赶上浪潮：论行波解在流行病学建模中的适用性。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-12-27 DOI: 10.1016/j.tpb.2024.12.004

Anna M. Langmüller , Joachim Hermisson , Courtney C. Murdock , Philipp W. Messer

{"title":"Catching a wave: On the suitability of traveling-wave solutions in epidemiological modeling","authors":"Anna M. Langmüller , Joachim Hermisson , Courtney C. Murdock , Philipp W. Messer","doi":"10.1016/j.tpb.2024.12.004","DOIUrl":"10.1016/j.tpb.2024.12.004","url":null,"abstract":"<div><div>Ordinary differential equation models such as the classical SIR model are widely used in epidemiology to study and predict infectious disease dynamics. However, these models typically assume that populations are homogeneously mixed, ignoring possible variations in disease prevalence due to spatial heterogeneity. To address this issue, reaction–diffusion models have been proposed as an alternative approach to modeling spatially continuous populations in which individuals move in a diffusive manner. In this study, we explore the conditions under which such spatial structure must be explicitly considered to accurately predict disease spread, and when the assumption of homogeneous mixing remains adequate. In particular, we derive a critical threshold for the diffusion coefficient below which disease transmission dynamics exhibit spatial heterogeneity. We validate our analytical results with individual-based simulations of disease transmission across a two-dimensional continuous landscape. Using this framework, we further explore how key epidemiological parameters such as the probability of disease establishment, its maximum incidence, and its final epidemic size are affected by incorporating spatial structure into SI, SIS, and SIR models. We discuss the implications of our findings for epidemiological modeling and identify design considerations and limitations for spatial simulation models of disease dynamics.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"162 ","pages":"Pages 1-12"},"PeriodicalIF":1.2,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Aggregation unveiled: A sequential modelling approach to bark beetle outbreaks 聚集揭幕：树皮甲虫爆发的连续建模方法。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-11-08 DOI: 10.1016/j.tpb.2024.10.002

Mahdi Salehzadeh, John M. Stockie, Ailene MacPherson

{"title":"Aggregation unveiled: A sequential modelling approach to bark beetle outbreaks","authors":"Mahdi Salehzadeh, John M. Stockie, Ailene MacPherson","doi":"10.1016/j.tpb.2024.10.002","DOIUrl":"10.1016/j.tpb.2024.10.002","url":null,"abstract":"<div><div>Tree-killing bark beetle infestations are a cause of massive coniferous forest mortality impacting forest ecosystems and the ecosystem services they provide. Models predicting bark beetle outbreaks are crucial for forest management and conservation, necessitating studies of the effect of epidemiological traits on the probability and severity of outbreaks. Due to the aggregation behaviour of beetles and host tree defence, this epidemiological interaction is highly non-linear and outbreak behaviour remains poorly understood, motivating questions about when an outbreak can occur, what determines outbreak severity, and how aggregation behaviour modulates these quantities. Here, we apply the principle of distributed delays to create a novel and mathematically tractable model for beetle aggregation in an epidemiological framework. We derive the critical outbreak threshold for the beetle emergence rate, which is a quantity analogous to the basic reproductive ratio, <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>, for epidemics. Beetle aggregation qualitatively impacts outbreak potential from depending on the emergence rate alone in the absence of aggregation to depending on both emergence rate and initial beetle density when aggregation is required. Finally, we use a stochastic model to confirm that our deterministic model predictions are robust in finite populations.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"160 ","pages":"Pages 62-69"},"PeriodicalIF":1.2,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An almost infinite sites model 几乎无限的场地模型

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-10-23 DOI: 10.1016/j.tpb.2024.10.001

Alejandra Avalos-Pacheco , Mathias C. Cronjäger , Paul A. Jenkins , Jotun Hein

{"title":"An almost infinite sites model","authors":"Alejandra Avalos-Pacheco , Mathias C. Cronjäger , Paul A. Jenkins , Jotun Hein","doi":"10.1016/j.tpb.2024.10.001","DOIUrl":"10.1016/j.tpb.2024.10.001","url":null,"abstract":"<div><h3>Motivation:</h3><div>A main challenge in molecular evolution is to find computationally efficient mutation models with flexible assumptions that properly reflect genetic variation. The infinite sites model assumes that each mutation event occurs at a site never previously mutant, i.e. it does not allow recurrent mutations. This is reasonable for low mutation rates and makes statistical inference much more tractable. However, recurrent mutations are common enough to be observable from genetic variation data, even in species with low per-site mutation rates such as humans. The finite sites model on the other hand allows for recurrent mutations but is computationally unfeasible to work with in most cases. In this work, we bridge these two approaches by developing a novel molecular evolution model, the almost infinite sites model, that both admits recurrent mutations and is tractable. We provide a recursive characterization of the likelihood of our proposed model under complete linkage and outline a parsimonious approximation scheme for computing it.</div></div><div><h3>Results:</h3><div>We show the usefulness of our model in simulated and human mitochondrial data. Our results show that the AISM, in combination with a constraint on the total number of mutation events, can recover accurate approximations to the maximum likelihood estimator of the mutation rate.</div></div><div><h3>Availability and implementation:</h3><div>An implementation of our model is freely available along with code for reproducing our computational experiments at <span><span>https://github.com/Cronjaeger/almost-infinite-sites-recursions</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"160 ","pages":"Pages 49-61"},"PeriodicalIF":1.2,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142511627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sharp habitat shifts, evolutionary tipping points and rescue: Quantifying the perilous path of a specialist species towards a refugium in a changing environment 栖息地的急剧变化、进化临界点和拯救：量化专一物种在不断变化的环境中走向避难所的危险之路。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-10-09 DOI: 10.1016/j.tpb.2024.09.001

Léonard Dekens

{"title":"Sharp habitat shifts, evolutionary tipping points and rescue: Quantifying the perilous path of a specialist species towards a refugium in a changing environment","authors":"Léonard Dekens","doi":"10.1016/j.tpb.2024.09.001","DOIUrl":"10.1016/j.tpb.2024.09.001","url":null,"abstract":"<div><div>Specialist species thriving under specific environmental conditions in narrow geographic ranges are widely recognized as heavily threatened by climate deregulation. Many might rely on both their potential to adapt and to disperse towards a refugium to avoid extinction. It is thus crucial to understand the influence of environmental conditions on the unfolding process of adaptation. Here, I study the eco-evolutionary dynamics of a sexually reproducing specialist species in a two-patch quantitative genetic model with moving optima. Thanks to a separation of ecological and evolutionary time scales and the phase-line study of the selection gradient, I derive the critical environmental speed for persistence, which reflects how the existence of a refugium impacts extinction patterns and how it relates to the cost of dispersal. Moreover, the analysis provides key insights about the dynamics that arise on the path towards this refugium. I show that after an initial increase of population size, there exists a critical environmental speed above which the species crosses a tipping point, resulting into an abrupt habitat switch. In addition, when selection for local adaptation is strong, this habitat switch passes through an evolutionary “death valley”, leading to a phenomenon related to evolutionary rescue, which can promote extinction for lower environmental speeds than the critical one.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"160 ","pages":"Pages 25-48"},"PeriodicalIF":1.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A simple model and rules for the evolution of microbial mutualistic symbiosis with positive fitness feedbacks 具有正能量反馈的微生物互助共生进化的简单模型和规则。

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-10-09 DOI: 10.1016/j.tpb.2024.09.002

Sosuke Iwai

{"title":"A simple model and rules for the evolution of microbial mutualistic symbiosis with positive fitness feedbacks","authors":"Sosuke Iwai","doi":"10.1016/j.tpb.2024.09.002","DOIUrl":"10.1016/j.tpb.2024.09.002","url":null,"abstract":"<div><div>The evolution of microbe–microbe mutualistic symbiosis is considered to be promoted by repeated exchanges of fitness benefits, which can generate positive fitness feedbacks (‘partner fidelity feedback’) between species. However, previous evolutionary models for mutualism have not captured feedback dynamics or coupling of fitness between species. Here, a simple population model is developed to understand the evolution of mutualistic symbiosis in which two microbial species (host and symbiont) continuously grow and exchange fitness benefits to generate feedback dynamics but do not strictly control each other. The assumption that individual microbes provide constant amounts of resources, which are equally divided among interacting partner individual, enables us to reveal a simple rule for the evolution of costly mutualism with positive fitness feedbacks: the product of the benefit-to-cost ratios for each species exceeds one. When this condition holds, high cooperative investment levels are favored in both species regardless of the amount invested by each partner. The model is then extended to examine how symbiont mutation, immigration, or switching affects the spread of selfish or cooperative symbionts, which decrease and increase their investment levels, respectively. In particular, when a host associates with numerous symbionts without enforcement, neither mutation nor immigration but rather random switching would allow the spread of cooperative symbionts. Examples using symbiont switching for evolution would include large ciliates hosting numerous intracellular endosymbionts. The simple model and rules would provide a basis for understanding the evolution of microbe–microbe mutualistic symbiosis with positive fitness feedbacks and without enforcement mechanisms.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"160 ","pages":"Pages 14-24"},"PeriodicalIF":1.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0