Theoretical Population Biology最新文献

Effect of competition on emergent phases and phase transitions in competitive systems.

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-12-28 DOI: 10.1016/j.tpb.2024.12.003

Shikun Wang, Yuanshi Wang, Hong Wu

引用次数: 0

Catching a wave: On the suitability of traveling-wave solutions in epidemiological modeling.

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":"https://doi.org/10.1016/j.tpb.2024.12.004","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":""},"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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The impact of simultaneous infections on phage-host ecology.

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-12-24 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":"<p><p>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 persist even though they cannot invade. 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.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":"42-49"},"PeriodicalIF":1.2,"publicationDate":"2024-12-24","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Editorial.

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-12-24 DOI: 10.1016/j.tpb.2024.12.001

引用次数: 0

Stochastic offspring distributions amplify selection bias in mutation accumulation experiments.

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-12-12 DOI: 10.1016/j.tpb.2024.11.002

Mojgan Ezadian, Lindi M Wahl

{"title":"Stochastic offspring distributions amplify selection bias in mutation accumulation experiments.","authors":"Mojgan Ezadian, Lindi M Wahl","doi":"10.1016/j.tpb.2024.11.002","DOIUrl":"10.1016/j.tpb.2024.11.002","url":null,"abstract":"<p><p>Mutation accumulation (MA) experiments play an important role in understanding evolution. For microbial populations, such experiments often involve periods of population growth, such that a single individual can make a visible colony, followed by severe bottlenecks. Previous work has quantified the effect of positive and negative selection on MA experiments, demonstrating for example that with 20 generations of growth between bottlenecks, big-benefit mutations can be over-represented by a factor of five or more (Wahl and Agashe, 2022). This previous work assumed a deterministic model for population growth. We now develop a fully stochastic model, including realistic offspring distributions that incorporate genetic drift and allow for the loss of rare lineages. We demonstrate that when stochastic offspring distributions are considered, selection bias is even stronger than previously predicted. We describe several analytical and numerical methods that offer an accurate correction for the effects of selection on the observed distribution of fitness effects, describe the practical considerations in implementing each method, and demonstrate the use of this correction on simulated MA data.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":"25-33"},"PeriodicalIF":1.2,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822826","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

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 : 2024-12-10 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":"<p><p>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. 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 in-silico evidence that under these conditions a defense trait can be altruistic and still spread in a structured population.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":"13-24"},"PeriodicalIF":1.2,"publicationDate":"2024-12-10","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A stochastic field theory for the evolution of quantitative traits in finite populations.

IF 1.2 4区生物学

Theoretical Population Biology Pub Date : 2024-11-26 DOI: 10.1016/j.tpb.2024.10.003

Ananda Shikhara Bhat

{"title":"A stochastic field theory for the evolution of quantitative traits in finite populations.","authors":"Ananda Shikhara Bhat","doi":"10.1016/j.tpb.2024.10.003","DOIUrl":"10.1016/j.tpb.2024.10.003","url":null,"abstract":"<p><p>Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modeling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which the total population size fluctuates due to demographic noise in births and deaths can behave qualitatively differently from constant or infinite population models due to density-dependent dynamics. In this paper, I present a stochastic field theory for the eco-evolutionary dynamics of finite populations bearing one-dimensional quantitative traits. I derive stochastic field equations that describe the evolution of population densities, trait frequencies, and the mean value of any trait in the population. These equations recover well-known results such as the replicator-mutator equation, Price equation, and gradient dynamics in the infinite population limit. For finite populations, the equations describe the intricate interplay between natural selection, noise-induced selection, eco-evolutionary feedback, and neutral genetic drift in determining evolutionary trajectories. My work uses ideas from statistical physics, calculus of variations, and SPDEs, providing alternative methods that complement the measure-theoretic martingale approach that is more common in the literature.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":"1-12"},"PeriodicalIF":1.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751658","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

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