Theoretical Population Biology最新文献_第5页

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 Q4 ECOLOGY

Theoretical Population Biology

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

Jaye Sudweeks , Christoph Hauert

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.

噬菌体利用细菌宿主资源进行复制，将噬菌体和宿主的生存内在地联系在一起。要了解噬菌体动力学，必须了解噬菌体-宿主生态学。这个生态系统的关键一步是细菌宿主的感染。以前的工作已经探索了单次和多次连续感染。在这里，我们专注于同时感染理论，其中多个噬菌体同时附着并感染一个细菌宿主细胞。同时感染是一个需要考虑的相关感染动态，特别是在高噬菌体密度时，当许多噬菌体在短时间内附着在单个宿主细胞上时。对于高细菌生长速率，同时感染可能导致双稳定：根据初始条件，噬菌体要么以稳定的密度灭绝，要么通过稳定极限环的周期性振荡与宿主共存。这对噬菌体应用（如噬菌体治疗）具有重要意义：即使噬菌体不能侵入，它们也可以持续存在。因此，通过噬菌体密度的峰值，即使噬菌体的基本繁殖数小于1，也有可能感染细菌种群。在稳定的极限环条件下，如果时间合适，可能只需要小密度的噬菌体。

{"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}

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 Q4 ECOLOGY

Theoretical Population Biology

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

Felix Jordan , Martin Hutzenthaler , Dirk Metzler

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.

我们模拟了在宿主（或猎物）种群中反寄生虫（或反捕食者）防御等位基因的自然选择或反寄生虫（或反捕食者）防御等位基因的自然选择。与同一巢穴中的非防御者（"作弊者"）相比，防御行为会使行为者付出健康代价，并局部降低寄生虫的生长率。Hutzenthaler 等人（2022 年）通过分析推导出了在大种群、多巢穴、弱选择和慢迁移条件下防御者固定或消亡的标准。在此，我们使用基于个体和基于扩散的模拟方法来分析相关模型。我们发现，该标准仍能准确预测有限数量种群和各种迁移模式的情况。提供防御性状益处的一个关键机制是由于繁殖和死亡事件的随机性而导致的遗传漂移，这导致了不同种群之间防御等位基因频率和宿主种群规模的差异。我们讨论了对这一机制的包容性拟合解释，并提出了在这些条件下防御性状可以利他并仍能在结构化种群中传播的内部证据。

{"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}

引用次数: 0

社论。

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

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

引用次数: 0

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 Q4 ECOLOGY

Theoretical Population Biology

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

Thomas Seidelmann, Sanaz Mostaghim

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.

尽管被广泛研究，生物多样性的维持仍然是当代生态学研究中一个备受争议和调查的话题。一些研究量化了各种共存机制对生物多样性的贡献。然而，通常随机的个人层面的相互作用是抽象出来的，或者是孤立地研究机制。因此，很少考虑机制之间的相互交织性质和相互影响，因为它们源于个人层面的相互作用。我们提出了一种基于中性理论的新型机制模拟模型，以捕获和量化由这种机制相互作用产生的紧急效应。它支持三种共存机制：存储效应、不可传递性和资源分区。我们证明了基本的中性动力学和孤立机制的相关模型可以被复制。除此之外，我们观察到难以预测，但显着的机制组合的紧急效应。在某些情况下，与单个机制性能相比，共存时间可能延长十倍以上。我们的研究结果表明，个体共存机制的研究可能是不充分的，并且在量化它们对生物多样性的总体影响方面确实具有误导性。机制及其相互作用的特殊组合似乎是至关重要的。

{"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}

引用次数: 0

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 Q4 ECOLOGY

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

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.

常微分方程模型，如经典的SIR模型，在流行病学中被广泛用于研究和预测传染病动力学。然而，这些模型通常假设种群是均匀混合的，忽略了由于空间异质性导致的疾病患病率的可能变化。为了解决这个问题，反应扩散模型被提出作为一种替代方法来模拟空间连续种群，其中个体以扩散的方式移动。在本研究中，我们探讨了在何种条件下必须明确考虑这种空间结构才能准确预测疾病传播，以及在何种情况下均匀混合假设仍然充分。特别是，我们推导了扩散系数的临界阈值，低于该阈值，疾病传播动态表现出空间异质性。我们通过二维连续景观中基于个体的疾病传播模拟来验证我们的分析结果。利用这一框架，通过将空间结构纳入SI、SIS和SIR模型，我们进一步探讨了疾病建立概率、最大发病率和最终流行规模等关键流行病学参数是如何受到影响的。我们讨论了我们的研究结果对流行病学建模的影响，并确定了疾病动力学空间模拟模型的设计考虑因素和局限性。

{"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}

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 Q4 ECOLOGY

Theoretical Population Biology

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

Mahdi Salehzadeh, John M. Stockie, Ailene MacPherson

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,

R_{0}

, 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.

树木致死性树皮甲虫灾害是针叶林大量死亡的原因之一，对森林生态系统及其提供的生态系统服务造成了影响。预测树皮甲虫爆发的模型对森林管理和保护至关重要，因此有必要研究流行病学特征对爆发概率和严重程度的影响。由于甲虫的聚集行为和寄主树的防御能力，这种流行病学的相互作用是高度非线性的，人们对爆发行为仍然知之甚少。在此，我们运用分布式延迟原理，在流行病学框架内创建了一个新颖、数学上可操作性强的甲虫聚集模型。我们推导出甲虫出现率的临界爆发阈值，该阈值类似于流行病的基本繁殖率 R0。甲虫聚集会对爆发潜力产生定性影响，从没有聚集时仅取决于甲虫出现率，到需要聚集时取决于甲虫出现率和初始甲虫密度。最后，我们使用随机模型来证实我们的确定性模型预测在有限种群中是可靠的。

{"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 Q4 ECOLOGY

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

Motivation:

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.

Results:

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.

Availability and implementation:

An implementation of our model is freely available along with code for reproducing our computational experiments at https://github.com/Cronjaeger/almost-infinite-sites-recursions.

动机分子进化的一个主要挑战是找到计算效率高、假设灵活、能正确反映遗传变异的突变模型。无限位点模型假设每次突变都发生在一个以前从未发生过突变的位点上，即不允许重复突变。这对低突变率来说是合理的，也使统计推断更加容易。然而，重复突变非常普遍，即使在人类等每个位点突变率较低的物种中，也能从遗传变异数据中观察到。另一方面，有限位点模型允许发生重复突变，但在大多数情况下计算上不可行。在这项研究中，我们开发了一种新的分子进化模型--几乎无限位点模型，它既允许重复突变，又易于操作，从而在这两种方法之间架起了一座桥梁。我们提供了我们提出的模型在完全关联条件下的可能性递归特征，并概述了计算该可能性的简便近似方案：我们在模拟数据和人类线粒体数据中展示了我们的模型的实用性。我们的结果表明，AISM 与突变事件总数的约束相结合，可以恢复突变率最大似然估计值的精确近似值：我们免费提供模型的实现以及用于重现计算实验的代码，请访问 https://github.com/Cronjaeger/almost-infinite-sites-recursions。

{"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 Q4 ECOLOGY

Theoretical Population Biology

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

Léonard Dekens

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.

人们普遍认为，在狭窄地理范围内特定环境条件下繁衍生息的专门物种受到气候失调的严重威胁。许多物种可能既要依靠自身的适应潜力，又要依靠向避难所扩散来避免灭绝。因此，了解环境条件对适应过程的影响至关重要。在这里，我在一个具有移动最优值的双片段定量遗传模型中研究了一种有性繁殖的专性物种的生态进化动态。得益于生态和进化时间尺度的分离以及对选择梯度的相线研究，我得出了持久性的临界环境速度，它反映了避难所的存在如何影响灭绝模式，以及它与扩散成本之间的关系。此外，该分析还提供了关于在通往该庇护所的道路上出现的动态变化的关键见解。我的研究表明，在最初的种群数量增加之后，存在一个临界环境速度，超过这个速度，物种就会越过一个临界点，导致栖息地的突然转换。此外，当对局部适应性的选择很强时，这种生境转换会经过一个进化的 "死亡谷"，从而导致一种与进化拯救有关的现象，这种现象会促使低于临界环境速度的物种灭绝。

{"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 Q4 ECOLOGY

Theoretical Population Biology

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

Sosuke Iwai

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.

微生物-微生物互利共生的进化被认为是通过重复交换适合度利益而促进的，这可以在物种之间产生正的适合度反馈（"伙伴忠诚度反馈"）。然而，以往的互惠进化模型并没有捕捉到物种间的反馈动态或适合度耦合。在这里，我们建立了一个简单的种群模型来理解互惠共生的进化过程，在这个过程中，两个微生物物种（宿主和共生体）不断生长并交换适合度收益，从而产生反馈动态，但并不严格控制对方。假定单个微生物提供恒定数量的资源，这些资源在相互作用的伙伴个体之间平均分配，这使我们能够揭示出具有正能量反馈的高成本互利共生进化的一个简单规则：每个物种的收益-成本比的乘积超过 1。当这一条件成立时，无论每个伙伴的投资额是多少，两个物种都会倾向于高合作投资水平。然后，我们将模型扩展到研究共生体变异、移民或转换如何影响自私共生体或合作共生体的传播，从而分别降低和提高它们的投资水平。特别是，当宿主与许多共生体建立联系而没有强制执行时，无论是突变还是移民，而是随机切换都不会使合作共生体扩散。利用共生体转换促进进化的例子包括寄生着大量胞内内生共生体的大型纤毛虫。这个简单的模型和规则将为理解具有正向适应性反馈且没有强制机制的微生物-微生物互利共生的进化提供一个基础。

{"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

Joint identity among loci under mutation and regular inbreeding 变异和正常近亲繁殖情况下基因位点间的共同特性

IF 1.2 4区生物学 Q4 ECOLOGY

Theoretical Population Biology

Pub Date : 2024-08-30 DOI: 10.1016/j.tpb.2024.08.002

Marcy K. Uyenoyama

This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci. Measures of association depend on genetic diversity rather than allelic frequencies, as do linkage disequilibrium and its relatives. Scaled indices designed to show monotonic dependence on rates of crossing-over, inbreeding, and mutation may prove useful for interpreting patterns of genome-scale variation.

本研究描述了一种简洁的方法，用于确定在遗传漂移、杂交、突变和常规近交（部分自交）条件下进化的种群中基因位点内和基因位点间的联合同态概率（IBS）。基因位点间关联的经典指数类似于这些联合特征的函数。这种基于凝聚的分析表明，多基因位点关联反映了各基因位点之间同时发生的凝聚事件。关联度的测量依赖于遗传多样性而非等位基因频率，这一点与连锁不平衡及其近亲一样。旨在显示对杂交率、近交率和变异率的单调依赖性的标度指数可能有助于解释基因组范围的变异模式。

引用次数: 0