Theoretical Population Biology最新文献

{"title":"Beyond fitness: The information imparted in population states by selection throughout lifecycles","authors":"Eric Smith","doi":"10.1016/j.tpb.2024.04.003","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.04.003","url":null,"abstract":"<div><p>We approach the questions, what part of evolutionary change results from selection, and what is the adaptive information flow into a population undergoing selection, as a problem of quantifying the divergence of typical trajectories realized under selection from the expected dynamics of their counterparts under a null stochastic-process model representing the absence of selection. This approach starts with a formulation of adaptation in terms of information and from that identifies selection from the genetic parameters that generate information flow; it is the reverse of a historical approach that defines selection in terms of fitness, and then identifies adaptive characters as those amplified in relative frequency by fitness. Adaptive information is a relative entropy on distributions of histories computed directly from the generators of stochastic evolutionary population processes, which in large population limits can be approximated by its leading exponential dependence as a large-deviation function. We study a particular class of generators that represent the genetic dependence of explicit transitions around reproductive cycles in terms of stoichiometry, familiar from chemical reaction networks. Following Smith (2023), which showed that partitioning evolutionary events among genetically distinct realizations of lifecycles yields a more consistent causal analysis through the Price equation than the construction from units of selection and fitness, here we show that it likewise yields more complete evolutionary information measures.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 86-117"},"PeriodicalIF":1.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000364/pdfft?md5=ab76042f06b1a1f92eb4084df971bd79&pid=1-s2.0-S0040580924000364-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140558903","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}

{"title":"Evolution of delayed dispersal with group size effect and population dynamics","authors":"Alan Flatrès,&nbsp;Geoff Wild","doi":"10.1016/j.tpb.2024.02.007","DOIUrl":"10.1016/j.tpb.2024.02.007","url":null,"abstract":"<div><p>Individuals delay natal dispersal for many reasons. There may be no place to disperse to; immediate dispersal or reproduction may be too costly; immediate dispersal may mean that the individual and their relatives miss the benefits of group living. Understanding the factors that lead to the evolution of delayed dispersal is important because delayed dispersal sets the stage for complex social groups and social behavior. Here, we study the evolution of delayed dispersal when the quality of the local environment is improved by greater numbers of individuals (<span><math><mrow><mi>e</mi><mo>.</mo><mi>g</mi><mo>.</mo></mrow></math></span>, safety in numbers). We assume that individuals who delay natal dispersal also expect to delay personal reproduction. In addition, we assume that improved environmental quality benefits manifest as changes to fecundity and survival. We are interested in how do the changes in these life-history features affect delayed dispersal. We use a model that ties evolution to population dynamics. We also aim to understand the relationship between levels of delayed dispersal and the probability of establishing as an independent breeder (a population-level feature) in response to changes in life-history details. Our model emphasizes kin selection and considers a sexual organism, which allows us to study parent–offspring conflict over delayed dispersal. At evolutionary equilibrium, fecundity and survival benefits of group size or quality promote higher levels of delayed dispersal over a larger set of life histories with one exception. The exception is for benefits of increased group size or quality reaped by the individuals who delay dispersal. There, the increased benefit does not change the life histories supporting delay dispersal. Next, in contrast to previous predictions, we find that a low probability of establishing in a new location is not always associated with a higher incidence of delayed dispersal. Finally, we find that increased personal benefits of delayed dispersal exacerbate the conflict between parents and their offspring. We discuss our findings in relation to previous theoretical and empirical work, especially work related to cooperative breeding.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 1-13"},"PeriodicalIF":1.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139991647","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}

{"title":"Mathematical model of rabies vaccination in the United States","authors":"Annalise Hassan ,&nbsp;Zoe A. Tapp ,&nbsp;Dan K. Tran ,&nbsp;Jan Rychtář ,&nbsp;Dewey Taylor","doi":"10.1016/j.tpb.2024.03.004","DOIUrl":"10.1016/j.tpb.2024.03.004","url":null,"abstract":"<div><p>Rabies is one of the oldest viral diseases and it has been present on every continent except Antarctica. Within the U.S. human rabies cases are quite rare. In the eastern USA, raccoons are the main reservoir hosts and pet vaccination serves as an important barrier against human rabies exposure. In this paper, we develop a compartmental model for rabies transmission amongst raccoons and domestic pets. We find the disease-free equilibria, reproduction numbers for the raccoons and domestic pets. We also determine the vaccination coverage/rates, both for raccoons and pets, needed to achieve the elimination of rabies.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 47-54"},"PeriodicalIF":1.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194935","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}

{"title":"Large effects and the infinitesimal model","authors":"Todd L. Parsons ,&nbsp;Peter L. Ralph","doi":"10.1016/j.tpb.2024.02.009","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.02.009","url":null,"abstract":"<div><p>The infinitesimal model of quantitative genetics relies on the Central Limit Theorem to stipulate that under additive models of quantitative traits determined by many loci having similar effect size, the difference between an offspring’s genetic trait component and the average of their two parents’ genetic trait components is Normally distributed and independent of the parents’ values. Here, we investigate how the assumption of similar effect sizes affects the model: if, alternatively, the tail of the effect size distribution is polynomial with exponent <span><math><mrow><mi>α</mi><mo>&lt;</mo><mn>2</mn></mrow></math></span>, then a different Central Limit Theorem implies that sums of effects should be well-approximated by a “stable distribution”, for which single large effects are often still important. Empirically, we first find tail exponents between 1 and 2 in effect sizes estimated by genome-wide association studies of many human disease-related traits. We then show that the independence of offspring trait deviations from parental averages in many cases implies the Gaussian aspect of the infinitesimal model, suggesting that non-Gaussian models of trait evolution must explicitly track the underlying genetics, at least for loci of large effect. We also characterize possible limiting trait distributions of the infinitesimal model with infinitely divisible noise distributions, and compare our results to simulations.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 117-129"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139992963","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}

{"title":"Evolution of spite versus evolution of altruism through a disbandment mechanism","authors":"Shun Kurokawa","doi":"10.1016/j.tpb.2024.02.008","DOIUrl":"10.1016/j.tpb.2024.02.008","url":null,"abstract":"<div><p>Altruism and spite are costly to the actor, making their evolution unlikely without specific mechanisms. Nonetheless, both altruistic and spiteful behaviors are present in individuals, which suggests the existence of an underlying mechanism that drives their evolution. If altruistic individuals are more likely to be recipients of altruism than non-altruistic individuals, then altruism can be favored by natural selection. Similarly, if spiteful individuals are less likely to be recipients of spite than non-spiteful individuals, then spite can be favored by natural selection. Spite is altruism's evil twin, ugly sister of altruism, or a shady relative of altruism. In some mechanisms, such as repeated interactions, if altruism is favored by natural selection, then spite is also favored by natural selection. However, there has been limited investigation into whether both behaviors evolve to the same extent. In this study, we focus on the mechanism by which individuals choose to keep or stop the interaction according to the opponent's behavior. Using the evolutionary game theory, we investigate the evolution of altruism and spite under this mechanism. Our model revealed that the evolution of spite is less likely than the evolution of altruism.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 131-147"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000170/pdfft?md5=f5fdcc6c7451516225dc75f174a3f509&pid=1-s2.0-S0040580924000170-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139924840","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}

{"title":"Pneumococcus and the stress-gradient hypothesis: A trade-off links R0 and susceptibility to co-colonization across countries","authors":"Ermanda Dekaj,&nbsp;Erida Gjini","doi":"10.1016/j.tpb.2024.02.001","DOIUrl":"10.1016/j.tpb.2024.02.001","url":null,"abstract":"<div><p>Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria <em>Streptococcus pneumoniae</em>, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of <em>S. pneumoniae</em> have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (<span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>) and susceptibility to co-colonization (<span><math><mi>k</mi></math></span>). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization <span><math><mrow><mi>μ</mi><mo>=</mo><mn>1</mn><mo>/</mo><mrow><mo>(</mo><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub><mo>−</mo><mn>1</mn><mo>)</mo></mrow><mi>k</mi></mrow></math></span>. From the mathematical model’s behavior, such conservation suggests preservation of ‘stability-diversity-complexity’ regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of <em>Streptococcus pneumoniae</em> from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 77-92"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000108/pdfft?md5=0247b897070fd207a00c036c6629322a&pid=1-s2.0-S0040580924000108-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139708355","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}

{"title":"Cultural transmission, competition for prey, and the evolution of cooperative hunting","authors":"Talia Borofsky ,&nbsp;Marcus W. Feldman ,&nbsp;Yoav Ram","doi":"10.1016/j.tpb.2023.12.005","DOIUrl":"10.1016/j.tpb.2023.12.005","url":null,"abstract":"<div><p>Although cooperative hunting is widespread among animals, its benefits are unclear. At low frequencies, cooperative hunting may allow predators to escape competition and access bigger prey that could not be caught by a lone cooperative predator. Cooperative hunting is a more successful strategy when it is common, but its spread can result in overhunting big prey, which may have a lower per-capita growth rate than small prey. We construct a one-predator species, two-prey species model in which predators either learn to hunt small prey alone or learn to hunt big prey cooperatively. Predators first learn vertically from parents, then horizontally (i.e. socially) from random individuals or siblings. After horizontal transmission, they hunt with their learning partner if both are cooperative, and otherwise they hunt alone. Cooperative hunting cannot evolve when initially rare unless predators (a) interact with siblings, or (b) horizontally transmit the cooperative behavior to potential hunting partners. Whereas competition for small prey favors cooperative hunting when this cooperation is initially rare, the frequency of cooperative hunting cannot reach 100% unless big prey is abundant. Furthermore, a mutant that increases horizontal learning can invade if cooperative hunting is present, but not at 100%, because horizontal learning allows pairs of predators to have the same strategy. Our results reveal that the interactions between prey availability, social learning, and degree of cooperation among predators may have important effects on ecosystems.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 12-21"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000017/pdfft?md5=a2ba6eb2f2f12050d6e18b09a4a9b34e&pid=1-s2.0-S0040580924000017-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139374264","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}

{"title":"Riding the waves from epidemic to endemic: Viral mutations, immunological change and policy responses","authors":"D. Grass ,&nbsp;S. Wrzaczek ,&nbsp;J.P. Caulkins ,&nbsp;G. Feichtinger ,&nbsp;R.F. Hartl ,&nbsp;P.M. Kort ,&nbsp;M. Kuhn ,&nbsp;A. Prskawetz ,&nbsp;M. Sanchez-Romero ,&nbsp;A. Seidl","doi":"10.1016/j.tpb.2024.02.002","DOIUrl":"10.1016/j.tpb.2024.02.002","url":null,"abstract":"<div><p>Nonpharmaceutical interventions (NPI) are an important tool for countering pandemics such as COVID-19. Some are cheap; others disrupt economic, educational, and social activity. The latter force governments to balance the health benefits of reduced infection and death against broader lockdown-induced societal costs. A literature has developed modeling how to optimally adjust lockdown intensity as an epidemic evolves. This paper extends that literature by augmenting the classic SIR model with additional states and flows capturing decay over time in vaccine-conferred immunity, the possibility that mutations create variants that erode immunity, and that protection against infection erodes faster than protecting against severe illness. As in past models, we find that small changes in parameter values can tip the optimal response between very different solutions, but the extensions considered here create new types of solutions. In some instances, it can be optimal to incur perpetual epidemic waves even if the uncontrolled infection prevalence would settle down to a stable intermediate level.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 46-65"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S004058092400011X/pdfft?md5=0d54423714faf727de2fa57b72322515&pid=1-s2.0-S004058092400011X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139663427","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}

{"title":"The impact of dormancy on evolutionary branching","authors":"Jochen Blath ,&nbsp;Tobias Paul ,&nbsp;András Tóbiás ,&nbsp;Maite Wilke Berenguer","doi":"10.1016/j.tpb.2024.02.003","DOIUrl":"10.1016/j.tpb.2024.02.003","url":null,"abstract":"<div><p>In this paper, we investigate the consequences of dormancy in the ‘rare mutation’ and ‘large population’ regime of stochastic adaptive dynamics. Starting from an individual-based micro-model, we first derive the Polymorphic Evolution Sequence of the population, based on a previous work by Baar and Bovier (2018). After passing to a second ‘small mutations’ limit, we arrive at the Canonical Equation of Adaptive Dynamics, and state a corresponding criterion for evolutionary branching, extending a previous result of Champagnat and Méléard (2011).</p><p>The criterion allows a quantitative and qualitative analysis of the effects of dormancy in the well-known model of Dieckmann and Doebeli (1999) for sympatric speciation. In fact, quite an intuitive picture emerges: Dormancy enlarges the parameter range for evolutionary branching, increases the carrying capacity and niche width of the post-branching sub-populations, and, depending on the model parameters, can either increase or decrease the ‘speed of adaptation’ of populations. Finally, dormancy increases diversity by increasing the genetic distance between subpopulations.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 66-76"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000121/pdfft?md5=ba7e1ab7af08a6f3d59914b2a2549f7e&pid=1-s2.0-S0040580924000121-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139703882","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}

{"title":"Maximum likelihood estimation and natural pairwise estimating equations are identical for three sequences and a symmetric 2-state substitution model","authors":"Asger Hobolth ,&nbsp;Carsten Wiuf","doi":"10.1016/j.tpb.2023.12.004","DOIUrl":"10.1016/j.tpb.2023.12.004","url":null,"abstract":"<div><p>Consider the problem of estimating the branch lengths in a symmetric 2-state substitution model with a known topology and a general, clock-like or star-shaped tree with three leaves. We show that the maximum likelihood estimates are analytically tractable and can be obtained from pairwise sequence comparisons. Furthermore, we demonstrate that this property does not generalize to larger state spaces, more complex models or larger trees. Our arguments are based on an enumeration of the free parameters of the model and the dimension of the minimal sufficient data vector. Our interest in this problem arose from discussions with our former colleague Freddy Bugge Christiansen.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 1-4"},"PeriodicalIF":1.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580923000837/pdfft?md5=426e44db4e15cbf41adb83d6740ba283&pid=1-s2.0-S0040580923000837-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139103662","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}