Theoretical Population Biology最新文献

{"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":"2024-03-21","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":"Demographic inference for spatially heterogeneous populations using long shared haplotypes","authors":"","doi":"10.1016/j.tpb.2024.03.002","DOIUrl":"10.1016/j.tpb.2024.03.002","url":null,"abstract":"<div><p>We introduce a modified spatial <span><math><mi>Λ</mi></math></span>-Fleming–Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 108-124"},"PeriodicalIF":1.2,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000285/pdfft?md5=83582755d2ad3c07d32cc176757e368e&pid=1-s2.0-S0040580924000285-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140979","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":"Neutral diversity in experimental metapopulations","authors":"Guilhem Doulcier ,&nbsp;Amaury Lambert","doi":"10.1016/j.tpb.2024.02.011","DOIUrl":"10.1016/j.tpb.2024.02.011","url":null,"abstract":"<div><p>New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth–death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 89-108"},"PeriodicalIF":1.4,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000200/pdfft?md5=f7a882f8520e75e3eb7e0ffeef1dcb3b&pid=1-s2.0-S0040580924000200-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144474","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 ancestral selection graph for a Λ-asymmetric Moran model","authors":"","doi":"10.1016/j.tpb.2024.02.010","DOIUrl":"10.1016/j.tpb.2024.02.010","url":null,"abstract":"<div><p>Motivated by the question of the impact of selective advantage in populations with skewed reproduction mechanisms, we study a Moran model with selection. We assume that there are two types of individuals, where the reproductive success of one type is larger than the other. The higher reproductive success may stem from either more frequent reproduction, or from larger numbers of offspring, and is encoded in a measure <span><math><mi>Λ</mi></math></span> for each of the two types. <span><math><mi>Λ</mi></math></span>-reproduction here means that a whole fraction of the population is replaced at a reproductive event. Our approach consists of constructing a <span><math><mi>Λ</mi></math></span>-asymmetric Moran model in which individuals of the two populations compete, rather than considering a Moran model for each population. Provided the measure are ordered stochastically, we can couple them. This allows us to construct the central object of this paper, the <span><math><mrow><mi>Λ</mi><mo>−</mo></mrow></math></span>asymmetric ancestral selection graph, leading to a pathwise duality of the forward in time <span><math><mi>Λ</mi></math></span>-asymmetric Moran model with its ancestral process. We apply the ancestral selection graph in order to obtain scaling limits of the forward and backward processes, and note that the frequency process converges to the solution of an SDE with discontinuous paths. Finally, we derive a Griffiths representation for the generator of the SDE and use it to find a semi-explicit formula for the probability of fixation of the less beneficial of the two types.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 91-107"},"PeriodicalIF":1.2,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000194/pdfft?md5=c0dce179bca40926eed0fec256704b68&pid=1-s2.0-S0040580924000194-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137404","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":"Phase-type distributions in mathematical population genetics: An emerging framework","authors":"Asger Hobolth ,&nbsp;Iker Rivas-González ,&nbsp;Mogens Bladt ,&nbsp;Andreas Futschik","doi":"10.1016/j.tpb.2024.03.001","DOIUrl":"10.1016/j.tpb.2024.03.001","url":null,"abstract":"<div><p>A phase-type distribution is the time to absorption in a continuous- or discrete-time Markov chain. Phase-type distributions can be used as a general framework to calculate key properties of the standard coalescent model and many of its extensions. Here, the ‘phases’ in the phase-type distribution correspond to states in the ancestral process. For example, the time to the most recent common ancestor and the total branch length are phase-type distributed. Furthermore, the site frequency spectrum follows a multivariate discrete phase-type distribution and the joint distribution of total branch lengths in the two-locus coalescent-with-recombination model is multivariate phase-type distributed. In general, phase-type distributions provide a powerful mathematical framework for coalescent theory because they are analytically tractable using matrix manipulations. The purpose of this review is to explain the phase-type theory and demonstrate how the theory can be applied to derive basic properties of coalescent models. These properties can then be used to obtain insight into the ancestral process, or they can be applied for statistical inference. In particular, we show the relation between classical first-step analysis of coalescent models and phase-type calculations. We also show how reward transformations in phase-type theory lead to easy calculation of covariances and correlation coefficients between e.g. tree height, tree length, external branch length, and internal branch length. Furthermore, we discuss how these quantities can be used for statistical inference based on estimating equations. Providing an alternative to previous work based on the Laplace transform, we derive likelihoods for small-size coalescent trees based on phase-type theory. Overall, our main aim is to demonstrate that phase-type distributions provide a convenient general set of tools to understand aspects of coalescent models that are otherwise difficult to derive. Throughout the review, we emphasize the versatility of the phase-type framework, which is also illustrated by our accompanying R-code. All our analyses and figures can be reproduced from code available on GitHub.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 14-32"},"PeriodicalIF":1.4,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000212/pdfft?md5=635096b59c3865e96b03602b5158c0b9&pid=1-s2.0-S0040580924000212-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068875","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":"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":"2024-02-27","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 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":"2024-02-27","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":"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":"2024-02-21","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":"Biographical sketch: Freddy Bugge Christiansen","authors":"Volker Loeschcke,&nbsp;Mikkel Heide Schierup","doi":"10.1016/j.tpb.2024.02.006","DOIUrl":"10.1016/j.tpb.2024.02.006","url":null,"abstract":"","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Page 130"},"PeriodicalIF":1.4,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139924713","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":"On multi-type Cannings models and multi-type exchangeable coalescents","authors":"Martin Möhle","doi":"10.1016/j.tpb.2024.02.005","DOIUrl":"10.1016/j.tpb.2024.02.005","url":null,"abstract":"<div><p>A multi-type neutral Cannings population model with migration and fixed subpopulation sizes is analyzed. Under appropriate conditions, as all subpopulation sizes tend to infinity, the ancestral process, properly time-scaled, converges to a multi-type coalescent sharing the exchangeability and consistency property. The proof gains from coalescent theory for single-type Cannings models and from decompositions of transition probabilities into parts concerning reproduction and migration respectively. The following section deals with a different but closely related multi-type Cannings model with mutation and fixed total population size but stochastically varying subpopulation sizes. The latter model is analyzed forward and backward in time with an emphasis on its behavior as the total population size tends to infinity. Forward in time, multi-type limiting branching processes arise for large population size. Its backward structure and related open problems are briefly discussed.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"156 ","pages":"Pages 103-116"},"PeriodicalIF":1.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000145/pdfft?md5=72409ec57f40736e3991c39dcda2e229&pid=1-s2.0-S0040580924000145-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898353","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}