Theoretical Population Biology最新文献

{"title":"Limits to selection on standing variation in an asexual population","authors":"Nick Barton , Himani Sachdeva","doi":"10.1016/j.tpb.2024.04.001","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.04.001","url":null,"abstract":"<div><p>We consider how a population of <span><math><mi>N</mi></math></span> haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values <span><math><mrow><msub><mrow><mi>z</mi></mrow><mrow><mn>1</mn></mrow></msub><mo>,</mo><mo>…</mo><mo>,</mo><msub><mrow><mi>z</mi></mrow><mrow><mi>N</mi></mrow></msub></mrow></math></span>, which are drawn from a distribution <span><math><mi>ψ</mi></math></span>; the fitness of individual <span><math><mi>i</mi></math></span> is proportional to <span><math><msup><mrow><mi>e</mi></mrow><mrow><msub><mrow><mi>z</mi></mrow><mrow><mi>i</mi></mrow></msub></mrow></msup></math></span>. For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance <span><math><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span>, and show that for large <span><math><mi>N</mi></math></span>, there is a scaling limit which depends on a single parameter <span><math><mrow><mi>N</mi><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt></mrow></math></span>. When selection is weak relative to drift (<span><math><mrow><mi>N</mi><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt><mo>≪</mo><mn>1</mn></mrow></math></span>), the variance decreases exponentially at rate <span><math><mrow><mn>1</mn><mo>/</mo><mi>N</mi></mrow></math></span>, and the expected ultimate gain in log fitness (scaled by <span><math><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt></math></span>), is just <span><math><mrow><mi>N</mi><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt></mrow></math></span>, which is the same as Robertson’s (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (<span><math><mrow><mi>N</mi><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt><mo>≫</mo><mn>1</mn></mrow></math></span>), the ultimate gain can be found by approximating the establishment of alleles by a branching process in which each allele competes independently with the population mean and the fittest allele to establish is certain to fix. Then, if the probability of survival to time <span><math><mrow><mi>t</mi><mo>∼</mo><mn>1</mn><mo>/</mo><msqrt><mrow><msub><mrow><mi>V</mi></mrow><mrow><mn>0</mn></mrow></msub></mrow></msqrt></mrow></math></span> of an allele with value <span><math><mi>z</mi></math></span> is <span><math><mrow><mi>P</mi><mrow><mo>(</mo><mi>z</mi><mo>)</mo></mrow></mrow></math></span>, with mean <span><math><mover><mrow><mi>P</mi></mrow><mo>¯</mo></mover></math></span>, the winning allele is the fittest of <span><math><mrow><mi>N</mi><mover><mrow><mi>P</mi></mrow><mo>¯</mo></mover></mrow></math></span> survivors drawn from a distribution <span><math><mrow><mi>ψ</mi><mi>P</mi><m","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 129-137"},"PeriodicalIF":1.4,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000340/pdfft?md5=11e7dda9fdc312e774cd76068c76d9e8&pid=1-s2.0-S0040580924000340-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140813631","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 mutation process on the ancestral line under selection","authors":"E. Baake ,&nbsp;F. Cordero ,&nbsp;E. Di Gaspero","doi":"10.1016/j.tpb.2024.04.004","DOIUrl":"10.1016/j.tpb.2024.04.004","url":null,"abstract":"<div><p>We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the distant past, far beyond the most recent common ancestor of the population (thus connecting population genetics to phylogeny), and analyse the mutation process along this line.</p><p>To this end, we use the pruned lookdown ancestral selection graph (Lenz et al., 2015), which consists of a set of potential ancestors of the sampled individual at any given time. Relative to the neutral case (that is, without selection), we obtain a general bias towards the beneficial type, an increase in the beneficial mutation rate, and a decrease in the deleterious mutation rate. This sheds new light on previous analytical results. We discuss our findings in the light of a well-known observation at the interface of phylogeny and population genetics, namely, the difference in the mutation rates (or, more precisely, mutation fluxes) estimated via phylogenetic methods relative to those observed in pedigree studies.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 60-75"},"PeriodicalIF":1.4,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000376/pdfft?md5=92245f3e3bf3575e7c165660cf7cbf4f&pid=1-s2.0-S0040580924000376-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140793784","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":"Indirect interaction between an endemic and an invading pathogen: A case study of Plasmodium and Usutu virus dynamics in a shared bird host population","authors":"Afonso Dimas Martins ,&nbsp;Mick Roberts ,&nbsp;Quirine ten Bosch ,&nbsp;Hans Heesterbeek","doi":"10.1016/j.tpb.2024.04.002","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.04.002","url":null,"abstract":"<div><p>Infectious disease agents can influence each other’s dynamics in shared host populations. We consider such influence for two mosquito-borne infections where one pathogen is endemic at the time that a second pathogen invades. We regard a setting where the vector has a bias towards biting host individuals infected with the endemic pathogen and where there is a cost to co-infected hosts. As a motivating case study, we regard <em>Plasmodium</em> spp., that cause avian malaria, as the endemic pathogen, and Usutu virus (USUV) as the invading pathogen. Hosts with malaria attract more mosquitoes compared to susceptible hosts, a phenomenon named vector bias. The possible trade-off between the vector-bias effect and the co-infection mortality is studied using a compartmental epidemic model. We focus first on the basic reproduction number <span><math><msub><mrow><mi>R</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span> for Usutu virus invading into a malaria-endemic population, and then explore the long-term dynamics of both pathogens once Usutu virus has become established. We find that the vector bias facilitates the introduction of malaria into a susceptible population, as well as the introduction of Usutu in a malaria-endemic population. In the long term, however, both a vector bias and co-infection mortality lead to a decrease in the number of individuals infected with either pathogen, suggesting that avian malaria is unlikely to be a promoter of Usutu invasion. This proposed approach is general and allows for new insights into other negative associations between endemic and invading vector-borne pathogens.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 118-128"},"PeriodicalIF":1.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000352/pdfft?md5=4284ef33f0fe5b3f5e85cb6433600d6b&pid=1-s2.0-S0040580924000352-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140618248","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":"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":"2024-04-13","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":"The expected sample allele frequencies from populations of changing size via orthogonal polynomials","authors":"Lynette Caitlin Mikula ,&nbsp;Claus Vogl","doi":"10.1016/j.tpb.2024.03.005","DOIUrl":"10.1016/j.tpb.2024.03.005","url":null,"abstract":"<div><p>In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by Hidden-Markov-Model (HMM) literature is used to compute exact sample allele frequency spectra for three demographic scenarios: single changes in (effective) population size, boom-bust dynamics, and stochastic fluctuations in (effective) population size. An approach for fully agnostic demographic inference from these sample allele spectra is explored, and sufficient statistics for stepwise changes in population size are found. Further, convergence behaviours of the polymorphic sample spectra for population size changes on different time scales are examined and discussed within the context of inference of the effective population size. Joint visual assessment of the sample spectra and the temporal coefficients of the spectral decomposition of the forward diffusion process is found to be important in determining departure from equilibrium. Stochastic changes in (effective) population size are shown to shape sample spectra particularly strongly.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 55-85"},"PeriodicalIF":1.4,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000339/pdfft?md5=b5dc535787bdc66776c8198cab2cd0d6&pid=1-s2.0-S0040580924000339-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140327303","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":"Interconnection between density-regulation and stability in competitive ecological network","authors":"Amit Samadder ,&nbsp;Arnab Chattopadhyay ,&nbsp;Anurag Sau ,&nbsp;Sabyasachi Bhattacharya","doi":"10.1016/j.tpb.2024.03.003","DOIUrl":"10.1016/j.tpb.2024.03.003","url":null,"abstract":"<div><p>In natural ecosystems, species can be characterized by the nonlinear density-dependent self-regulation of their growth profile. Species of many taxa show a substantial density-dependent reduction for low population size. Nevertheless, many show the opposite trend; density regulation is minimal for small populations and increases significantly when the population size is near the carrying capacity. The theta-logistic growth equation can portray the intraspecific density regulation in the growth profile, theta being the density regulation parameter. In this study, we examine the role of these different growth profiles on the stability of a competitive ecological community with the help of a mathematical model of competitive species interactions. This manuscript deals with the random matrix theory to understand the stability of the classical theta-logistic models of competitive interactions. Our results suggest that having more species with strong density dependence, which self-regulate at low densities, leads to more stable communities. With this, stability also depends on the complexity of the ecological network. Species network connectance (link density) shows a consistent trend of increasing stability, whereas community size (species richness) shows a context-dependent effect. We also interpret our results from the aspect of two different life history strategies: r and K-selection. Our results show that the stability of a competitive network increases with the fraction of r-selected species in the community. Our result is robust, irrespective of different network architectures.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 33-46"},"PeriodicalIF":1.4,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194934","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":"2024-03-21","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}