Theoretical Population Biology最新文献

{"title":"Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities.","authors":"Xiran Liu, Zarif Ahsan, Noah A Rosenberg","doi":"10.1016/j.tpb.2025.05.002","DOIUrl":"https://doi.org/10.1016/j.tpb.2025.05.002","url":null,"abstract":"<p><p>Allele-sharing dissimilarity (ASD) statistics are measures of genetic differentiation for pairs of individuals or populations. Given the allele-frequency distributions of two populations-possibly the same population-the expected value of an ASD statistic is computed by evaluating the expectation of the pairwise dissimilarity between two individuals drawn at random, each from its associated allele-frequency distribution. For each of two ASD statistics, which we term D₁ and D₂, we investigate the extent to which the expected ASD is constrained by allele frequencies in the two populations; in other words, how is the magnitude of the measure bounded as a function of the frequency of the most frequent allelic type? We first consider dissimilarity of a population with itself, obtaining bounds on expected ASD in terms of the frequency of the most frequent allelic type in the population. We then examine pairs of populations that might or might not possess the same most frequent allelic type. Across the unit interval for the frequency of the most frequent allelic type, the expected allele-sharing dissimilarity has a range that is more restricted than the [0,1] interval. The mathematical constraints on expected ASD assist in explaining a pattern observed empirically in human populations, namely that when averaging across loci, allele-sharing dissimilarities between pairs of individuals often tend to vary only within a relatively narrow range.</p>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":" ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144486686","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":"Parthenogenesis, sexual conflict, and selection on fertilization rates in switching environments","authors":"Xiaoyuan Liu ,&nbsp;Jon W. Pitchford ,&nbsp;George W.A. Constable","doi":"10.1016/j.tpb.2025.05.001","DOIUrl":"10.1016/j.tpb.2025.05.001","url":null,"abstract":"<div><div>In the face of varying environments, organisms exhibit a variety of reproductive modes, from asexuality to obligate sexuality. Should reproduction be sexual, the morphology of the sex cells (gametes) produced by these organisms has important evolutionary implications; these cells can be the same size (isogamy), one larger and one smaller (anisogamy), and finally the larger cell can lose its capacity for motility (oogamy, the familiar sperm–egg system). Understanding the origin of the sexes, which lies in the types of gametes they produce, thus amounts to explaining these evolutionary transitions. Here we extend classic results in this area by exploring these transitions in a model in which organisms can reproduce both sexually and asexually. This reproductive mode is present in many algae and is accompanied by suppressed pheromone production in female populations of the brown alga <em>Scytosiphon lomentaria</em>. Our model investigates the co-evolution of gamete cell size with fertilization rate, which is a proxy for motility and pheromone production but is often held constant in anisogamy models. Using adaptive dynamics generalized to the case of switching environments, we find that isogamy can evolve to anisogamy through evolutionary branching, and that anisogamy can evolve to oogamy or suppressed pheromone production through a further branching driven by sexual conflict. We also derive analytic conditions on the model parameters required to arrest evolution on this isogamy–oogamy trajectory, with low fertilization rates and stochastically switching environments stabilizing isogamy under a bet-hedging strategy, and low fertilization costs stabilizing anisogamy and pheromone production.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 37-56"},"PeriodicalIF":1.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183263","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 bounds on r2 and the effect size in case-control genome-wide association studies","authors":"Sanjana M. Paye ,&nbsp;Michael D. Edge","doi":"10.1016/j.tpb.2025.04.003","DOIUrl":"10.1016/j.tpb.2025.04.003","url":null,"abstract":"<div><div>Case-control genome-wide association studies (GWAS) are often used to find associations between genetic variants and diseases. When case-control GWAS are conducted, researchers must make decisions regarding how many cases and how many controls to include in the study. Connections between variants and diseases are made using association statistics, including <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>. Previous work in population genetics has shown that LD statistics, including <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>, are bounded by the allele frequencies in the population being studied. Since varying the case fraction changes sample allele frequencies, we use the known bounds on <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> to explore how the fraction of cases included in a study can affect statistical power to detect associations. We analyze a simple mathematical model and use simulations to study a quantity proportional to the <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> noncentrality parameter, which is closely related to <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>, under various conditions. Varying the case fraction changes the <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> noncentrality parameter, and by extension the statistical power, with effects depending on the dominance, penetrance, and frequency of the risk allele. Our framework explains previously observed results, such as asymmetries in power to detect risk vs. protective alleles, and the fact that a balanced sample of cases and controls does not always give the best power to detect associations, particularly for highly penetrant minor risk alleles that are either dominant or recessive. We show by simulation that our results can be used as a rough guide to statistical power for association tests other than <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> tests of independence.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 1-11"},"PeriodicalIF":1.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089593","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 between two competing macrophyte populations along a resource gradient leads to collapse in a bistable lake ecosystem","authors":"Sirine Boucenna ,&nbsp;Gael Raoul ,&nbsp;Vasilis Dakos","doi":"10.1016/j.tpb.2025.04.001","DOIUrl":"10.1016/j.tpb.2025.04.001","url":null,"abstract":"<div><div>While it is known that shallow lake ecosystems may experience abrupt shifts (ie tipping points) from a clear water state to a contrasting turbid alternative state as a result of eutrophication, the role of evolutionary processes and the impact of trait variation in this context remain largely unexplored. It is crucial to elucidate how eco-evolutionary feedbacks affect abrupt ecological transitions in shallow lakes and more in general in bistable ecosystems. These feedbacks can significantly alter the dynamics of aquatic plants competition, community structure, and species diversity, potentially affecting the existence of alternative states or either delay or expedite the thresholds at which these ecological shifts occur. In this paper, we explore the eco-evolutionary dynamics of submerged and floating macrophytes in a shallow lake ecosystem under asymmetric competition for nutrients and light along a gradient of nutrient diffusion. We use Adaptive Dynamics and a structured population model to analyze the evolution of the growth depth of the submerged and floating macrophytes populations, which influences their competitive ability for the two resources. We show how trait evolution can result in complex dynamics including evolutionary oscillations, extensive diversification and evolutionary suicide. Furthermore, we find that the co-evolution of the two competing populations plays a stabilizing role, but does not significantly alter the dynamics compared to when only one of the two populations is evolving. Overall, our study contributes to the understanding of the effects of evolution on the ecological dynamics of bistable ecosystems.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 23-36"},"PeriodicalIF":1.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081485","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":"Muller’s ratchet and gene duplication","authors":"Fabian Freund ,&nbsp;Johannes Wirtz ,&nbsp;Yichen Zheng ,&nbsp;Yannick Schäfer ,&nbsp;Thomas Wiehe","doi":"10.1016/j.tpb.2025.04.002","DOIUrl":"10.1016/j.tpb.2025.04.002","url":null,"abstract":"<div><div>Copy number of genes in gene families can be highly variable among individuals and may continue to change across generations. Here, we study a model of duplication–selection interaction, which is related to Haigh’s mutation–selection model of Muller’s ratchet. New gene copies are generated by duplication but fitness of individuals decreases as copy number increases. Our model comes in two flavors: duplicates are copied either from a single template or from any existing copy. A duplication–selection equilibrium exists in both cases for infinite size populations and is given by a shifted Poisson or a negative binomial distribution. Unless counteracted by synergistic epistasis, finite populations suffer from loss of low copy-number haplotypes by drift, forcing them into a regime called ‘run-away evolution’ in which new copies accumulate without bound nor equilibrium. We discuss a few empirical examples and interpret them in the light of our models. Generally, large gene families appear too over-dispersed to fit the single template model suggesting a dynamic, and potentially accelerating, duplication process.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"164 ","pages":"Pages 12-22"},"PeriodicalIF":1.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081493","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":"Eco-evolutionary dynamics of anthelmintic resistance in soil-transmitted helminths","authors":"Swati Patel ,&nbsp;Kelsey Lyberger ,&nbsp;Carolin Vegvari ,&nbsp;Hayriye Gulbudak","doi":"10.1016/j.tpb.2025.03.006","DOIUrl":"10.1016/j.tpb.2025.03.006","url":null,"abstract":"<div><div>Anthelmintic resistance (AR) of soil-transmitted helminth parasites against the most widely available drugs is an ongoing concern for both human-infecting and livestock-infecting species. There has been substantial evidence of AR in livestock but less in humans, which may be due to a variety of reasons. In this paper, we develop an eco-evolutionary model that couples the life cycle of these parasites with their underlying evolution in a single biallelic genetic locus that confers resistance to treatment drugs. We determine the critical treatment frequency needed to effectively eliminate the population, for a fixed drug efficacy (without evolution) and use this to classify three qualitative distinct behaviors of the eco-evolutionary model. Then, we describe how aspects of the life cycle influence which qualitative outcome is achieved and the rate of spread of the resistance allele, comparing across parameterized models of human-infecting and livestock-infecting species. For all but one species, we find that lower fecundity rates and lower contact rates speed the spread of resistance, while lower larval death slows it down. The life cycle parameters of <em>Ancylostoma duodenale</em> and <em>Ostertagia circumcincta</em> are associated with the fastest and slowest spread of resistance, respectively. We discuss the mechanistic reason for these results.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 80-90"},"PeriodicalIF":1.2,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844549","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":"A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model","authors":"Asger Hobolth ,&nbsp;Simon Boitard ,&nbsp;Andreas Futschik ,&nbsp;Raphael Leblois","doi":"10.1016/j.tpb.2025.03.002","DOIUrl":"10.1016/j.tpb.2025.03.002","url":null,"abstract":"<div><div>In this paper we develop a general framework for calculating the probability of a genetic sample under a time-homogeneous coalescent process and the infinite sites mutation model. The evolutionary model that we consider can be characterized as a two-step procedure: A coalescent process that describes the ancestral relatedness of the samples and a sprinkling of mutations in separate sites on the ancestral tree according to a Poisson process. The coalescent process is defined using multivariate phase-type theory. The requirements are a rate matrix that determines the transition rates between the ancestral states, an initial state probability vector, and a reward matrix that informs about the characteristics of the ancestral states. For example, the reward matrix could contain information about the number of singleton, doubleton or higher-order lineages in the ancestral states. We analyze the probability generating function for the evolutionary model as a function of the initial state probability vector, the transition rate matrix, the reward matrix, and the mutation rate. The matrix-analytical expression of the probability generating function allows us to develop a general method for calculating the probability of a population genetic data set. We demonstrate that the method is computationally attractive for a small number of mutations and provide a simple and easy-to-implement algorithm for determining the probability of a sample from the evolutionary model. The method is computationally stable and only involves a single inverse matrix operation, matrix multiplications and matrix additions. We provide comprehensive understanding of the procedure by detailed calculations and discussions of several elementary examples. These examples include different sample representations (labeled samples and the site frequency spectrum) and different demographic and genetic models (the structured coalescent and the Beta-coalescent). We apply the sampling formula to calculate probabilities of spectra for the Kingman coalescent and the Beta-coalescent. Even for a small number of samples and mutations we find that the probabilities for spectra vary in huge orders of magnitudes. We compare the probabilities of the spectra to the values of Tajima’s <span><math><mi>D</mi></math></span>-statistics, and find that the <span><math><mi>D</mi></math></span>-statistic is a poor predictor for the probability of a spectrum. Finally, we investigate how the probabilities of the spectra vary with the parametrization of the Beta-coalescent.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 62-79"},"PeriodicalIF":1.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781871","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":"Connectivity, conservation and catch: Understanding the effects of dispersal between harvested and protected patches","authors":"Femke N. Reurik ,&nbsp;Juan Segura ,&nbsp;Frank M. Hilker","doi":"10.1016/j.tpb.2025.03.005","DOIUrl":"10.1016/j.tpb.2025.03.005","url":null,"abstract":"<div><div>Overharvesting is a pressing global problem, and spatial management, such as protecting designated areas, is one proposed solution. This study examines how connectivity (in terms of dispersal rate) between protected and harvested areas affects the asymptotic total population size and the asymptotic yield, which are key questions for conservation management and the design of protected areas. We utilise a two-patch model with heterogeneous habitat qualities, symmetric dispersal and density-dependent growth functions in both discrete and continuous time. One patch is subject to proportional harvesting, while the other one is protected.</div><div>Our results show that increased dispersal does not always increase the asymptotic total population size or the asymptotic yield. Depending on the circumstances, dispersal enables the protected patch to rescue the harvested patch from overexploitation, potentially increasing both total population size and yield. However, high levels of dispersal can also lead to a lower total population size or even cause extinction of both patches if harvesting pressure is strong. The population in the protected patch needs to have high reproductive potential and the protected patch needs to be the effectively larger patch in order to benefit monotonically from increased dispersal. These findings provide a fundamental understanding of how dispersal influences dynamics in fragmented landscapes under harvesting pressure.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 91-105"},"PeriodicalIF":1.2,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732485","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":"Spatial evolutionary public goods game theory applied to optimal resource allocation and defense strategies in herbaceous plants","authors":"Molly Creagar ,&nbsp;Richard Rebarber ,&nbsp;Brigitte Tenhumberg","doi":"10.1016/j.tpb.2025.02.003","DOIUrl":"10.1016/j.tpb.2025.02.003","url":null,"abstract":"<div><div>Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, the payoff for allocating to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We use a combination of spatial evolutionary game theory and stochastic dynamic programming to predict the proportion of plants in the population investing in defense (cooperators) and the proportion of plants that do not (defectors). Our model accounts for metabolic costs of maintenance of stored resources when predicting optimal resource allocation to growth, reproduction, and storage; this cost is not commonly accounted for in previous models. For both annual and perennial plants, our model predicts an evolutionarily stable proportion of cooperators and defectors (mixed stable strategy), but the proportion of cooperators is higher in a population of perennial plants than in a population of annual plants. We also show that including a metabolic cost of maintaining stored resources does not change the proportion of cooperators but does decrease plant fitness and allocation to overwinter storage.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 36-49"},"PeriodicalIF":1.2,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694258","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":"Exact calculation of the expected SFS in structured populations","authors":"Armando Arredondo ,&nbsp;Josué Corujo ,&nbsp;Camille Noûs ,&nbsp;Simon Boitard ,&nbsp;Lounès Chikhi ,&nbsp;Olivier Mazet","doi":"10.1016/j.tpb.2025.03.003","DOIUrl":"10.1016/j.tpb.2025.03.003","url":null,"abstract":"<div><div>The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in a panmictic population under the infinite-site model of mutation has been known in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We show here how to obtain this expected SFS as the solution of a linear system. More precisely, we propose a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system using an iterative method. We then build a specialization for the simplest case of the symmetrical <span><math><mi>n</mi></math></span>-island model to arrive at a ready-to-use software called <em>SISiFS</em> from which a demographic parameters inference framework could easily be developed.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"163 ","pages":"Pages 50-61"},"PeriodicalIF":1.2,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694257","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}