Theoretical Population Biology最新文献

{"title":"Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing","authors":"Maximillian Newman ,&nbsp;John Wakeley ,&nbsp;Wai-Tong (Louis) Fan","doi":"10.1016/j.tpb.2025.05.003","DOIUrl":"10.1016/j.tpb.2025.05.003","url":null,"abstract":"<div><div>We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the genealogical relationships of a sample of two gene copies at a genetic locus. Specifically, we consider a diploid Moran model with constant population size <span><math><mi>N</mi></math></span> over time, in which a proportion of offspring are produced by selfing. We show that the conditional distribution of the pairwise coalescence time at a single locus given the random pedigree converges to a limit law as <span><math><mi>N</mi></math></span> tends to infinity. The distribution of coalescence times obtained in this way predicts variation among unlinked loci in a sample of individuals. Traditional coalescent analyses implicitly average over pedigrees and generally make different predictions. We describe three different behaviors in the limit depending on the relative strengths, from large to small, of selfing versus outcrossing: partial selfing, limited outcrossing, and negligible outcrossing. In the case of partial selfing, coalescence times are related to the Kingman coalescent, similar to what is found in traditional analyses. In the case of limited outcrossing, the retained pedigree information forms a random graph, with coalescence times given by the meeting times of random walks on this graph. In the case of negligible outcrossing, which represents complete or nearly complete selfing, coalescence times are determined entirely by the fixed times to common ancestry of diploid individuals in the pedigree.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 29-44"},"PeriodicalIF":1.2,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602077","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":"Identity-by-descent segments in large samples","authors":"Seth D. Temple ,&nbsp;Elizabeth A. Thompson","doi":"10.1016/j.tpb.2025.06.003","DOIUrl":"10.1016/j.tpb.2025.06.003","url":null,"abstract":"<div><div>If two haplotypes share the same alleles for an extended gene tract, these haplotypes are likely to be derived identical-by-descent from a recent common ancestor. Identity-by-descent segment lengths are correlated via unobserved ancestral tree and recombination processes, which commonly presents challenges to the derivation of theoretical results in population genetics. We show that the proportion of detectable identity-by-descent segments around a locus is normally distributed when the sample size and the scaled population size are large. We generalize this central limit theorem to cover flexible demographic scenarios, multi-way identity-by-descent segments, and multivariate identity-by-descent rates. The regularity conditions on sample size and scaled population size are unlikely to hold in genetic data from real populations, but provide intuition for when the Gaussian distribution may be a reasonable approximate model for the IBD rate. We use efficient simulations to study the distributional behavior of the detectable identity-by-descent rate. One consequence of non-normality in finite samples is that a genome-wide scan looking for excess identity-by-descent rates may be subject to anti-conservative control of family-wise error rates.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 10-21"},"PeriodicalIF":1.2,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585410","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":"The TMRCA of general genealogies in populations with deterministically varying size","authors":"Alejandro H. Wences ,&nbsp;Lizbeth Peñaloza ,&nbsp;Matthias Steinrücken ,&nbsp;Arno Siri-Jégousse","doi":"10.1016/j.tpb.2025.06.002","DOIUrl":"10.1016/j.tpb.2025.06.002","url":null,"abstract":"<div><div>We study the time to the most recent common ancestor (TMRCA) of a sample of finite size in a wide class of genealogical models for populations with deterministically varying size. This is made possible by recently developed results on inhomogeneous phase-type random variables, allowing us to obtain the density and the moments of the TMRCA of time-dependent coalescent processes in terms of matrix formulas. We also provide matrix simplifications permitting a more straightforward calculation. With these results, the TMRCA provides an explanatory variable to distinguish different evolutionary scenarios, and to infer model parameters.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 1-9"},"PeriodicalIF":1.2,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565359","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 redirected help with stepping-stone dispersal","authors":"Alan Flatrès,&nbsp;Geoff Wild","doi":"10.1016/j.tpb.2025.06.001","DOIUrl":"10.1016/j.tpb.2025.06.001","url":null,"abstract":"<div><div>Individuals can be subject to brood failure for many reasons, e.g. egg predation. Some species have adopted a strategy to compensate for fitness loss due to brood failure. In some bird species, individuals that experience brood failure can help a related neighbor care for their offspring. This behavior is known as redirected helping and it compensates for the loss of fitness by improving inclusive fitness. However, inclusive fitness gains associated with redirected helping are counteracted in a ‘viscous’ population, where individuals remain close to their natal site, by increased competition among kin. In a previous model, we investigated how population viscosity affects the evolution of redirected help by building an infinite-island model that lacked explicit spatial structure and emphasized dispersal on a global scale. Here, we revisit the role of population viscosity in the evolution of redirected help with a spatially explicit stepping-stone dispersal model. The dispersal pattern in this new framework is much more constrained than in the infinite-island case, strengthening the population viscosity we are interested in. In contrast to previous work, we find that localized dispersal can prevent the evolution of redirected help and even lead to the evolution of spiteful behavior in some specific cases. Our predictions are sensitive to the scale of dispersal, survival rate and the benefits provided by helping. We discuss our findings with regard to the previous literature investigating the evolution of helping in a viscous population.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"165 ","pages":"Pages 22-28"},"PeriodicalIF":1.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561735","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":"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":"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}