Theoretical Population Biology最新文献

{"title":"The grapheme-valued Wright–Fisher diffusion with mutation","authors":"Andreas Greven ,&nbsp;Frank den Hollander ,&nbsp;Anton Klimovsky ,&nbsp;Anita Winter","doi":"10.1016/j.tpb.2024.04.007","DOIUrl":"10.1016/j.tpb.2024.04.007","url":null,"abstract":"<div><p>In Athreya et al. (2021), models from population genetics were used to define stochastic dynamics in the space of graphons arising as continuum limits of dense graphs. In the present paper we exhibit an example of a simple neutral population genetics model for which this dynamics is a Markovian diffusion that can be characterized as the solution of a martingale problem. In particular, we consider a Markov chain in the space of finite graphs that resembles a Moran model with resampling and mutation. We encode the finite graphs as graphemes, which can be represented as a triple consisting of a vertex set (or more generally, a topological space), an adjacency matrix, and a sampling (Borel) measure. We equip the space of graphons with convergence of sample subgraph densities and show that the grapheme-valued Markov chain converges to a grapheme-valued diffusion as the number of vertices goes to infinity. We show that the grapheme-valued diffusion has a stationary distribution that is linked to the Griffiths–Engen–McCloskey (GEM) distribution. In a companion paper (Greven et al. 2023), we build up a general theory for obtaining grapheme-valued diffusions via genealogies of models in population genetics.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 76-88"},"PeriodicalIF":1.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000406/pdfft?md5=f9d4f022450b2756df0c49347ac9761c&pid=1-s2.0-S0040580924000406-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141184653","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":"Latent mutations in the ancestries of alleles under selection","authors":"Wai-Tong (Louis) Fan ,&nbsp;John Wakeley","doi":"10.1016/j.tpb.2024.04.008","DOIUrl":"10.1016/j.tpb.2024.04.008","url":null,"abstract":"<div><p>We consider a single genetic locus with two alleles <span><math><msub><mrow><mi>A</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> and <span><math><msub><mrow><mi>A</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright–Fisher diffusion and have reached stationarity, we describe the asymptotic behaviors of the conditional gene genealogy and the latent mutations of a sample with known allele counts, when the count <span><math><msub><mrow><mi>n</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> of allele <span><math><msub><mrow><mi>A</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> is fixed, and when either or both the sample size <span><math><mi>n</mi></math></span> and the selection strength <span><math><mrow><mo>|</mo><mi>α</mi><mo>|</mo></mrow></math></span> tend to infinity. Our study extends previous work under neutrality to the case of non-neutral rare alleles, asserting that when selection is not too strong relative to the sample size, even if it is strongly positive or strongly negative in the usual sense (<span><math><mrow><mi>α</mi><mo>→</mo><mo>−</mo><mi>∞</mi></mrow></math></span> or <span><math><mrow><mi>α</mi><mo>→</mo><mo>+</mo><mi>∞</mi></mrow></math></span>), the number of latent mutations of the <span><math><msub><mrow><mi>n</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> copies of allele <span><math><msub><mrow><mi>A</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> follows the same distribution as the number of alleles in the Ewens sampling formula. On the other hand, very strong positive selection relative to the sample size leads to neutral gene genealogies with a single ancient latent mutation. We also demonstrate robustness of our asymptotic results against changing population sizes, when one of <span><math><mrow><mo>|</mo><mi>α</mi><mo>|</mo></mrow></math></span> or <span><math><mi>n</mi></math></span> is large.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 1-20"},"PeriodicalIF":1.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867955","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":"Corrigendum to “Fixation and effective size in a haploid–diploid population with asexual reproduction” [Theoretical Population Biology 143 (2022) 30–45]","authors":"Kazuhiro Bessho ,&nbsp;Sarah P. Otto","doi":"10.1016/j.tpb.2024.04.005","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.04.005","url":null,"abstract":"","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Page 138"},"PeriodicalIF":1.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000388/pdfft?md5=f5b68b0069966146ee9e2da2038b0757&pid=1-s2.0-S0040580924000388-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140816123","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":"Polygenic dynamics underlying the response of quantitative traits to directional selection","authors":"Hannah Götsch ,&nbsp;Reinhard Bürger","doi":"10.1016/j.tpb.2024.04.006","DOIUrl":"10.1016/j.tpb.2024.04.006","url":null,"abstract":"<div><p>We study the response of a quantitative trait to exponential directional selection in a finite haploid population, both at the genetic and the phenotypic level. We assume an infinite sites model, in which the number of new mutations per generation in the population follows a Poisson distribution (with mean <span><math><mi>Θ</mi></math></span>) and each mutation occurs at a new, previously monomorphic site. Mutation effects are beneficial and drawn from a distribution. Sites are unlinked and contribute additively to the trait. Assuming that selection is stronger than random genetic drift, we model the initial phase of the dynamics by a supercritical Galton–Watson process. This enables us to obtain time-dependent results. We show that the copy-number distribution of the mutant in generation <span><math><mi>n</mi></math></span>, conditioned on non-extinction until <span><math><mi>n</mi></math></span>, is described accurately by the deterministic increase from an initial distribution with mean 1. This distribution is related to the absolutely continuous part <span><math><msup><mrow><mi>W</mi></mrow><mrow><mo>+</mo></mrow></msup></math></span> of the random variable, typically denoted <span><math><mi>W</mi></math></span>, that characterizes the stochasticity accumulating during the mutant’s sweep. A suitable transformation yields the approximate dynamics of the mutant frequency distribution in a Wright–Fisher population of size <span><math><mi>N</mi></math></span>. Our expression provides a very accurate approximation except when mutant frequencies are close to 1. On this basis, we derive explicitly the (approximate) time dependence of the expected mean and variance of the trait and of the expected number of segregating sites. Unexpectedly, we obtain highly accurate approximations for all times, even for the quasi-stationary phase when the expected per-generation response and the trait variance have equilibrated. The latter refine classical results. In addition, we find that <span><math><mi>Θ</mi></math></span> is the main determinant of the pattern of adaptation at the genetic level, i.e., whether the initial allele-frequency dynamics are best described by sweep-like patterns at few loci or small allele-frequency shifts at many. The number of segregating sites is an appropriate indicator for these patterns. The selection strength determines primarily the rate of adaptation. The accuracy of our results is tested by comprehensive simulations in a Wright–Fisher framework. We argue that our results apply to more complex forms of directional selection.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 21-59"},"PeriodicalIF":1.4,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S004058092400039X/pdfft?md5=8757c8dd3a942c9f0c1e627b25941dbb&pid=1-s2.0-S004058092400039X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855705","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":"Limits to selection on standing variation in an asexual population","authors":"Nick Barton ,&nbsp;Himani Sachdeva","doi":"10.1016/j.tpb.2024.04.001","DOIUrl":"https://doi.org/10.1016/j.tpb.2024.04.001","url":null,"abstract":"&lt;div&gt;&lt;p&gt;We consider how a population of &lt;span&gt;&lt;math&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;z&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mo&gt;…&lt;/mo&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;z&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;, which are drawn from a distribution &lt;span&gt;&lt;math&gt;&lt;mi&gt;ψ&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt;; the fitness of individual &lt;span&gt;&lt;math&gt;&lt;mi&gt;i&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; is proportional to &lt;span&gt;&lt;math&gt;&lt;msup&gt;&lt;mrow&gt;&lt;mi&gt;e&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;z&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;i&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msup&gt;&lt;/math&gt;&lt;/span&gt;. For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;, and show that for large &lt;span&gt;&lt;math&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt;, there is a scaling limit which depends on a single parameter &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;. When selection is weak relative to drift (&lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;mo&gt;≪&lt;/mo&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;), the variance decreases exponentially at rate &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;mo&gt;/&lt;/mo&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;, and the expected ultimate gain in log fitness (scaled by &lt;span&gt;&lt;math&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;/math&gt;&lt;/span&gt;), is just &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;, which is the same as Robertson’s (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (&lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;mo&gt;≫&lt;/mo&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;), 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 &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;mo&gt;∼&lt;/mo&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;mo&gt;/&lt;/mo&gt;&lt;msqrt&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;V&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/msqrt&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; of an allele with value &lt;span&gt;&lt;math&gt;&lt;mi&gt;z&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; is &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;P&lt;/mi&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mi&gt;z&lt;/mi&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;, with mean &lt;span&gt;&lt;math&gt;&lt;mover&gt;&lt;mrow&gt;&lt;mi&gt;P&lt;/mi&gt;&lt;/mrow&gt;&lt;mo&gt;¯&lt;/mo&gt;&lt;/mover&gt;&lt;/math&gt;&lt;/span&gt;, the winning allele is the fittest of &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;N&lt;/mi&gt;&lt;mover&gt;&lt;mrow&gt;&lt;mi&gt;P&lt;/mi&gt;&lt;/mrow&gt;&lt;mo&gt;¯&lt;/mo&gt;&lt;/mover&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; survivors drawn from a distribution &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mi&gt;ψ&lt;/mi&gt;&lt;mi&gt;P&lt;/mi&gt;&lt;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}