Theoretical Population Biology最新文献

{"title":"The coalescent in finite populations with arbitrary, fixed structure","authors":"Benjamin Allen ,&nbsp;Alex McAvoy","doi":"10.1016/j.tpb.2024.06.004","DOIUrl":"10.1016/j.tpb.2024.06.004","url":null,"abstract":"<div><p>The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial, age, and class structure, along with other features of real-world populations. To further extend the range of population structures to which coalescent theory applies, we formulate a coalescent process for a broad class of neutral drift models with arbitrary – but fixed – spatial, age, sex, and class structure, haploid or diploid genetics, and any fixed mating pattern. Here, the coalescent is represented as a random sequence of mappings <span><math><mrow><mi>C</mi><mo>=</mo><msubsup><mrow><mfenced><mrow><msub><mrow><mi>C</mi></mrow><mrow><mi>t</mi></mrow></msub></mrow></mfenced></mrow><mrow><mi>t</mi><mo>=</mo><mn>0</mn></mrow><mrow><mi>∞</mi></mrow></msubsup></mrow></math></span> from a finite set <span><math><mi>G</mi></math></span> to itself. The set <span><math><mi>G</mi></math></span> represents the “sites” (in individuals, in particular locations and/or classes) at which these alleles can live. The state of the coalescent, <span><math><mrow><msub><mrow><mi>C</mi></mrow><mrow><mi>t</mi></mrow></msub><mo>:</mo><mi>G</mi><mo>→</mo><mi>G</mi></mrow></math></span>, maps each site <span><math><mrow><mi>g</mi><mo>∈</mo><mi>G</mi></mrow></math></span> to the site containing <span><math><mi>g</mi></math></span>’s ancestor, <span><math><mi>t</mi></math></span> time-steps into the past. Using this representation, we define and analyze coalescence time, coalescence branch length, mutations prior to coalescence, and stationary probabilities of identity-by-descent and identity-by-state. For low mutation, we provide a recipe for computing identity-by-descent and identity-by-state probabilities via the coalescent. Applying our results to a diploid population with arbitrary sex ratio <span><math><mi>r</mi></math></span>, we find that measures of genetic dissimilarity, among any set of sites, are scaled by <span><math><mrow><mn>4</mn><mi>r</mi><mrow><mo>(</mo><mn>1</mn><mo>−</mo><mi>r</mi><mo>)</mo></mrow></mrow></math></span> relative to the even sex ratio case.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 150-169"},"PeriodicalIF":1.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000649/pdfft?md5=a09fbbcdb9b66c124896eb3ccc9340db&pid=1-s2.0-S0040580924000649-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332353","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 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":"2024-08-01","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":"Unifying quantification methods for sexual selection and assortative mating using information theory","authors":"A. Carvajal-Rodríguez","doi":"10.1016/j.tpb.2024.06.007","DOIUrl":"10.1016/j.tpb.2024.06.007","url":null,"abstract":"<div><p>Sexual selection plays a crucial role in modern evolutionary theory, offering valuable insight into evolutionary patterns and species diversity. Recently, a comprehensive definition of sexual selection has been proposed, defining it as any selection that arises from fitness differences associated with nonrandom success in the competition for access to gametes for fertilization. Previous research on discrete traits demonstrated that non-random mating can be effectively quantified using Jeffreys (or symmetrized Kullback-Leibler) divergence, capturing information acquired through mating influenced by mutual mating propensities instead of random occurrences. This novel theoretical framework allows for detecting and assessing the strength of sexual selection and assortative mating.</p><p>In this study, we aim to achieve two primary objectives. Firstly, we demonstrate the seamless alignment of the previous theoretical development, rooted in information theory and mutual mating propensity, with the aforementioned definition of sexual selection. Secondly, we extend the theory to encompass quantitative traits. Our findings reveal that sexual selection and assortative mating can be quantified effectively for quantitative traits by measuring the information gain relative to the random mating pattern. The connection of the information indices of sexual selection with the classical measures of sexual selection is established.</p><p>Additionally, if mating traits are normally distributed, the measure capturing the underlying information of assortative mating is a function of the square of the correlation coefficient, taking values within the non-negative real number set [0, +∞).</p><p>It is worth noting that the same divergence measure captures information acquired through mating for both discrete and quantitative traits. This is interesting as it provides a common context and can help simplify the study of sexual selection patterns.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 206-215"},"PeriodicalIF":1.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000650/pdfft?md5=a22dea1ed5eeb299ff36e9cf8734d81b&pid=1-s2.0-S0040580924000650-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452035","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":"Host control and species interactions jointly determine microbiome community structure","authors":"Eeman Abbasi,&nbsp;Erol Akçay","doi":"10.1016/j.tpb.2024.06.006","DOIUrl":"10.1016/j.tpb.2024.06.006","url":null,"abstract":"<div><p>The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 185-194"},"PeriodicalIF":1.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460283","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 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":"2024-06-01","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":"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":"2024-06-01","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":"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":"2024-06-01","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":"Phase-type distributions in mathematical population genetics: An emerging framework","authors":"Asger Hobolth ,&nbsp;Iker Rivas-González ,&nbsp;Mogens Bladt ,&nbsp;Andreas Futschik","doi":"10.1016/j.tpb.2024.03.001","DOIUrl":"10.1016/j.tpb.2024.03.001","url":null,"abstract":"<div><p>A phase-type distribution is the time to absorption in a continuous- or discrete-time Markov chain. Phase-type distributions can be used as a general framework to calculate key properties of the standard coalescent model and many of its extensions. Here, the ‘phases’ in the phase-type distribution correspond to states in the ancestral process. For example, the time to the most recent common ancestor and the total branch length are phase-type distributed. Furthermore, the site frequency spectrum follows a multivariate discrete phase-type distribution and the joint distribution of total branch lengths in the two-locus coalescent-with-recombination model is multivariate phase-type distributed. In general, phase-type distributions provide a powerful mathematical framework for coalescent theory because they are analytically tractable using matrix manipulations. The purpose of this review is to explain the phase-type theory and demonstrate how the theory can be applied to derive basic properties of coalescent models. These properties can then be used to obtain insight into the ancestral process, or they can be applied for statistical inference. In particular, we show the relation between classical first-step analysis of coalescent models and phase-type calculations. We also show how reward transformations in phase-type theory lead to easy calculation of covariances and correlation coefficients between e.g. tree height, tree length, external branch length, and internal branch length. Furthermore, we discuss how these quantities can be used for statistical inference based on estimating equations. Providing an alternative to previous work based on the Laplace transform, we derive likelihoods for small-size coalescent trees based on phase-type theory. Overall, our main aim is to demonstrate that phase-type distributions provide a convenient general set of tools to understand aspects of coalescent models that are otherwise difficult to derive. Throughout the review, we emphasize the versatility of the phase-type framework, which is also illustrated by our accompanying R-code. All our analyses and figures can be reproduced from code available on GitHub.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"157 ","pages":"Pages 14-32"},"PeriodicalIF":1.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000212/pdfft?md5=635096b59c3865e96b03602b5158c0b9&pid=1-s2.0-S0040580924000212-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"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":"2024-06-01","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":"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":"2024-06-01","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}