Theoretical Population Biology最新文献

{"title":"Patterns of spawning and settlement of reef fishes as strategic responses to post-settlement competition","authors":"Erik G. Noonburg ,&nbsp;Suzanne H. Alonzo ,&nbsp;Craig W. Osenberg ,&nbsp;Stephen E. Swearer ,&nbsp;Jeffrey S. Shima","doi":"10.1016/j.tpb.2024.08.001","DOIUrl":"10.1016/j.tpb.2024.08.001","url":null,"abstract":"<div><p>Settlement is a critical transition in the life history of reef fish, and the timing of this event can have a strong effect on fitness. Key factors that influence settlement timing are predictable lunar cyclic variation in tidal currents, moonlight, and nocturnal predation risk as larvae transition from pelagic to benthic environments. However, populations typically display wide variation in the arrival of settlers over the lunar cycle. This variation is often hypothesized to result from unpredictable conditions in the pelagic environment and bet-hedging by spawning adults. Here, we consider the hypothesis that the timing of spawning and settlement is a strategic response to post-settlement competition. We use a game theoretic model to predict spawning and settlement distributions when fish face a tradeoff between minimizing density-independent predation risk while crossing the reef crest vs. avoiding high competitor density on settlement habitat. In general, we expect competition to spread spawning over time such that settlement is distributed around the lunar phase with the lowest predation risk, similar to an ideal free distribution in which competition spreads competitors across space. We examine the effects of overcompensating density dependence, age-dependent competition, and competition among daily settler cohorts. Our model predicts that even in the absence of stochastic variation in the larval environment, competition can result in qualitative divergence between spawning and settlement distributions. Furthermore, we show that if competitive strength increases with settler age, competition results in covariation between settler age and settlement date, with older larvae settling when predation risk is minimal. We predict that competition between daily cohorts delays peak settlement, with priority effects potentially selecting for a multimodal settlement distribution.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"160 ","pages":"Pages 1-13"},"PeriodicalIF":1.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057074","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 invasion of cooperative parasites","authors":"","doi":"10.1016/j.tpb.2024.07.001","DOIUrl":"10.1016/j.tpb.2024.07.001","url":null,"abstract":"<div><p>In this paper we study invasion probabilities and invasion times of cooperative parasites spreading in spatially structured host populations. The spatial structure of the host population is given by a random geometric graph on <span><math><msup><mrow><mrow><mo>[</mo><mn>0</mn><mo>,</mo><mn>1</mn><mo>]</mo></mrow></mrow><mrow><mi>n</mi></mrow></msup></math></span>, <span><math><mrow><mi>n</mi><mo>∈</mo><mi>N</mi></mrow></math></span>, with a Poisson<span><math><mrow><mo>(</mo><mi>N</mi><mo>)</mo></mrow></math></span>-distributed number of vertices and in which vertices are connected over an edge when they have a distance of at most <span><math><msub><mrow><mi>r</mi></mrow><mrow><mi>N</mi></mrow></msub></math></span> with <span><math><msub><mrow><mi>r</mi></mrow><mrow><mi>N</mi></mrow></msub></math></span> of order <span><math><msup><mrow><mi>N</mi></mrow><mrow><mrow><mo>(</mo><mi>β</mi><mo>−</mo><mn>1</mn><mo>)</mo></mrow><mo>/</mo><mi>n</mi></mrow></msup></math></span> for some <span><math><mrow><mn>0</mn><mo>&lt;</mo><mi>β</mi><mo>&lt;</mo><mn>1</mn></mrow></math></span>. At a host infection many parasites are generated and parasites move along edges to neighbouring hosts. We assume that parasites have to cooperate to infect hosts, in the sense that at least two parasites need to attack a host simultaneously. We find lower and upper bounds on the invasion probability of the parasites in terms of survival probabilities of branching processes with cooperation. Furthermore, we characterize the asymptotic invasion time.</p><p>An important ingredient of the proofs is a comparison with infection dynamics of cooperative parasites in host populations structured according to a complete graph, i.e. in well-mixed host populations. For these infection processes we can show that invasion probabilities are asymptotically equal to survival probabilities of branching processes with cooperation. Furthermore, we build on proof techniques developed in Brouard and Pokalyuk (2022), where an analogous invasion process has been studied for host populations structured according to a configuration model.</p><p>We substantiate our results with simulations.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 35-58"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000686/pdfft?md5=7baf961ab53e2f51f9344de949b836db&pid=1-s2.0-S0040580924000686-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141591851","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":"A Wright–Fisher graph model and the impact of directional selection on genetic variation","authors":"Ingemar Kaj ,&nbsp;Carina F. Mugal ,&nbsp;Rebekka Müller-Widmann","doi":"10.1016/j.tpb.2024.07.004","DOIUrl":"10.1016/j.tpb.2024.07.004","url":null,"abstract":"<div><p>We introduce a multi-allele Wright–Fisher model with mutation and selection such that allele frequencies at a single locus are traced by the path of a hybrid jump–diffusion process. The state space of the process is given by the vertices and edges of a topological graph, i.e. edges are unit intervals. Vertices represent monomorphic population states and positions on the edges mark the biallelic proportions of ancestral and derived alleles during polymorphic segments. In this setting, mutations can only occur at monomorphic loci. We derive the stationary distribution in mutation–selection–drift equilibrium and obtain the expected allele frequency spectrum under large population size scaling. For the extended model with multiple independent loci we derive rigorous upper bounds for a wide class of associated measures of genetic variation. Within this framework we present mathematically precise arguments to conclude that the presence of directional selection reduces the magnitude of genetic variation, as constrained by the bounds for neutral evolution.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 13-24"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000777/pdfft?md5=c7ea20aafbe501d42760b57841f9e368&pid=1-s2.0-S0040580924000777-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635177","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":"Joint identity among loci under mutation and regular inbreeding","authors":"Marcy K. Uyenoyama","doi":"10.1016/j.tpb.2024.08.002","DOIUrl":"10.1016/j.tpb.2024.08.002","url":null,"abstract":"<div><p>This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci. Measures of association depend on genetic diversity rather than allelic frequencies, as do linkage disequilibrium and its relatives. Scaled indices designed to show monotonic dependence on rates of crossing-over, inbreeding, and mutation may prove useful for interpreting patterns of genome-scale variation.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 74-90"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114062","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 ancestral selection graph for a Λ-asymmetric Moran model","authors":"","doi":"10.1016/j.tpb.2024.02.010","DOIUrl":"10.1016/j.tpb.2024.02.010","url":null,"abstract":"<div><p>Motivated by the question of the impact of selective advantage in populations with skewed reproduction mechanisms, we study a Moran model with selection. We assume that there are two types of individuals, where the reproductive success of one type is larger than the other. The higher reproductive success may stem from either more frequent reproduction, or from larger numbers of offspring, and is encoded in a measure <span><math><mi>Λ</mi></math></span> for each of the two types. <span><math><mi>Λ</mi></math></span>-reproduction here means that a whole fraction of the population is replaced at a reproductive event. Our approach consists of constructing a <span><math><mi>Λ</mi></math></span>-asymmetric Moran model in which individuals of the two populations compete, rather than considering a Moran model for each population. Provided the measure are ordered stochastically, we can couple them. This allows us to construct the central object of this paper, the <span><math><mrow><mi>Λ</mi><mo>−</mo></mrow></math></span>asymmetric ancestral selection graph, leading to a pathwise duality of the forward in time <span><math><mi>Λ</mi></math></span>-asymmetric Moran model with its ancestral process. We apply the ancestral selection graph in order to obtain scaling limits of the forward and backward processes, and note that the frequency process converges to the solution of an SDE with discontinuous paths. Finally, we derive a Griffiths representation for the generator of the SDE and use it to find a semi-explicit formula for the probability of fixation of the less beneficial of the two types.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 91-107"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000194/pdfft?md5=c0dce179bca40926eed0fec256704b68&pid=1-s2.0-S0040580924000194-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mean-field interacting multi-type birth–death processes with a view to applications in phylodynamics","authors":"William S. DeWitt ,&nbsp;Steven N. Evans ,&nbsp;Ella Hiesmayr ,&nbsp;Sebastian Hummel","doi":"10.1016/j.tpb.2024.07.002","DOIUrl":"10.1016/j.tpb.2024.07.002","url":null,"abstract":"<div><p>Multi-type birth–death processes underlie approaches for inferring evolutionary dynamics from phylogenetic trees across biological scales, ranging from deep-time species macroevolution to rapid viral evolution and somatic cellular proliferation. A limitation of current phylogenetic birth–death models is that they require restrictive linearity assumptions that yield tractable message-passing likelihoods, but that also preclude interactions between individuals. Many fundamental evolutionary processes – such as environmental carrying capacity or frequency-dependent selection – entail interactions, and may strongly influence the dynamics in some systems. Here, we introduce a multi-type birth–death process in mean-field interaction with an ensemble of replicas of the focal process. We prove that, under quite general conditions, the ensemble’s stochastically evolving interaction field converges to a <em>deterministic</em> trajectory in the limit of an infinite ensemble. In this limit, the replicas effectively decouple, and self-consistent interactions appear as nonlinearities in the infinitesimal generator of the focal process. We investigate a special case that is rich enough to model both carrying capacity and frequency-dependent selection while yielding tractable message-passing likelihoods in the context of a phylogenetic birth–death model.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 1-12"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000753/pdfft?md5=449649d0ee10fbb5ed718ac4824a76ef&pid=1-s2.0-S0040580924000753-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635178","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":"Duality and the well-posedness of a martingale problem","authors":"Andrej Depperschmidt ,&nbsp;Andreas Greven ,&nbsp;Peter Pfaffelhuber","doi":"10.1016/j.tpb.2024.07.003","DOIUrl":"10.1016/j.tpb.2024.07.003","url":null,"abstract":"&lt;div&gt;&lt;p&gt;For two Polish state spaces &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt; and &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;, and an operator &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;G&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;, we obtain existence and uniqueness of a &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;G&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;-martingale problem provided there is a bounded continuous duality function &lt;span&gt;&lt;math&gt;&lt;mi&gt;H&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; on &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; together with a dual process &lt;span&gt;&lt;math&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; on &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt; which is the unique solution of a &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;G&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;-martingale problem. For the corresponding solutions &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt; and &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;, duality with respect to a function &lt;span&gt;&lt;math&gt;&lt;mi&gt;H&lt;/mi&gt;&lt;/math&gt;&lt;/span&gt; in its simplest form means that the relation &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;x&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mrow&gt;&lt;mo&gt;[&lt;/mo&gt;&lt;mi&gt;H&lt;/mi&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;y&lt;/mi&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;mo&gt;]&lt;/mo&gt;&lt;/mrow&gt;&lt;mo&gt;=&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mrow&gt;&lt;mo&gt;[&lt;/mo&gt;&lt;mi&gt;H&lt;/mi&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mi&gt;x&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;mo&gt;]&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; holds for all &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mi&gt;x&lt;/mi&gt;&lt;mo&gt;,&lt;/mo&gt;&lt;mi&gt;y&lt;/mi&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;mo&gt;∈&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;E&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; and &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;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt;. While duality is well-known to imply uniqueness of the &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;G&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;X&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/math&gt;&lt;/span&gt;-martingale problem, we give here a set of conditions under which duality also implies existence without using approximating sequences of processes of a different kind (e.g. jump processes to approximate diffusions) which is a widespread strategy for proving existence of solutions of martingale problems. Given the process &lt;span&gt;&lt;math&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;msub&gt;&lt;mrow&gt;&lt;mi&gt;Y&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mi&gt;t&lt;/mi&gt;&lt;mo&gt;≥&lt;/mo&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/mrow&gt;&lt;/msub&gt;&lt;/mat","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 59-73"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000765/pdfft?md5=3a0d0ba95ef090a854236fc78278e994&pid=1-s2.0-S0040580924000765-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001150","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":"One hundred years of influenza A evolution","authors":"Bjarke Frost Nielsen ,&nbsp;Christian Berrig ,&nbsp;Bryan T. Grenfell ,&nbsp;Viggo Andreasen","doi":"10.1016/j.tpb.2024.07.005","DOIUrl":"10.1016/j.tpb.2024.07.005","url":null,"abstract":"<div><p>Leveraging the simplicity of nucleotide mismatch distributions, we provide an intuitive window into the evolution of the human influenza A ‘nonstructural’ (NS) gene segment. In an analysis suggested by the eminent Danish biologist Freddy B. Christiansen, we illustrate the existence of a continuous genetic “backbone” of influenza A NS sequences, steadily increasing in nucleotide distance to the 1918 root over more than a century. The 2009 influenza A/H1N1 pandemic represents a clear departure from this enduring genetic backbone. Utilizing nucleotide distance maps and phylogenetic analyses, we illustrate remaining uncertainties regarding the origin of the 2009 pandemic, highlighting the complexity of influenza evolution. The NS segment is interesting precisely because it experiences less pervasive positive selection, and departs less strongly from neutral evolution than e.g. the HA antigen. Consequently, sudden deviations from neutral diversification can indicate changes in other genes via the hitchhiking effect. Our approach employs two measures based on nucleotide mismatch counts to analyze the evolutionary dynamics of the NS gene segment. The <em>rooted Hamming map</em> of distances between a reference sequence and all other sequences over time, and the unrooted temporal Hamming distribution which captures the distribution of genotypic distances between simultaneously circulating viruses, thereby revealing patterns of nucleotide diversity and epi-evolutionary dynamics.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 25-34"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demographic inference for spatially heterogeneous populations using long shared haplotypes","authors":"","doi":"10.1016/j.tpb.2024.03.002","DOIUrl":"10.1016/j.tpb.2024.03.002","url":null,"abstract":"<div><p>We introduce a modified spatial <span><math><mi>Λ</mi></math></span>-Fleming–Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"159 ","pages":"Pages 108-124"},"PeriodicalIF":1.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000285/pdfft?md5=83582755d2ad3c07d32cc176757e368e&pid=1-s2.0-S0040580924000285-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Muller’s ratchet in a near-critical regime: Tournament versus fitness proportional selection","authors":"J.L. Igelbrink ,&nbsp;A. González Casanova ,&nbsp;C. Smadi ,&nbsp;A. Wakolbinger","doi":"10.1016/j.tpb.2024.06.001","DOIUrl":"10.1016/j.tpb.2024.06.001","url":null,"abstract":"<div><p>Muller’s ratchet, in its prototype version, models a haploid, asexual population whose size <span><math><mi>N</mi></math></span> is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. The classical variant considers <em>fitness proportional</em> selection, but other fitness schemes are conceivable as well. Inspired by the work of Etheridge et al. (2009) we propose a parameter scaling which fits well to the “near-critical” regime that was in the focus of Etheridge et al. (2009) (and in which the mutation–selection ratio diverges logarithmically as <span><math><mrow><mi>N</mi><mo>→</mo><mi>∞</mi></mrow></math></span>). Using a Moran model, we investigate the“rule of thumb” given in Etheridge et al. (2009) for the click rate of the “classical ratchet” by putting it into the context of new results on the long-time evolution of the size of the best class of the ratchet with (binary) tournament selection. This variant of Muller’s ratchet was introduced in González Casanova et al. (2023), and was analysed there in a subcritical parameter regime. Other than that of the classical ratchet, the size of the best class of the tournament ratchet follows an autonomous dynamics up to the time of its extinction. It turns out that, under a suitable correspondence of the model parameters, this dynamics coincides with the so called Poisson profile approximation of the dynamics of the best class of the classical ratchet.</p></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"158 ","pages":"Pages 121-138"},"PeriodicalIF":1.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0040580924000613/pdfft?md5=39cd36b5168e3c4b5182ac2584e304f9&pid=1-s2.0-S0040580924000613-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285183","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}