Theoretical Population Biology最新文献

{"title":"Corrigendum to “Exact calculation of the expected SFS in structured populations” [Theoretical Population Biology Volume 163(2025) 50-61]","authors":"Armando Arredondo , Josué Corujo , Simon Boitard , Lounès Chikhi , Olivier Mazet","doi":"10.1016/j.tpb.2026.04.001","DOIUrl":"10.1016/j.tpb.2026.04.001","url":null,"abstract":"","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"169 ","pages":"Page 39"},"PeriodicalIF":1.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148044261","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":"Interacting Partially Observable DBN to model the dynamics of partially observable metapopulations: Opportunities and open challenges","authors":"Hanna Bacave ,&nbsp;Pierre-Olivier Cheptou ,&nbsp;Nathalie Peyrard","doi":"10.1016/j.tpb.2025.12.004","DOIUrl":"10.1016/j.tpb.2025.12.004","url":null,"abstract":"<div><div>Among the mathematical approaches used to model population dynamics, Hidden Markov Models (HMM) are well adapted to the case where the species of interest is difficult to observe. For a broader application of HMM in ecology, two limits need to be overcome. While HMMs can deal with detection errors, another important situation is when only some life stages of the population can be observed while the others remain hidden. The metapopulation level, rather than a single population, makes it possible to incorporate dispersal processes, often linked to hidden life stages. Therefore, there is a need to extend the HMM framework to the case of several couples of hidden and observed life stages interacting via dispersal. We propose a conceptual guide to model and estimate such dynamics using the framework of interacting Partially Observable Dynamic Bayesian Networks (PO-DBN). We show that only four interaction structures are needed to describe the main metapopulation models. We illustrate them on concrete examples. Well known computational challenges apply to inference in metapopulation models with partial observation, due to the problem dimension. We discuss parameter estimation using the EM algorithm and we establish that for two structures the complexity of EM is actually linear in the number of patches, which means that estimation is easily accessible for the associated metapopulations. For the two other structures, the EM complexity is exponential and we discuss methods for approximate inference. This study provides the practical foundations for modelling and estimating the dynamics of a metapopulation with hidden life stages.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"168 ","pages":"Pages 19-31"},"PeriodicalIF":1.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145851266","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":"Strategies for resolving cellular phylogenies from sequential lineage tracing data","authors":"Nicola Mulberry ,&nbsp;Tanja Stadler","doi":"10.1016/j.tpb.2026.01.001","DOIUrl":"10.1016/j.tpb.2026.01.001","url":null,"abstract":"<div><div>A combination of recent advancements in molecular recording devices and sequencing technologies has made it possible to generate lineage tracing data on the order of thousands of cells. Dynamic lineage recorders are able to generate random, heritable mutations which accumulate continuously on the timescale of developmental processes; this genetic information is then recovered using single-cell RNA sequencing. These data have the potential to hold rich phylogenetic information due to the irreversible nature of the editing process, a key feature of the employed CRISPR-based systems that deviates from traditional assumptions about molecular mutation processes. Recent technologies have furthermore made it possible for mutations to be acquired sequentially. Understanding the information content of these recorders remains an open area of investigation. Here, we model a sequentially-edited recording system and analyse the experimental conditions over which exact phylogenetic reconstruction occurs with high probability. We find, using simulation and theory, explicit parameter regimes over which simple and efficient distance-based reconstruction methods can accurately resolve the cellular phylogeny. We furthermore illustrate how our theoretical results could be used to help inform experimental design.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"168 ","pages":"Pages 32-43"},"PeriodicalIF":1.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146004778","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":"Evolving genealogies in cultural evolution, the descendant process, and the number of cultural traits","authors":"Joe Yuichiro Wakano ,&nbsp;Hisashi Ohtsuki ,&nbsp;Yutaka Kobayashi ,&nbsp;Ellen Baake","doi":"10.1016/j.tpb.2025.12.003","DOIUrl":"10.1016/j.tpb.2025.12.003","url":null,"abstract":"<div><div>We consider a Moran-type model of cultural evolution, which describes how traits emerge, are transmitted, and get lost in populations. Our analysis focuses on the underlying cultural genealogies; they were first described by Aguilar and Ghirlanda (2015) and are closely related to the ancestral selection graph of population genetics, wherefore we call them <em>ancestral learning graphs</em>. We investigate their dynamical behaviour, that is, we are concerned with <em>evolving genealogies</em>. In particular, we consider the total length of the genealogy of the entire population as a function of the (forward) time where we start looking back. This quantity shows a sawtooth-like dynamics with linear increase interrupted by collapses to near-zero at random times. We relate this to the metastable behaviour of the stochastic logistic model, which describes the evolution of the number of ancestors as well as the number of descendants of a given sample.</div><div>We superpose types to the model by assuming that new inventions appear independently in every individual, and all traits of the cultural parent are transmitted to the learner in any given learning event. The set of traits of an individual then agrees with the set of innovations along its genealogy. The properties of the genealogy thus translate into the properties of the trait set of a sample. In particular, the moments of the number of traits are obtained from the moments of the total length of the genealogy.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"168 ","pages":"Pages 1-18"},"PeriodicalIF":1.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145851308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A clarification of historical concepts of effective population size and their applicability to subdivided populations","authors":"Warren Ewens ,&nbsp;Ola Hössjer","doi":"10.1016/j.tpb.2025.12.002","DOIUrl":"10.1016/j.tpb.2025.12.002","url":null,"abstract":"<div><div>The great population geneticist Sewall Wright had a lifelong interest in animal breeding programs. He was concerned that, in these programs, genetic variation would tend to be lost (as measured by him in a tendency for genetic heterozygosity to decrease) when a small number of males is mated to a comparatively large number of females. The calculations in his great 1931 paper were designed to quantify this tendency. Decades later other authors noted further cases when population genetic heterozygosity tended to be lost, a classic example being that of a population whose size changes cyclically with some small population sizes arising during the cycle. These observations led to several definitions of the effective population size. Perhaps the two most frequently discussed in the literature are the inbreeding effective population size and the variance effective population size. The first aim of this note is to show that Wright’s (1931) calculations for two-sex populations relate to neither of these, and instead to the far less discussed eigenvalue effective population size. The second aim is to critically assess all three effective population sizes and put two-sex populations into a wider concept of subdivided populations. This analysis reveals some new results, and for two-sex populations without other types of subdivision, we conclude that the eigenvalue effective size is the most relevant type of effective size.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"167 ","pages":"Pages 11-21"},"PeriodicalIF":1.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145709995","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":"Correlation of coalescence times in a diploid Wright–Fisher model with recombination and selfing","authors":"David Kogan ,&nbsp;Dimitrios Diamantidis ,&nbsp;John Wakeley ,&nbsp;Louis Wai-Tong Fan","doi":"10.1016/j.tpb.2025.11.003","DOIUrl":"10.1016/j.tpb.2025.11.003","url":null,"abstract":"<div><div>The correlation among the gene genealogies at different loci is crucial in biology, yet challenging to understand because such correlation depends on many factors including genetic linkage, recombination, natural selection and population structure. Based on a diploid Wright–Fisher model with partial selfing and a single mating type for a constant large population of size <span><math><mi>N</mi></math></span>, we quantify the combined effects of genetic drift and two competing factors, recombination and selfing, on the correlation of coalescence times at two linked loci for samples of size two. Recombination decouples the genealogies at different loci and decreases the correlation while selfing increases the correlation. We obtain explicit asymptotic formulas for the correlation under four different scaling scenarios depending on whether the selfing probability and the recombination probability are of order <span><math><mrow><mi>O</mi><mrow><mo>(</mo><mn>1</mn><mo>/</mo><mi>N</mi><mo>)</mo></mrow></mrow></math></span> or <span><math><mrow><mi>O</mi><mrow><mo>(</mo><mn>1</mn><mo>)</mo></mrow></mrow></math></span> as <span><math><mi>N</mi></math></span> tends to infinity. Our analytical results show that the asymptotic lower bound in King et al. (2018) is sharp when the loci are unlinked and when there is no selfing, and provide a number of new formulas for other scaling scenarios that have not been considered before. We present asymptotic results for the variance of Tajima’s estimator of the population mutation rate for infinitely many loci as <span><math><mi>N</mi></math></span> tends to infinity. When the selfing probability is of order <span><math><mrow><mi>O</mi><mrow><mo>(</mo><mn>1</mn><mo>)</mo></mrow></mrow></math></span> and is equal to a positive constant <span><math><mi>s</mi></math></span> for all <span><math><mi>N</mi></math></span> and if the samples at both loci are in the same individual, then the variance of the Tajima’s estimator tends to <span><math><mrow><mi>s</mi><mo>/</mo><mn>2</mn></mrow></math></span> (hence remains positive) even when the recombination rate, the number of loci and the population size all tend to infinity.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"167 ","pages":"Pages 40-68"},"PeriodicalIF":1.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745457","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":"Strong information delay as a driver of epidemic waves: Mathematical modeling for drug trends and epidemic bio-preparedness","authors":"Martina Bouka ,&nbsp;W. Christopher Strickland","doi":"10.1016/j.tpb.2025.11.002","DOIUrl":"10.1016/j.tpb.2025.11.002","url":null,"abstract":"<div><div>Avoidance behaviors can have a substantial influence on both the spread of an infectious disease and on the long-term dynamics of substance use disorder. However, this behavior is typically reactive based on delayed information related to personal risk as well as both the length of exposure to and retention of that information. This suggests that in epidemic models, feedback delays should be strong — that is, not exponentially distributed (Erlang-1) but instead peaking at a point strictly in the past (Erlang-2 or greater). However, almost all studies of infectivity feedback delays are exponential with qualitatively different results than are seen with strong delays. To address this gap, we analyze two compartmental models for infectious disease epidemiology. Our results demonstrate that sustained oscillations in the total number of active cases may appear even as early as the first two years of an outbreak, suggesting that human behavior may be an explanatory factor for periodic fluctuations evident in recent pandemic time-series data (e.g. COVID-19). We then extend our analysis to a study of the role of information feedback on substance use disorder epidemiology, with a focus on both the transient and asymptotic dynamics of drug waves. We show that under certain conditions, oscillations in substance use disorder can become sustained and that models without strong feedback delays can fail to produce important qualitative transient behavior in substance use incidence rates. To our knowledge, this work represents the first mathematical model exhibiting oscillations with non-contact (linear) pathways to substance use disorder.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"167 ","pages":"Pages 22-39"},"PeriodicalIF":1.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145702781","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":"What drives bacterial extinction? The role of bacteriophages","authors":"Mark M. Tanaka ,&nbsp;Lindi M. Wahl","doi":"10.1016/j.tpb.2025.12.001","DOIUrl":"10.1016/j.tpb.2025.12.001","url":null,"abstract":"<div><div>Bacterial lineages are relatively short-lived on geological timescales, according to phylogenetic analyses, implying that bacterial extinction occurs at high rates. Since the vast majority of bacteria live in large populations in oceans and soils, many well-studied extinction mechanisms, such as demographic or environmental stochasticity, seem unlikely to drive this pattern. We outline mechanisms for the extinction of large bacterial populations, and discuss the emergence of a new virus as a possible cause of extinction. We use deterministic and stochastic models to characterise the persistence of a bacterial population, demonstrating that when resistance to a new virus does not emerge, large populations are more likely to go extinct than small populations, which contrasts with classically studied extinction mechanisms. When they go extinct, large populations also reach extinction more quickly. When phage-resistant bacteria appear, extinction is rare but its probability increases with population size in some parameter regimes. We also quantify bacterial extinction in spatially distinct subpopulations. We conclude that large bacterial populations are robust to many extinction mechanisms, and typically evolve resistance to new phages, as observed empirically. For bacterial lineages that have gone extinct, however, the failure to evolve resistance to a novel phage is a likely underlying mechanism.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"167 ","pages":"Pages 1-10"},"PeriodicalIF":1.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145712493","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":"An equal-tempered measure of linkage disequilibrium","authors":"Mark M. Tanaka","doi":"10.1016/j.tpb.2025.09.002","DOIUrl":"10.1016/j.tpb.2025.09.002","url":null,"abstract":"<div><div>Linkage disequilibrium (LD), the association of alleles at two loci, is defined in multiple ways. Because LD measures depend on allele frequencies, it is difficult to compare LD values between populations or loci with different allele frequencies. Here, I consider a geometric interpretation of a commonly used LD measure <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span> which suggests a modification that is frequency-independent in the sense that equal evolutionary forces lead to the same effect at different frequencies. This new measure is a very simple expression that is known elsewhere as the Hamann coefficient and the G index of agreement; it is a linear transformation of the simple matching coefficient. I explore properties of this quantity in comparison with <span><math><mi>D</mi></math></span> and <span><math><msup><mrow><mi>r</mi></mrow><mrow><mn>2</mn></mrow></msup></math></span>, and discuss its interpretation, advantages and disadvantages.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"166 ","pages":"Pages 36-43"},"PeriodicalIF":1.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066188","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":"Consistency and central limit results for the maximum likelihood estimator in the Admixture Model","authors":"Carola Sophia Heinzel","doi":"10.1016/j.tpb.2025.10.001","DOIUrl":"10.1016/j.tpb.2025.10.001","url":null,"abstract":"<div><div>In the Admixture Model, the probability of an individual having a certain number of alleles at a specific marker depends on the allele frequencies in <span><math><mi>K</mi></math></span> ancestral populations and the fraction of the individual’s genome originating from these ancestral populations.</div><div>This study investigates consistency and central limit results of maximum likelihood estimators (MLEs) for the ancestry and the allele frequencies in the Admixture Model, complimenting previous work by Pfaff et al. (2004); Pfaffelhuber and Rohde (2022). Specifically, we prove consistency of the MLE, if we estimate the allele frequencies and the ancestries. Furthermore, we prove central limit theorems, if we estimate the ancestry of a finite number of individuals and the allele frequencies of finitely many markers, also addressing the case where the true ancestry lies on the boundary of the parameter space.</div><div>Finally, we use the new theory to quantify the uncertainty of the MLEs for the data of the 1000 Genomes Project.</div></div>","PeriodicalId":49437,"journal":{"name":"Theoretical Population Biology","volume":"166 ","pages":"Pages 70-79"},"PeriodicalIF":1.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145270191","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}