In the present article, we investigate the effects of dormancy on an abstract population genetic level. We first provide a short review of seed bank models in population genetics, and the role of dormancy for the interplay of evolutionary forces in general, before we discuss two recent paradigmatic models, referring to spontaneous resp. simultaneous switching of individuals between the active and the dormant state. We show that both mechanisms give rise to non-trivial mathematical objects, namely the (continuous) seed bank diffusion and the seed bank diffusion with jumps, as well as their dual processes, the seed bank coalescent and the seed bank coalescent with simultaneous switching.
In this paper, we investigate the consequences of dormancy in the `rare mutation' and `large population' regime of stochastic adaptive dynamics. Starting from an individual-based micro-model, we first derive the polymorphic evolution sequence of the population, based on previous work by Baar and Bovier (2018). After passing to a second `small mutations' limit, we arrive at the canonical equation of adaptive dynamics, and state a corresponding criterion for evolutionary branching, extending a previous result of Champagnat and Méléard (2011). The criterion allows a quantitative and qualitative a…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated defence mechanism was described in Bautista et al (2015) for an archaeal host, while Jackson and Fineran (2019) and Meeske et al (2019) describe a related, CRISPR-Cas induced, dormancy defense of bacterial hosts to curb phage epidemics. We first analyse the effect of the dormancy-related model parameters on the probability and time of invasion of a newly arriv…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it combines the recent model of Champagnat, Méléard and Tran (2021) involving HGT with the model for competition-induced dormancy of Blath and Tóbiás (2020). Our main result is a convergence theorem which describes the evolution of the different traits in the population on a `doubly logarithmic scale' as piece-wise affine functions. Interestingly, even for a relativ…
Consider a population evolving from year to year through three seasons: spring, summer and winter. Every spring starts with $N$ dormant individuals waking up independently of each other according to a given distribution. Once an individual is awake, it starts reproducing at a constant rate. By the end of spring, all individuals are awake and continue reproducing independently as Yule processes during the whole summer. In the winter, $N$ individuals chosen uniformly at random go to sleep until the next spring, and the other individuals die. We show that because an individual that wakes up unusu…
Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University（亚利桑那州立大学生物设计研究所进化机制中心）；School of Mathematical and Statistical Sciences, Arizona State University（亚利桑那州立大学数学与统计科学学院）；Centro de Investigaciones en Matemáticas（数学研究中心）；Center for Genomic Sciences, Universidad Nacional Autónoma de México（墨西哥国立自治大学生命科学中心）
The interplay of selection and dormancy in a Moran model can lead to coexistence of types
Goethe-Universität Frankfurt（法兰克福歌德大学）；Budapest University of Technology and Economics（布达佩斯技术与经济大学）；HUN-REN Alfréd Rényi Institute of Mathematics（匈牙利研究与教育网络阿尔弗雷德·雷尼数学研究所）
We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial communities, affecting their dynamics in important ways. Recently, they have each moved (separately) into the focus of stochastic individual-based modelling (Billiard et al. 2016, 2018; Champagnat, Méléard and Tran, 2021; Blath and Tóbiás 2020). Here, we examine their combined effects in a unified model. Indeed, we consider the (idealized) scenario of two sub-popu…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the frequency of neutural mutations in exponentially growing multitype branching processes that have been widely used in cancer modeling. Our results yield a simple new population genetics result for the site frequency spectrum of a sample from an exponentially growing population.
We examine genetic statistics used in the study of structured populations. In a 1999 paper, Wakeley observed that the coalescent process associated with the finite island model can be decomposed into a scattering phase and a collecting phase. In this paper, we introduce a class of population structure models, which we refer to as G/KC models, that obey such a decomposition. In a large population, large sample limit we derive the distribution of the statistic Fst for all G/KC models under the assumptions of strong or weak mutation. We show that in the large population, large sample limit the is…
We study the following model for a diploid population of constant size $N$: Every individual carries a random number of (genetic) elements. Upon a reproduction event each of the two parents passes each element independently with probability $\tfrac 12$ on to the offspring. We study the process $X^N = (X^N(1), X^N(2),...)$, where $X_t^N(k)$ is the frequency of individuals at time $t$ that carry $k$ elements, and prove convergence (in some weak sense) of $X^N$ jointly with its empirical first moment $Z^N$ to the ``slow-fast'' system $(Z,X)$, where $X_t = \text{Poi}(Z_t)$ and $Z$ evolves accordin…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed \textit{a priori} known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interactions and asexual reproduction. We develop an inferential procedure fo…
Mathematical population genetics is only one of Kingman's many research interests. Nevertheless, his contribution to this field has been crucial, and moved it in several important new directions. Here we outline some aspects of his work which have had a major influence on population genetics theory.
Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in the genetic signature left by a selective sweep induced by recurrent mutations at a given locus from an allele A to an allele a, depending on the mutation frequency. We distinguish three possible scales for the mutation probability per reproductive event, which entail distinct genetic signatures. Besides, we study the hydrodynamic limit of the A- and a-populat…
In the context of population genetics, active information can be extended to measure the change of information of a given event (e.g., fixation of an allele) from a neutral model in which only genetic drift is taken into account to a non-neutral model that includes other sources of frequency variation (e.g., selection and mutation). In this paper we illustrate active information in population genetics through the Wright-Fisher model.
In this article, three models are considered, they are the infinitely-many-neutral-alleles model \cite{MR615945}, infinite dimensional diffusion associated with two-parameter Poisson-Dirichlet distribution \cite{MR2596654} and the infinitely-many-alleles model with symmetric dominance \cite{MR1626158}. The new representations of the transition transition densities are obtained for the first two models. Lastly, the ergodic inequalities of these three models are provided.
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values in bacteria and cancer cell populations, we take the mutation rate to zero and the final number of cells to infinity. We prove that almost every site (entry of the nucleotide sequence) is mutated in only a finite number of cells, and these numbers are independent across sites. However independence breaks down for the rare sites which are mutated in a positive…
This article is concerned with the long time behavior of neutral genetic population models, with fixed population size. We design an explicit, finite, exact, genealogical tree based representation of stationary populations that holds both for finite and infinite types (or alleles) models. We then analyze the decays to the equilibrium of finite populations in terms of the convergence to stationarity of their first common ancestor. We estimate the Lyapunov exponent of the distribution flows with respect to the total variation norm. We give bounds on these exponents only depending on the stabilit…
We consider a population of haploid individuals reproducing sexually, i.e. for which the genome of each individual is a random mixture of the genome of its two parents. We assume that initially one individual carries a mutation at one locus, and that individuals carrying this mutation have an advantage regarding genome transmission. Our aim is to study the long time effect of this mutation on the genetic composition of the population, when population size is large.
The goal of this paper is to develop a theory of graphon-valued stochastic processes, and to construct and analyse a natural class of such processes arising from population genetics. We consider finite populations where individuals change type according to Wright-Fisher resampling. At any time, each pair of individuals is linked by an edge with a probability that is given by a type-connection matrix, whose entries depend on the current empirical type distribution of the entire population via a fitness function. We show that, in the large-population-size limit and with an appropriate scaling of…
We provide a detailed description of the structure of the transition probabilities and of the hitting distributions of boundary components of a manifold with corners for a degenerate strong Markov process arising in population genetics. The Markov processes that we study are a generalization of the classical Wright-Fisher process. The main ingredients in our proofs are based on the analysis of the regularity properties of solutions to a forward Kolmogorov equation defined on a compact manifold with corners, which is degenerate in the sense that it is not strictly elliptic and the coefficients …
Starting from a sequence of independent Wright-Fisher diffusion processes on $[0,1]$, we construct a class of reversible infinite dimensional diffusion processes on $\DD_\infty:= \{{\bf x}\in [0,1]^\N: \sum_{i\ge 1} x_i=1\}$ with GEM distribution as the reversible measure. Log-Sobolev inequalities are established for these diffusions, which lead to the exponential convergence to the corresponding reversible measures in the entropy. Extensions are made to a class of measure-valued processes over an abstract space $S$. This provides a reasonable alternative to the Fleming-Viot process which does…
We describe the processes obtained by time reversal of a class of stationary jump-diffusion processes that model the dynamics of genetic variation in populations subject to repeated bottlenecks. Assuming that only one lineage survives each bottleneck, the forward process is a diffusion on [0,1] that jumps to the boundary before diffusing back into the interior. We show that the behavior of the time-reversed process depends on whether the boundaries are accessible to the diffusive motion of the forward process. If a boundary point is inaccessible to the forward diffusion, then time reversal lea…
In this paper, we discuss the construction of a multivariate generalisation of the Dirichlet-multinomial distribution. An example from forensic genetics in the statistical analysis of DNA mixtures motivates the study of this multivariate extension. In forensic genetics, adjustment of the match probabilities due to remote ancestry in the population is often done using the so-called θ-correction. This correction increases the probability of observing multiple copies of rare alleles and thereby reduces the weight of the evidence for rare genotypes. By numerical examples, we show how the θ-correct…
We apply our general method of duality, introduced in [Giardina', Kurchan, Redig, J. Math. Phys. 48, 033301 (2007)], to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman's type, as well as for models with finite population size. Next, using SU(1,1) raising and lowering operators, we find new dualities between the Wright-Fisher diffusion with $d$ types and the Moran model, both in presence and absence of…
