arXiv subjects

Sylvie Méléard

Publications and source records attributed to Sylvie Méléard.

At least 37 records · Page 2Linked to original sources

arXiv2019

Horizontal gene transfer: numerical comparison between stochastic and deterministic approaches

Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that this phenomenon plays an essential role in the evolution of certain bacterias. In particular, HT is believed to be the main instrument of developing the antibiotic resistance. In this work, we consider several models which describe this phenomenon: a stochastic jump process (individual-based) and the deterministic nonlinear integrod-ifferential equation obtained as a limit for large populations. We also consider a Hamilton-Jacobi equation, obtained as a limit of the deterministic model under the assumption of small mutations. The goal of this paper is to compare these models with the help of numerical simulations. More specifically, our goal is to understand to which extent the Hamilton-Jacobi model reproduces the qualitative behavior of the stochastic model and the phenomenon of evolutionary rescue in particular.

q-bio.PE↗

arXiv2019

A birth-death model of ageing: from individual-based dynamics to evolutive differential inclusions

Ageing's sensitivity to natural selection has long been discussed because of its apparent negative effect on individual's fitness. Thanks to the recently described (Smurf) 2-phase model of ageing we were allowed to propose a fresh angle for modeling the evolution of ageing. Indeed, by coupling a dramatic loss of fertility with a high-risk of impending death - amongst other multiple so-called hallmarks of ageing - the Smurf phenotype allowed us to consider ageing as a couple of sharp transitions. The birth-death model (later called bd-model) we describe here is a simple life-history trait model where each asexual and haploid individual is described by its fertility period $x_b$ and survival period $x_d$. We show that, thanks to the Lansing effect, $x_b$ and $x_d$ converge during evolution to configurations $x_b-x_d\approx 0$. This guarantees that a certain proportion of the population maintains the Lansing effect which in turn, confers higher evolvability to individuals. \\To do so, we built an individual-based stochastic model which describes the age and trait distribution dynamics of such a finite population. Then we rigorously derive the adaptive dynamics models, which describe the trait dynamics at the evolutionary time-scale. We extend the Trait Substitution Sequence with age structure to take into account the Lansing effect. Finally, we study the limiting behaviour of this jump process when mutations are small. We show that the limiting behaviour is described by a differential inclusion whose solutions $x(t)=(x_b(t),x_d(t))$ reach the diagonal $\lbrace x_b=x_d\rbrace$ in finite time and then remain on it. This differential inclusion is a natural way to extend the canonical equation of adaptive dynamics in order to take into account the lack of regularity of the invasion fitness function on the diagonal $\lbrace x_b=x_d\rbrace$.

math.PR↗

arXiv2018

Scaling limits of general population processes - Wright-Fisher and branching processes in random environment

Our motivation comes from the large population approximation of individual based models in population dynamics and population genetics. We propose a general method to investigate scaling limits of finite dimensional population size Markov chains to diffusion with jumps. The statements of tightness, identification and convergence in law are based on the convergence of suitable characteristics of the transition of the chain and strongly exploit the structure of the population processes defined recursively as sums of independent random variables. These results allow to reduce the convergence of characteristics of semimartingales to analytically tractable functional spaces. We develop two main applications. First, we extend the classical Wright-Fisher diffusion approximation to independent and identically distributed random environment. Second, we obtain the convergence in law of generalized Galton-Watson processes with interactions and random environment to the solution of stochastic differential equations with jumps.

math.PR↗

arXiv2017

Diffusions from Infinity

In this paper we consider diffusions on the half line (0, $\infty$) such that the expectation of the arrival time at the origin is uniformly bounded in the initial point. This implies that there is a well defined diffusion process starting from infinity, which takes finite values at positive times. We study the behaviour of hitting times of large barriers and in a dual way, the behaviour of the process starting at infinity for small time. In particular we prove that the process coming down from infinity is in small time governed by a specific deterministic function. Suitably normalized fluctuations of the hitting times are asymptotically Gaussian. We also derive the tail of the distribution of the hitting time of the origin and a Yaglom limit for the diffusion starting from infinity. We finally prove that the distribution of this process killed at the origin is absolutely continuous with respect to the speed measure. The density is expressed in terms of the eigenvalues and eigenfunctions of the generator of the killed diffusion.

math.PR↗

arXiv2017

Stochastic dynamics for adaptation and evolution of microorganisms

We present a model for the dynamics of a population of bacteria with a continuum of traits, who compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait with possible mutations. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We consider a stochastic individual-based pure jump process taking values in the space of point measures, and whose jump events describe the individual reproduction, transfer and death mechanisms. In a large population scale, the stochastic process is proved to converge to the solution of a nonlinear integro-differential equation. When there are only two different traits and no mutation, this equation reduces to a non-standard two-dimensional dynamical system. We show how crucial the forms of the transfer rates are for the long-term behavior of its solutions. We describe the dynamics of invasion and fixation when one of the two traits is initially rare, and compute the invasion probabilities. Then, we study the process under the assumption of rare mutations. We prove that the stochastic process at the mutation time scale converges to a jump process which describes the successive invasions of successful mutants. We show that the horizontal transfer can have a major impact on the distribution of the successive mutational fixations, leading to dramatically different behaviors, from expected evolution scenarios to evolutionary suicide. Simulations are given to illustrate these phenomena.

math.PR↗

arXiv2017

Some stochastic models for structured populations : scaling limits and long time behavior

The first chapter concerns monotype population models. We first study general birth and death processes and we give non-explosion and extinction criteria, moment computations and a pathwise representation. We then show how different scales may lead to different qualitative approximations, either ODEs or SDEs. The prototypes of these equations are the logistic (deterministic) equation and the logistic Feller diffusion process. The convergence in law of the sequence of processes is proved by tightness-uniqueness argument. In these large population approximations, the competition between individuals leads to nonlinear drift terms. We then focus on models without interaction but including exceptional events due either to demographic stochasticity or to environmental stochasticity. In the first case, an individual may have a large number of offspring and we introduce the class of continuous state branching processes. In the second case, catastrophes may occur and kill a random fraction of the population and the process enjoys a quenched branching property. We emphasize on the study of the Laplace transform, which allows us to classify the long time behavior of these processes. In the second chapter, we model structured populations by measure-valued stochastic differential equations. Our approach is based on the individual dynamics. The individuals are characterized by parameters which have an influence on their survival or reproduction ability. Some of these parameters can be genetic and are inheritable except when mutations occur, but they can also be a space location or a quantity of parasites. The individuals compete for resources or other environmental constraints. We describe the population by a point measure-valued Markov process. We study macroscopic approximations of this process depending on the interplay between different scalings and obtain in the limit either integro-differential equations or reaction-diffusion equations or nonlinear super-processes. In each case, we insist on the specific techniques for the proof of convergence and for the study of the limiting model. The limiting processes offer different models of mutation-selection dynamics. Then, we study two-level models motivated by cell division dynamics, where the cell population is discrete and characterized by a trait, which may be continuous. In 1 particular, we finely study a process for parasite infection and the trait is the parasite load. The latter grows following a Feller diffusion and is randomly shared in the two daughter cells when the cell divides. Finally, we focus on the neutral case when the rate of division of cells is constant but the trait evolves following a general Markov process and may split in a random number of cells. The long time behavior of the structured population is then linked and derived from the behavior a well chosen SDE (monotype population).

math.PR↗

arXiv2017

Perpetual integrals convergence and extinctions in population dynamics

In this article we use a criterion for the integrability of paths of one-dimensional diffusion processes from which we derive new insights on allelic fixation in several situations. This well known criterion involves a simple necessary and sufficient condition based on scale function and speed measure. We provide a new simple proof for this result and also obtain explicit bounds for the moments of such integrals. We also extend this criterion to non-homogeneous processes by use of Girsanov's transform. We apply our results to multi-type population dynamics: using the criterion with appropriate time changes, we characterize the behavior of proportions of each type before population extinction in different situations.

math.PR↗

arXiv2016

Non local Lotka-Volterra system with cross-diffusion in an heterogeneous medium

We introduce a stochastic individual model for the spatial behavior of an animal population of dispersive and competitive species, considering various kinds of biological effects, such as heterogeneity of environmental conditions, mutual attractive or repulsive interactions between individuals or competition between them for resources. As a consequence of the study of the large population limit, global existence of a nonnegative weak solution to a multidimensional parabolic strongly coupled model of competing species is proved. The main new feature of the corresponding integro-differential equation is the nonlocal nonlinearity appearing in the diffusion terms, which may depend on the spatial densities of all population types. Moreover, the diffusion matrix is generally not strictly positive definite and the cross-diffusion effect allows for linearly growing influences of the subpopulations' sizes. We prove uniqueness of the finite measure-valued solution and give conditions under which the solution takes values in a functional space. We then make the competition kernels converge to a Dirac measure and obtain the existence of a solution to a locally competitive version of the previous equation. The large population limit is obtained by means of weak convergence tools for measure valued processes. The techniques employed in the study of the liming equation are novel, and are essentially based on the underlying stochastic flow related to the dispersive part of the dynamics, together with the use of suitable dual distances in the space of finite measures. This is an extended version of the paper "Non local Lotka-Volterra system with cross-diffusion in a heterogeneous medium" appeared in J. Math. Biol (2015) 70:829-854.

math.PR↗

arXiv2015

The effect of competition and horizontal trait inheritance on invasion, fixation and polymorphism

Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present a modeling framework for the dynamics of two populations that compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We capture this feedback with a stochastic individual-based model, from which we derive a deterministic approximation for large populations. The interaction between horizontal transfer and competition makes possible the stable (or bi-stable) polymorphic maintenance of deleterious traits (including costly plasmids). When transfer rates are of a general density-dependent form, transfer stochasticity contributes strongly to population fluctuations. For an initially rare trait, we describe the probabilistic dynamics of invasion and fixation. Acceleration of fixation by HT is faster when competition is weak in the resident population. Thus, HT can have a major impact on the distribution of mutational effects that are fixed, and our model provides a basis for a general theory of the influence of HT on eco-evolutionary dynamics and adaptation.

q-bio.PE↗

arXiv2015

Speed of coming down from infinity for birth and death processes

We finely describe the speed of "coming down from infinity" for birth and death processes which eventually become extinct. Under general assumptions on the birth and death rates, we firstly determine the behavior of the successive hitting times of large integers. We put in light two different regimes depending on whether the mean time for the process to go from $n+1$ to $n$ is negligible or not compared to the mean time to reach $n$ from infinity. In the first regime, the coming down from infinity is very fast and the convergence is weak. In the second regime, the coming down from infinity is gradual and a law of large numbers and a central limit theorem for the hitting times sequence hold. By an inversion procedure, we deduce that the process is a.s. equivalent to a non-increasing function when the time goes to zero. Our results are illustrated by several examples including applications to population dynamics and population genetics. The particular case where the death rate varies regularly is studied in details.

math.PR↗

arXiv2015

Stochastic eco-evolutionary model of a prey-predator community

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the Polymorphic Evolutionary Sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.

q-bio.PE↗

arXiv2014

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

math.PR↗

arXiv2014

Singular limits for reaction-diffusion equations with fractional Laplacian and local or nonlocal nonlinearity

We perform an asymptotic analysis of models of population dynamics with a fractional Laplacian and local or nonlocal reaction terms. The first part of the paper is devoted to the long time/long range rescaling of the fractional Fisher-KPP equation. This rescaling is based on the exponential speed of propagation of the population. In particular we show that the only role of the fractional Laplacian in determining this speed is at the initial layer where it determines the thickness of the tails of the solutions. Next, we show that such rescaling is also possible for models with non-local reaction terms, as selection-mutation models. However, to obtain a more relevant qualitative behavior for this second case, we introduce, in the second part of the paper, a second rescaling where we assume that the diffusion steps are small. In this way, using a WKB ansatz, we obtain a Hamilton-Jacobi equation in the limit which describes the asymptotic dynamics of the solutions, similarly to the case of selection-mutation models with a classical Laplace term or an integral kernel with thin tails. However, the rescaling introduced here is very different from the latter cases. We extend these results to the multidimensional case.

math.AP↗

arXiv2013

How do birth and death processes come down from infinity?

We finely describe the "coming down from infinity" for birth and death processes which eventually become extinct. Our biological motivation is to study the decrease of regulated populations which are initially large. Under general assumptions on the birth and death rates, we describe the behavior of the hitting time of large integers. We let two regimes appear and derive an expression of the speed of coming down from infinity. In the case of death rates with regular variations, we also get a central limit theorem and the asymptotic probability of extinction in small times. Finally, we apply our results to birth and death processes in varying environment in whose the environment influences the competition.

math.PR↗

arXiv2013

Adaptation in a stochastic multi-resources chemostat model

We are interested in modeling the Darwinian evolution resulting from the interplay of phenotypic variation and natural selection through ecological interactions, in the specific scales of the biological framework of adaptive dynamics. Adaptive dynamics so far has been put on a rigorous footing only for direct competition models (Lotka-Volterra models) involving a competition kernel which describes the competition pressure from one individual to another one. We extend this to a multi-resources chemostat model, where the competition between individuals results from the sharing of several resources which have their own dynamics. Starting from a stochastic birth and death process model, we prove that, when advantageous mutations are rare, the population behaves on the mutational time scale as a jump process moving between equilibrium states (the polymorphic evolution sequence of the adaptive dynamics literature). An essential technical ingredient is the study of the long time behavior of a chemostat multi-resources dynamical system. In the small mutational steps limit this process in turn gives rise to a differential equation in phenotype space called canonical equation of adaptive dynamics. From this canonical equation and still assuming small mutation steps, we prove a rigorous characterization of the evolutionary branching points.

math.PR↗

arXiv2012

Nonlinear historical superprocess approximations for population models with past dependence

We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend on the trait of the ancestors and on its past and allows interactions between individuals through their lineages. We define an interacting historical particle process describing the genealogies of the living individuals; it takes values in the space of point measures on an infinite dimensional càdlàg path space. This individual-based process can be approximated by a nonlinear historical superprocess, under the assumptions of large populations, small individuals and allometric demographies. Because of the interactions, the branching property fails and we use martingale problems and fine couplings between our population and independent branching particles. Our convergence theorem is illustrated by two examples of current interest in biology. The first one relates the biodiversity history of a population and its phylogeny, while the second treats a spatial model with competition between individuals through their past trajectories.

math.PR↗

arXiv2011

Quasi-stationary distributions and population processes

This survey concerns the study of quasi-stationary distributions with a specific focus on models derived from ecology and population dynamics. We are concerned with the long time behavior of different stochastic population size processes when 0 is an absorbing point almost surely attained by the process. The hitting time of this point, namely the extinction time, can be large compared to the physical time and the population size can fluctuate for large amount of time before extinction actually occurs. This phenomenon can be understood by the study of quasi-limiting distributions. In this paper, general results on quasi-stationarity are given and examples developed in detail. One shows in particular how this notion is related to the spectral properties of the semi-group of the process killed at 0. Then we study different stochastic population models including nonlinear terms modeling the regulation of the population. These models will take values in countable sets (as birth and death processes) or in continuous spaces (as logistic Feller diffusion processes or stochastic Lotka-Volterra processes). In all these situations we study in detail the quasi-stationarity properties. We also develop an algorithm based on Fleming-Viot particle systems and show a lot of numerical pictures.

math.PR↗

arXiv2011

A rigorous model study of the adaptative dynamics of Mendelian diploids

Adaptive dynamics so far has been put on a rigorous footing only for clonal inheritance. We extend this to sexually reproducing diploids, although admittedly still under the restriction of an unstructured population with Lotka-Volterra-like dynamics and single locus genetics (as in Kimura's 1965 infinite allele model). We prove under the usual smoothness assumptions, starting from a stochastic birth and death process model, that, when advantageous mutations are rare and mutational steps are not too large, the population behaves on the mutational time scale (the 'long' time scale of the literature on the genetical foundations of ESS theory) as a jump process moving between homozygous states (the trait substitution sequence of the adaptive dynamics literature). Essential technical ingredients are a rigorous estimate for the probability of invasion in a dynamic diploid population, a rigorous, geometric singular perturbation theory based, invasion implies substitution theorem, and the use of the Skorohod $M_1$ topology to arrive at a functional convergence result. In the small mutational steps limit this process in turn gives rise to a differential equation in allele or in phenotype space of a type referred to in the adaptive dynamics literature as 'canonical equation'.

math.PR↗