Gene flow across geographical barriers - scaling limits of random walks with obstacles

In this paper, we study the scaling limit of a class of random walks which behave like simple random walks outside of a bounded region around the origin and which are subject to a partial reflection near the origin. If the probability of crossing the barrier scales as $1/\sqrt{n}$ as we rescale space by $\sqrt{n}$ and time by $n$, we obtain a non trivial scaling limit which behaves like reflected Brownian motion until its local time at the origin reaches an independent exponential variable. It then follows reflected Brownian motion on the other side of the origin until its local time at the origin reaches another exponential level, and so on. We give a martingale problem characterisation of this process as well as another construction and an explicit formula for its transition density. This result has applications in the field of population genetics where such a random walk is used to trace the position of one's ancestor in the past in the presence of a barrier to gene flow.Comment: Stochastic Processes and Their Applications, in pres

A measure-valued stochastic model for vector-borne viruses

In this work we propose a measure-valued stochastic process representing the dynamics of a virus population, structured by phenotypic traits and geographical space, and where viruses are transported between spatial locations by mechanical vectors. As a first example of the use of this model, we show how to use this model to infer results on the probability of extinction of the virus population. Later, by combining various scalings on population sizes, speed of diffusion of vectors, and other relevant model parameters, we show the emergence of two systems of integro-differential equations as Macroscopic descriptions of the system. Under the existence of densities at time zero, we also show the propagation of this property for later times, and derive the strong formulation of the limiting systems of IDEs. These strong formulations, in a sense, correspond to spatial Lotka-Volterra competition models with mutation and vector-borne dispersal.Comment: 39 page

Epidemic models with varying infectivity

We introduce an epidemic model with varying infectivity and general exposed and infectious periods, where the infectivity of each individual is a random function of the elapsed time since infection, those function being i.i.d. for the various individuals in the population. This approach models infection-age dependent infectivity, and extends the classical SIR and SEIR models. We focus on the infectivity process (total force of infection at each time), and prove a functional law of large number (FLLN). In the deterministic limit of this LLN, the infectivity process and the susceptible process are determined by a two-dimensional deterministic integral equation. From its solutions, we then derive the exposed, infectious and recovered processes, again using integral equations. For the early phase, we study the stochastic model directly by using an approximate (non--Markovian) branching process, and show that the epidemic grows at an exponential rate on the event of non-extinction, which matches the rate of growth derived from the deterministic linearized equations. We also use these equations to derive the basic reproduction number $R_0$ during the early stage of an epidemic, in terms of the average individual infectivity function and the exponential rate of growth of the epidemic

Structure spatiale de la diversité génétique : influence de la sélection naturelle et d'un environnement hétérogène

This thesis deals with the spatial structure of genetic diversity. We first study a measure-valued process describing the evolution of the genetic composition of a population subject to natural selection. We show that this process satisfies a central limit theorem and that its fluctuations are given by the solution to a stochastic partial differential equation. We then use this result to obtain an estimate of the drift load in spatially structured populations.Next we investigate the genetic composition of a populations whose individuals move more freely in one part of space than in the other (a situation called dispersal heterogeneity). We show in this case the convergence of allele frequencies via the convergence of ancestral lineages to a system of skew Brownian motions.We then detail the effect of a barrier to gene flow dividing the habitat of a population. We show that ancestral lineages follow partially reflected Brownian motions, of whom we give several constructions.To apply these results, we adapt a method for demographic inference to the setting of dispersal heterogeneity. This method makes use of long blocks of genome along which pairs of individuals share a common ancestry, and allows to estimate several demographic parameters when they vary accross space. To conclude, we demonstrate the accuracy of our method on simulated datasets.Cette thèse porte sur la structure spatiale de la diversité génétique. Dans un premier temps, nous étudions un processus à valeurs mesure décrivant l'évolution de la composition génétique d'une population soumise à la sélection naturelle. Nous montrons que ce processus satisfait un théorème de la limite centrale, et que ses fluctuations sont données par la solution d'une équation aux dérivées partielles stochastique. Nous utilisons ce résultat pour donner une estimation du fardeau de dérive au sein d'une population structurée en espace.Dans un deuxième temps, nous nous intéressons à la composition génétique d'une population lorsque les individus se déplacent plus facilement dans une région de l'espace que dans l'autre (on parle alors de dispersion hétérogène). Nous démontrons dans ce cas la convergence des fréquences alléliques via la convergence des lignées ancestrales vers un système de mouvements browniens de Walsh.Nous détaillons également l'impact d'une barrière géographique traversant l'habitat d'une population sur sa diversité génétique. Nous montrons que les lignées ancestrales décrivent dans ce cas des mouvements browniens partiellement réfléchis, dont nous donnons plusieurs constructions.Dans le but d'appliquer ces travaux, nous adaptons une méthode d'inférence démographique au cas de la dispersion hétérogène. Cette méthode utilise les blocs continus de génome hérités d'un même ancêtre entre les paires d'individus dans l'échantillon et permet d'estimer les caractéristiques démographiques d'une population lorsque celles-ci varient dans l'espace. Pour terminer nous démontrons l'efficacité de notre méthode sur des données simulées

The stepping stone model in a random environment and the effect of local heterogneities on isolation by distance patterns

International audienceWe study a one-dimensional spatial population model where the population sizes of the subpopulations are chosen according to a translation invariant and ergodic distribution and are uniformly bounded away from 0 and infinity. We suppose that the frequencies of a particular genetic type in the colonies evolve according to a system of interacting diffusions, following the stepping stone model of Kimura. We show that, over large spatial and temporal scales, this model behaves like the solution to a stochastic heat equation with Wright-Fisher noise with constant coefficients. These coefficients are the effective diffusion rate of genes within the population and the effective local population density. We find that, in our model, the local heterogeneity leads to a slower effective diffusion rate and a larger effective population density than in a uniform population. Our proof relies on duality techniques, an invariance principle for reversible random walks in a random environment and a convergence result for a system of coalescing random walks in a random environment

Dispersal heterogeneity in the spatial Lambda-Fleming-Viot process

We study the evolution of gene frequencies in a spatially distributed population when the dispersal of individuals is not uniform in space. We adapt the \slfv to this setting and consider that individuals spread their offspring farther from themselves at each generation in one halfspace than in the other. We study the large scale behaviour of this process and show that the motion of ancestral lineages is asymptotically close to a family of skew Brownian motions which coalesce upon meeting in one dimension, but never meet in higher dimension. This leads to a generalization of a result due to Nagylaki on the scaling limits of the gene frequencies: the non-uniform dispersal causes a discontinuity in the slope of the gene frequencies but the gene frequencies themselves are continuous across the interface

Household epidemic models and McKean-Vlasov Poisson driven SDEs

This paper presents a new view of household epidemic models, where the interaction between the households is of mean field type. We thus obtain in the limit of infinitely many households a nonlinear Markov process solution of a McKean - Vlasov type Poisson driven SDE, and a propagation of chaos result. We also define a basic reproduction number R0, and show that if R0>1, then the nonlinear Markov process has a unique non trivial ergodic invariant probability measure, whereas if R0<=1, it converges to 0 as t tends to infinity

Multi-patch multi-group epidemic model with varying infectivity

International audienceThis paper presents a law of large numbers result, as the size of the population tends to infinity, of SIR stochastic epidemic models, for a population distributed over L distinctpatches(withmigrationsbetweenthem)and K distinctgroups(possiblyagegroups). The limit is a set of Volterra-type integral equations, and the result shows the effects of both spatial and population heterogeneity. The novelty of the model is that the infectivity of an infected individual is infection age dependent. More precisely, to each infected individual is attached a random infection-age dependent infectivity function, such that the various random functions attached to distinct individuals are i.i.d.The proof involves a novel construction of a sequence of i.i.d. processes to invoke the law of large numbers for processes in D, by using the solution of a MacKean-Vlasov type Poisson-driven stochastic equation (as in the propagation of chaos theory). We also establish an identity using the Feynman-Kac formula for an adjoint backward ODE. The advantage of this approach is that it assumes much weaker conditions on the random infectivity functions than our earlier work for the homogeneous model in [20], where standard tightness criteria for convergence of stochastic processes were employed. To illustrate this new approach, we first explain the new proof under the weak assumptions for the homogeneous model, and then describe the multipatch-multigroup model and prove the law of large numbers for that model

Outside the wild: Risks and mechanisms of host jumps of endive necrotic mosaic potyvirus

National audienc

Outside the wild: Risks and mechanisms of host jumps of endive necrotic mosaic potyvirus

National audienc