arXiv subjects

Amandine Veber

Publications and source records attributed to Amandine Veber.

9 recordsLinked to original sources

arXiv2023

Measure-valued growth processes in continuous space and growth properties starting from an infinite interface

The k-parent and infinite-parent spatial Lambda-Fleming Viot processes (or SLFV), introduced in Louvet (2023), form a family of stochastic models for spatially expanding populations. These processes are akin to a continuous-space version of the classical Eden growth model (but with local backtracking of the occupied area allowed when k is finite), while being associated to a dual process encoding ancestry. In this article, we focus on the growth properties of the area occupied by individuals of type 1 (type 0 encoding units of empty space). To do so, we first define the quantities that we shall use to quantify the speed of growth of the occupied area. Using the associated dual process and a comparison with a first-passage percolation problem, we show that the growth of the occupied region in the infinite-parent SLFV is linear in time. Because of the possibility of local backtracking of the occupied area, the result we obtain for the k-parent SLFV is slightly weaker. It gives an upper bound on the probability that a given location is occupied at time t, which also shows that growth in the k-parent SLFV is linear in time. We use numerical simulations to approximate the growth speed for the infinite-parent SLFV, and we observe that the actual speed may be higher than the speed expected from simple first-moment calculations due to the characteristic front dynamics.

math.PR↗

arXiv2022

A spatial measure-valued model for chemical reaction networks in heterogeneous systems

We propose a novel measure valued process which models the behaviour of chemical reaction networks in spatially heterogeneous systems. It models reaction dynamics between different molecular species and continuous movement of molecules in space. Reactions rates at a spatial location are proportional to the mass of different species present locally and to a location specific chemical rate, which may be a function of the local or global species mass as well. We obtain asymptotic limits for the process, with appropriate rescaling depending on the abundance of different molecular types. In particular, when the mass of some species in the scaling limit is discrete while the mass of the others is continuous, we obtain a new type of spatial random evolution process. This process can be shown, in some situations, to correspond to a measure-valued piecewise deterministic Markov process in which the discrete mass of the process evolves stochastically, and the continuous mass evolves in a deterministic way between consecutive jump times of the discrete part.

math.PR↗

arXiv2021

The Tajima heterochronous n-coalescent: inference from heterochronously sampled molecular data

The observed sequence variation at a locus informs about the evolutionary history of the sample and past population size dynamics. The Kingman coalescent is used in a generative model of molecular sequence variation to infer evolutionary parameters. However, it is well understood that inference under this model does not scale well with sample size. Here, we build on recent work based on a lower resolution coalescent process, the Tajima coalescent, to model longitudinal samples. While the Kingman coalescent models the ancestry of labeled individuals, the heterochronous Tajima coalescent models the ancestry of individuals labeled by their sampling time. We propose a new inference scheme for the reconstruction of effective population size trajectories based on this model with the potential to improve computational efficiency. Modeling of longitudinal samples is necessary for applications (e.g. ancient DNA and RNA from rapidly evolving pathogens like viruses) and statistically desirable (variance reduction and parameter identifiability). We propose an efficient algorithm to calculate the likelihood and employ a Bayesian nonparametric procedure to infer the population size trajectory. We provide a new MCMC sampler to explore the space of heterochronous Tajima's genealogies and model parameters. We compare our procedure with state-of-the-art methodologies in simulations and applications.

stat.ME↗

arXiv2020

Rescaling limits of the spatial Lambda-Fleming-Viot process with selection

We consider the spatial Lambda-Fleming-Viot process model for frequencies of genetic types in a population living in R^d, with two types of individuals (0 and 1) and natural selection favouring individuals of type 1. We first prove that the model is well-defined and provide a measure-valued dual process encoding the locations of the `potential ancestors' of a sample taken from such a population. We then consider two cases, one in which the dynamics of the process are driven by events of bounded radii and one incorporating large-scale events whose radii have a polynomial tail distribution. In both cases, we consider a sequence of spatial Lambda-Fleming-Viot processes indexed by n, and we assume that the fraction of individuals replaced during a reproduction event and the relative frequency of events during which natural selection acts tend to 0 as n tends to infinity. We choose the decay of these parameters in such a way that when reproduction is only local, the measure-valued process describing the local frequencies of the less favoured type converges in distribution to a (measure-valued) solution to the stochastic Fisher-KPP equation in one dimension, and to a (measure-valued) solution to the deterministic Fisher-KPP equation in more than one dimension. When large-scale extinction-recolonisation events occur, the sequence of processes converges instead to the solution to the analogous equation in which the Laplacian is replaced by a fractional Laplacian. We also consider the process of `potential ancestors' of a sample of individuals taken from these populations, which we see as a system of branching and coalescing symmetric jump processes. We show their convergence in distribution towards a system of Brownian or stable motions which branch at some finite rate. In one dimension, in the limit, pairs of particles also coalesce at a rate proportional to their collision local time.

math.PR↗

arXiv2016

A Beta-splitting model for evolutionary trees

In this article, we construct a generalization of the Blum-François Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification `potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the Generating, Organizing and Deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the Generating, Organizing and Deleting processes where tree topology and branch-lengths are jointly modeled and provide code in SageMath/python for these algorithms.

math.PR↗

arXiv2013

The spatial Lambda-Fleming-Viot process: an event-based construction and a lookdown representation

We construct a measure-valued equivalent to the spatial Lambda-Fleming-Viot process (SLFV) introduced in [Eth08]. In contrast with the construction carried out in [Eth08], we fix the realization of the sequence of reproduction events and obtain a quenched evolution of the local genetic diversities. To this end, we use a particle representation which highlights the role of the genealogies in the attribution of types (or alleles) to the individuals of the population. This construction also enables us to clarify the state-space of the SLFV and to derive several path properties of the measure-valued process as well as of the labeled trees describing the genealogical relations between a sample of individuals. We complement it with a look-down construction which provides a particle system whose empirical distribution at time t, seen as a process in t, has the law of the quenched SLFV. In all these results, the facts that we work with a fixed configuration of events and that reproduction occurs only locally in space introduce serious technical issues that are overcome by controlling the number of events occurring and of particles present in a given area over macroscopic time intervals.

math.PR↗

arXiv2011

Escape probabilities for branching Brownian motion among mild obstacles

We derive asymptotics for the quenched probability that a critical branching Brownian motion killed at a small rate in Poissonian obstacles exits a large domain. Results are formulated in terms of the solution to a semilinear partial differential equation with singular boundary conditions. The proofs depend on a quenched homogenization theorem for branching Brownian motion among mild obstacles.

math.PR↗

arXiv2009

Quenched convergence of a sequence of superprocesses in R^d among Poissonian obstacles

We prove a convergence theorem for a sequence of super-Brownian motions moving among hard Poissonian obstacles, when the intensity of the obstacles grows to infinity but their diameters shrink to zero in an appropriate manner. The superprocesses are shown to converge in probability for the law $\mathbf{P}$ of the obstacles, and $\mathbf{P}$-almost surely for a subsequence, towards a superprocess with underlying spatial motion given by Brownian motion and (inhomogeneous) branching mechanism $ψ(u,x)$ of the form $ψ(u,x)= u^2+ κ(x)u$, where $κ(x)$ depends on the density of the obstacles. This work draws on similar questions for a single Brownian motion. In the course of the proof, we establish precise estimates for integrals of functions over the Wiener sausage, which are of independent interest.

math.PR↗

arXiv2008

Coalescent processes in subdivided populations subject to recurrent mass extinctions

We investigate the infinitely many demes limit of the genealogy of a sample of individuals from a subdivided population subject to sporadic mass extinction events. By exploiting a separation of timescales property of Wright's island model, we show that as the number of demes tends to infinity the limiting form of the genealogy can be described in terms of the alternation of instantaneous 'scattering' phases dominated by local demographic processes, and extended 'collecting' phases dominated by global processes. When extinction and recolonization events are local, this genealogy is given by Kingman's coalescent and the scattering phase influences only the overall rate of the process. In contrast, if the vacant demes left by a mass extinction event can be recolonized by individuals emerging from a small number of demes, then the limiting genealogy is a colaescent with simultaneous multiple mergers. In this case, the details of the within-deme population dynamics influence not only the overall rate of the coalescent process, but also the statistics of the complex mergers that can occur within sample genealogies. This study gives some insight into the genealogical consequences of mass extinction in structured populations.

math.PR↗