Related papers: The Expected Sample Allele Frequencies from Popula…
Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
We analyse numerically the effects of small population size in the initial transient regime of a simple example population dynamics. These effects play an important role for the numerical determination of large deviation functions of…
In population genetics, extant samples are usually used for inference of past population genetic forces. With the Kingman coalescent and the backward diffusion equation, inference of the marginal likelihood proceeds from an extant sample…
In this article, a stochastic individual-based model describing Darwinian evolution of asexual, phenotypic trait-structured population, is studied. We consider a large population with constant population size characterised by a resampling…
A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences. In particular,…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
This work is devoted to the study of a stochastic logistic growth model with and without the Allee effect. Such a model describes the evolution of a population under environmental stochastic fluctuations and is in the form of a stochastic…
Understanding the time evolution of fragmented animal populations and their habitats, connected by migration, is a problem of both theoretical and practical interest. This paper presents a method for calculating the time evolution of the…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
We study the population genetics of two neutral alleles under reversible mutation in the \Lambda-processes, a population model that features a skewed offspring distribution. We describe the shape of the equilibrium allele frequency…
It is becoming routine to obtain datasets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study…
Our models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new situation by multiple…
Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to…
We introduce a modified spatial $\Lambda$-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective…
We investigate the large population dynamics of a family of stochastic particle systems with three-state cyclic individual behaviour and parameter-dependent transition rates. On short time scales, the dynamics turns out to be approximated…
A strong demographic Allee effect in which the expected population growth rate is negative below a certain critical population size can cause high extinction probabilities in small introduced populations. However, many species are…
Frequency dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency dependent selection, the average fitness of the population may increase or decrease based on…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…