Related papers: Statistical tools for seed bank detection
We identify a new natural coalescent structure, which we call the seed-bank coalescent, that describes the gene genealogy of populations under the influence of a strong seed-bank effect, where "dormant forms" of individuals (such as seeds…
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…
We present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered…
Seed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with…
We consider a population constituted by two types of individuals; each of them can produce offspring in two different islands (as a particular case the islands can be interpreted as active or dormant individuals). We model the evolution of…
Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species.…
We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct…
Kingman's coalescent is one of the most popular models in population genetics. It describes the genealogy of a population whose genetic composition evolves in time according to the Wright-Fisher model, or suitable approximations of it…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…
Consider a structured population consisting of $d$ colonies, with migration rates proportional to a positive parameter $K$. We sample $N_K$ individuals, distributed evenly across the $d$ colonies, and trace their ancestral lineages backward…
This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of…
In this article, we introduce a random (directed) graph model for the simultaneous forwards and backwards description of a rather broad class of Cannings models with a seed bank mechanism. This provides a simple tool to establish a sampling…
We derive the asymptotic behavior of the total, active and inactive branch lengths of the seed bank coalescent, when the size of the initial sample grows to infinity. Those random variables have important applications for populations…
Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe…
Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has…
This paper generalizes the strong seed-bank model introduced in arXiv:1411.4747 to allow for more general dormancy time distributions, such as a type of Pareto distribution. Inspired by the method of approximation using models with…
The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial,…
We investigate the behaviour of the genealogy of a Wright-Fisher population model under the influence of a strong seed-bank effect. More precisely, we consider a simple seed-bank age distribution with two atoms, leading to either classical…
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enables inference of past population dynamics directly from…
Statistical properties of the site frequency spectrum associated with Lambda-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier…