Related papers: The quasispecies distribution
Modern statistical software and machine learning libraries are enabling semi-automated statistical inference. Within this context, it appears easier and easier to try and fit many models to the data at hand, reversing thereby the Fisherian…
We present a hybrid algorithm between an evolution strategy and a quasi Newton method. The design is based on the Hessian Estimation Evolution Strategy, which iteratively estimates the inverse square root of the Hessian matrix of the…
We describe a simple model of evolution which incorporates the branching and extinction of species lines, and also includes abiotic influences. A first principles approach is taken in which the probability for speciation and extinction are…
Background. In a number of recent experiments with food-and-mouth disease virus, a deleterious mutant, was found to avoid extinction and remain in the population for long periods of time. This observation was called quasispecies memory. The…
This paper develops a formulation of the quasispecies equations appropriate for polysomic, semiconservatively replicating genomes. This paper is an extension of previous work on the subject, which considered the case of haploid genomes.…
The controversy concerning both the definition of the species and methods for inferring the boundaries and numbers of species has occupied biologists for centuries, and the debate itself has become known as the species problem. The modern…
An analytical approximation is derived for the Zero Sum Multinomial distribution which gives the Species Abundance Distribution in Neutral Community Models. The obtained distribution function describes well computer simulation results on…
Stochastic models, based on random processes, may lead to power law distributions, which provide long range correlations. The observation of power law behavior and the presence of long range correlations in biological systems has been…
We study a continuous-time nearest-neighbor branching random walk on the $d$-dimensional $b$-ary hypercube $\{0,1,\dots,b-1\}^d$ as a model for viral quasispecies evolution under mutation and replication. Motivated by mutagenic antiviral…
We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an…
Global pointwise estimates are obtained for quasilinear Lane-Emden-type systems involving measures in the "sublinear growth" rate. We give necessary and sufficient conditions for existence expressed in terms of Wolff's potential. Our…
We study a classical multitype Galton--Watson process with mutation and selection. The individuals are sequences of fixed length over a finite alphabet. On the sharp peak fitness landscape together with independent mutations per locus, we…
The goal of this work is to propose a finite population counterpart to Eigen's model, which incorporates stochastic effects. We consider a Moran model describing the evolution of a population of size $m$ of chromosomes of length $\ell$ over…
The simplest model of a smart spatial redistribution of individuals is proposed. A single-species population is considered, to be composed of two discrete subpopulations inhabiting two stations; migration is a transfer between them. The…
A Bayesian nonparametric approach to the study of species diversity based on choosing a random discrete distribution as a prior model for the unknown relative abundances of species has been recently introduced in Lijoi et al. (2007, 2008).…
1. Joint species distribution models (JSDMs) have gained considerable traction among ecologists over the past decade, due to their capacity to answer a wide range of questions at both the species- and the community-level. The family of…
In the setting of stochastic dynamical systems that eventually go extinct, the quasi-stationary distributions are useful to understand the long-term behavior of a system before evanescence. For a broad class of applicable continuous-time…
The aim of this work is twofold. First, we survey the techniques developed in (Perthame, Zubelli, 2007) and (Doumic, Perthame, Zubelli, 2008) to reconstruct the division (birth) rate from the cell volume distribution data in certain…
We consider a branching model introduced by Kimmel for cell division with parasite infection. Cells contain proliferating parasites which are shared randomly between the two daughter cells when they divide. We determine the probability that…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…