Related papers: Genealogical constructions of population models
The paper reviews the results obtained for spatial population models and the evolution of the genealogies of these populations during the last decade by the author and his coworkers. The focus is on their large scale behaviour and on the…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of…
Complex processes ranging from protein folding to nuclear fission often follow a low-dimension reaction path parameterized in terms of a few collective variables. In nuclear theory, variables related to the shape of the nuclear density in a…
We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…
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…
We consider an approximating sequence of interacting population models with branching, mutation and competition. Each individual is characterized by its trait and the traits of its ancestors. Birth- and death-events happen at exponential…
We consider a continuous-time Bienaym\'e-Galton-Watson process with logistic competition in a regime of weak competition, or equivalently of a large carrying capacity. Individuals reproduce at random times independently of each other but…
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 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,…
A simulation model of a population having internal (genetic) structure is presented. The population is subject to selection pressure coming from the environment which is the same in the whole system but changes in time. Reproduction has a…
Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can…
We consider a generic class of stochastic particle-based models whose state at an instant in time is described by a set of continuous degrees of freedom (e.g. positions), and the length of this set changes stochastically in time due to…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
There exists a wide variety of works on the dynamics of large populations ranging from simple heuristic modeling to those based on advanced computer supported methods. Their interconnections, however, remain mostly vague, which…
New experimental methods make it possible to measure the expression levels of many genes, simultaneously, in snapshots from thousands or even millions of individual cells. Current approaches to analyze these experiments involve clustering…
Probabilistic graphical models (PGMs) are widely used to discover latent structure in data, but their success hinges on selecting an appropriate model design. In practice, model specification is difficult and often requires iterative…
Generative AI (GenAI) has revolutionized data-driven modeling by enabling the synthesis of high-dimensional data across various applications, including image generation, language modeling, biomedical signal processing, and anomaly…
The goal of this paper is to study the lookdown model with selection in the case of a population containing two types of individuals, with a reproduction model which is dual to the $\Lambda$-coalescent. In particular we formulate the…
Recently we have introduced a simplified model of ecosystem assembly (Capitan et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper…