Related papers: Finite populations with frequency-dependent select…
Kingman's coalescent is a random tree that arises from classical population genetic models such as the Moran model. The individuals alive in these models correspond to the leaves in the tree and the following two laws of large numbers…
Populations evolving under the joint influence of recombination and resampling (traditionally known as genetic drift) are investigated. First, we summarise and adapt a deterministic approach, as valid for infinite populations, which assumes…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
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…
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we…
We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the…
The purpose of this Note is twofold: First, we introduce the general formalism of evolutionary genetics dynamics involving fitnesses, under both the deterministic and stochastic setups, and chiefly in discrete-time. In the process, we…
The entropy rates of the Wright-Fisher process, the Moran process, and generalizations are computed and used to compare these processes and their dependence on standard evolutionary parameters. Entropy rates are measures of the variation…
In population genetics, diffusions on the unit interval are often used to model the frequency path of an allele. In this setting we derive approximations for fixation probabilities, expected hitting times and the expected…
We study a class of processes that are akin to the Wright-Fisher model, with transition probabilities weighted in terms of the frequency-dependent fitness of the population types. By considering an approximate weak formulation of the…
We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
$\Lambda$-Wright--Fisher processes provide a robust framework to describe the type-frequency evolution of an infinite neutral population. We add a polynomial drift to the corresponding stochastic differential equation to incorporate…
Temporal environmental variations are ubiquitous in nature, yet most of the theoretical works in population genetics and evolution assume fixed environment. Here we analyze the effect of variations in carrying capacity on the fate of a…
Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is…
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.…
Modern developments in population dynamics emphasize the role of the turnover of individuals. In the new approaches stable population size is a dynamic equilibrium between different mortality and fecundity factors instead of an arbitrary…
We consider a continuous population whose dynamics is described by the standard stationary Fleming-Viot process, so that the genealogy of $n$ uniformly sampled individuals is distributed as the Kingman $n$-coalescent. In this note, we study…
This work is a systematic study of discrete Markov chains that are used to describe the evolution of a two-types population. Motivated by results valid for the well-known Moran (M) and Wright-Fisher (WF) processes, we define a general class…