Related papers: A master equation approach to the n-coalescent pro…
$\Lambda$-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…
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…
Multiple-merger coalescents, e.g. $\Lambda$-$n$-coalescents, have been proposed as models of the genealogy of $n$ sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's…
Consider an arbitrary large population at the present time, originated at an unspecified arbitrary large time in the past, where individuals in the same generation reproduce independently, forward in time, with the same offspring…
Coalescent processes, including mutation, are derived from Moran type population models admitting large offspring numbers. Including mutation in the coalescent process allows for quantifying the turnover of alleles by computing the…
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially…
We revisit the spatial ${\lambda}$-Fleming-Viot process introduced in [1]. Particularly, we are interested in the time $T_0$ to the most recent common ancestor for two lineages. We distinguish between the case where the process acts on the…
A detailed study is presented for a large class of uncoupled continuous-time random walks (CTRWs). The master equation is solved for the Mittag-Leffler survival probability. The properly scaled diffusive limit of the master equation is…
The goal of cancer genome sequencing projects is to determine the genetic alterations that cause common cancers. Many malignancies arise during the clonal expansion of a benign tumor which motivates the study of recurrent selective sweeps…
We investigate the distribution of the coalescence time (most recent common ancestor) for two individuals picked at random (uniformly) in the current generation of a continuous time Bienaym\'e-Galton-Watson process founded $t$ units of time…
The goal of this paper is to prove rigorous results for the behavior of genealogies in a one-dimensional long range biased voter model introduced by Hallatschek and Nelson [25]. The first step, which is easily accomplished using results of…
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…
Duality plays an important role in population genetics. It can relate results from forwards-in-time models of allele frequency evolution with those of backwards-in-time genealogical models; a well known example is the duality between the…
When identical particles on a line collide, they merge and continue as one. Exact determinantal formulas have long been available for particles conditioned never to collide, but collisions change the number of particles, and exact…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
Consider a two-type Moran population of size $N$ with selection and mutation, where the selective advantage of the fit individuals is amplified at extreme environmental conditions. Assume selection and mutation are weak with respect to $N$,…
Motivated by sample path decomposition of the stationary continuous state branching process with immigration, a general population model is considered using the idea of immortal individual. We compute the joint distribution of the random…
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 consider a single genetic locus which carries two alleles, labelled P and Q. This locus experiences selection and mutation. It is linked to a second neutral locus with recombination rate r. If r=0, this reduces to the study of a single…