Related papers: Integral representation of probabilities in Kingma…
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…
The classical model for the genealogies of a neutrally evolving population in a fixed environment is due to Kingman. Kingman's coalescent process, which produces a binary tree, universally emerges from many microscopic models in which the…
The nested Kingman coalescent describes the ancestral tree of a population undergoing neutral evolution at the level of individuals and at the level of species, simultaneously. We study the speed at which the number of lineages descends…
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…
For a one-locus haploid infinite population with discrete generations, the celebrated Kingman's model describes the evolution of fitness distributions under the competition of selection and mutation, with a constant mutation probability.…
The observed sequence variation at a locus informs about the evolutionary history of the sample and past population size dynamics. The Kingman coalescent is used in a generative model of molecular sequence variation to infer evolutionary…
Kingman's model describes the evolution of a one-locus haploid population of infinite size and discrete generations under the competition of selection and mutation. A random generalisation has been made in a previous paper which assumes all…
Full likelihood inference under Kingman's coalescent is a computationally challenging problem to which importance sampling (IS) and the product of approximate conditionals (PAC) method have been applied successfully. Both methods can be…
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…
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their…
We propose a new algorithm to do posterior sampling of Kingman's coalescent, based upon the Particle Markov Chain Monte Carlo methodology. Specifically, the algorithm is an instantiation of the Particle Gibbs Sampling method, which…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
Kingman's coalescent is a widely used process to model sample genealogies in population genetics. Recently there have been studies on the inference of quantities related to the genealogy of additional individuals given a known sample. This…
Kingman derived the Ewens sampling formula for random partitions describing the genetic variation in a neutral mutation model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process, and…
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the…
We consider a model of a population in which individuals are sampled from different species. The Yule-Kingman nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a…
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…
The evolving Kingman coalescent is the tree-valued process which records the time evolution undergone by the genealogies of Moran populations. We consider the associated process of total external tree length of the evolving Kingman…
Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of…
Take a continuous-time Galton-Watson tree. If the system survives until a large time $T$, then choose $k$ particles uniformly from those alive. What does the ancestral tree drawn out by these $k$ particles look like? Some special cases are…