Related papers: Selection and Coalescence in a Finite State Model
We consider a three dimensional system consisting of a large number of small spherical particles, distributed in a range of sizes and heights (with uniform distribution in the horizontal direction). Particles move vertically at a…
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…
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…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
We study the effect of biological confounders on the model selection problem between Kingman coalescents with population growth, and Xi-coalescents involving simultaneous multiple mergers. We use a low dimensional, computationally tractable…
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,…
Coalescence processes have received a lot of attention in the context of conditional branching processes with fixed population size and non-overlapping generations. Here we focus on similar problems in the context of the standard…
Study sample sizes in human genetics are growing rapidly, and in due course it will become routine to analyze samples with hundreds of thousands if not millions of individuals. In addition to posing computational challenges, such large…
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 show that genealogical trees arising from a broad class of non-neutral models of population evolution converge to the Kingman coalescent under a suitable rescaling of time. As well as non-neutral biological evolution, our results apply…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
The classical linear ordering problem seeks a single ranking representing a given preference matrix. While suitable for homogeneous populations, it fails when observed preferences arise from several latent groups with distinct ranking…
When particles on a line collide, they may coalesce into one. Such systems arise in the voter model, where boundaries between opinion clusters perform coalescing random walks, and in reaction-diffusion theory, where diffusing particles…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
We consider the mutation--selection differential equation with pairwise interaction (or, equivalently, the diploid mutation--selection equation) and establish the corresponding ancestral process, which is a random tree and a variant of the…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
We present a novel preference learning framework to capture participant preferences efficiently within limited interaction rounds. It involves three main contributions. First, we develop a variational Bayesian approach to infer the…
The Wright-Fisher model and the Moran model are both widely used in population genetics. They describe the time evolution of the frequency of an allele in a well-mixed population with fixed size. We propose a simple and tractable model…
Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, inferential algorithms do not scale to available data sets. A…
A multi-type neutral Cannings population model with mutation and fixed subpopulation sizes is analyzed. Under appropriate conditions, as all subpopulation sizes tend to infinity, the ancestral process, properly time-scaled, converges to a…