相关论文: Statistical properties of the site-frequency spect…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
Sweepstakes reproduction refers to a highly skewed individual recruitment success without involving natural selection and may apply to individuals in broadcast spawning populations characterised by Type III survivorship. We consider an…
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…
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 introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct…
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 propose a change in focus from the prevalent paradigm based on the branching property as a tool to analyze the structure of population models, to one based on the self-similarity property, which we also introduce for the first time in…
We present a robust method which translates information on the speed of coming down from infinity of a genealogical tree into sampling formulae for the underlying population. We apply these results to population dynamics where the genealogy…
The results in this paper provide new information on asymptotic properties of classical models: the neutral Kingman coalescent under a general finite-alleles, parent-dependent mutation mechanism, and its generalisation, the ancestral…
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…
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…
Bayesian inference for spatial point patterns is often hindered computationally by intractable likelihoods. In the frequentist literature, estimating equations utilizing pseudolikelihoods have long been used for simulation-free parameter…
It is becoming routine to obtain datasets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study…
We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or…
In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models…
We consider the problem of making nonparametric inference in a class of multi-dimensional diffusions in divergence form, from low-frequency data. Statistical analysis in this setting is notoriously challenging due to the intractability of…
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…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
Coalescents with multiple collisions, also known as $\Lambda$-coalescents, were introduced by Pitman and Sagitov in 1999. These processes describe the evolution of particles that undergo stochastic coagulation in such a way that several…
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that…