Related papers: Multiple merger coalescent inference of effective …
Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology, but is particularly…
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enables inference of past population dynamics directly from…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
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…
Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the…
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…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…
Trees corresponding to $\Lambda$- and $\Xi$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting…
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories…
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…
Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past…
Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the population size history to genealogies. The high computational cost…
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…
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…
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…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
We study coalescent processes conditional on the population pedigree under the exchangeable diploid bi-parental population model of \citet{BirknerEtAl2018}. While classical coalescent models average over all reproductive histories, thereby…
We consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
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…