相关论文: The coalescent and its descendants

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…

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…

Bertoin and Le Gall (2003) introduced a certain probability measure valued Markov process that describes the evolution of a population, such that a sample from this population would exhibit a genealogy given by the so-called…

We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we…

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…

Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe…

Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…

We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the…

In this work we describe a new model for the evolution of a diploid structured population backwards in time that allows for large migrations and uneven offspring distributions. The model generalizes both the mean-field model of Birkner et…

Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species.…

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…

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…

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…

Reconstructing past population size from present day genetic data is a major goal of population genetics. Recent empirical studies infer population size history using coalescent-based models applied to a small number of individuals. Here we…

Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…

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…

Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard coalescent, is used to infer the sample's bifurcating…

In a series of recent works it has been shown that a class of simple models of evolving populations under selection leads to genealogical trees whose statistics are given by the Bolthausen-Sznitman coalescent rather than by the well known…

Coalescent theory is the study of random processes where particles may join each other to form clusters as time evolves. These notes provide an introduction to some aspects of the mathematics of coalescent processes and their applications…

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…