Related papers: Ancestral lines under recombination
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
We introduce and study the dynamics of an \emph{immortal} critical branching process. In the classic, critical branching process, particles give birth to a single offspring or die at the same rates. Even though the average population is…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…
The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…
Population stratification is a problem encountered in several areas of biology and public health. We tackle this problem by mapping a population and its elements attributes into a hypergraph, a natural extension of the concept of graph or…
Graph coloring is a challenging combinatorial optimization problem with a wide range of applications. In this paper, a distribution evolutionary algorithm based on a population of probability model (DEA-PPM) is developed to address it…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But…
Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a…
$\Lambda$-Wright--Fisher processes provide a robust framework to describe the type-frequency evolution of an infinite neutral population. We add a polynomial drift to the corresponding stochastic differential equation to incorporate…
Understanding how stochastic and non-linear deterministic processes interact is a major challenge in population dynamics theory. After a short review, we introduce a stochastic individual-centered particle model to describe the evolution in…
The evolutionary process has been modelled in many ways using both stochastic and deterministic models. We develop an algebraic model of evolution in a population of asexually reproducing organisms in which we represent a stochastic walk in…
We are interested in a stochastic model of trait and age-structured population undergoing mutation and selection. We start with a continuous time, discrete individual-centered population process. Taking the large population and rare…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…
In this paper, we review recent results of ours concerning branching processes with general lifetimes and neutral mutations, under the infinitely many alleles model, where mutations can occur either at birth of individuals or at a constant…
Increasingly good statistical data on the galaxy population at high and low redshift enable the development of new phenomenological approaches to galaxy evolution based on application of the simplest continuity equations. This has given new…
We consider catalytic branching populations. They consist of a catalyst population evolving according to a critical binary branching process in continuous time with a constant branching rate and a reactant population with a branching rate…
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 study the common ancestor type distribution in a $2$-type Moran model with population size $N$, mutation and selection, and in the deterministic limit regime arising in the former when $N$ tends to infinity, without any rescaling of…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…