Related papers: Lines of descent under selection
We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing Machines that we introduced in a previous article. The use of Turing Machines allows for very simple mechanisms of code growth and code…
We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
The presence of phenomena analogous to phase transition in Statistical Mechanics, has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
We review and extend results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic…
In many indigenous societies, people are categorised into several cultural groups, or clans, within which they believe to share ancestors. Clan attributions provide certain rules for marriage and descent. Such rules between clans constitute…
We consider a stationary continuous model of random size population with non-neutral mutations using a continuous state branching process with non-homogeneous immigration. We assume the type (or mutation) of the immigrants is random given…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Spatial models where growth is limited to the edge of the expansions have been instrumental to understand the population dynamics and the clone size distribution in growing cellular populations, such as microbial colonies and avascular…
We define a multi-type coalescent point process of a general branching process with finitely many types. This multi-type coalescent fully describes the genealogy of the (quasi-stationary) standing population, providing types along ancestral…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
In stochastic evolutionary dynamics, the replacement of an existing genotype or cultural trait by a newly introduced mutant is typically characterized by the quantities of fixation probability and fixation time. But in a structured…
We develop the theory of linear evolution equations associated with the adjacency matrix of a graph, focusing in particular on infinite graphs of two kinds: uniformly locally finite graphs as well as locally finite line graphs. We discuss…
Cancer progression is an evolutionary process that is driven by mutation and selection in a population of tumor cells. We discuss mathematical models of cancer progression, starting from traditional multistage theory. Each stage is…
Increasing effort is put into the development of methods for learning mechanistic models from data. This task entails not only the accurate estimation of parameters but also a suitable model structure. Recent work on the discovery of…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…