Related papers: Measure representation of evolving genealogies
In recent years, with the advent of highly scalable artificial-neural-network-based text representation methods the field of natural language processing has seen unprecedented growth and sophistication. It has become possible to distill…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
With recent progress in deep generative models, the problem of identifying synthetic data and comparing their underlying generative processes has become an imperative task for various reasons, including fighting visual misinformation and…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
We consider a population with non-overlapping generations, whose size goes to infinity. It is described by a discrete genealogy which may be time non-homogeneous and we pay special attention to branching trees in varying environments. A…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population in contrast with the linear growth of…
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…
Genetic and evolution algebras arise naturally from applied probability and stochastic processes. Gibbs measures describe interacting systems commonly studied in thermodynamics and statistical mechanics with applications in several fields.…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…
We construct a measure-valued equivalent to the spatial Lambda-Fleming-Viot process (SLFV) introduced in [Eth08]. In contrast with the construction carried out in [Eth08], we fix the realization of the sequence of reproduction events and…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…
A fundamental problem in technological studies is how to measure the evolution of technology. The literature has suggested several approaches to measuring the level of technology (or state-of-the-art) and changes in technology. However, the…
We introduce a broad class of spatial models to describe how spatially heterogeneous populations live, die, and reproduce. Individuals are represented by points of a point measure, whose birth and death rates can depend both on spatial…