Related papers: Measure representation of evolving genealogies
We calculate the density and expectation for the number of lineages in a reconstructed tree with $n$ extant species. This is done with conditioning on the age of the tree as well as with assuming a uniform prior for the age of the tree.
We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
We consider weighted particle systems in which new generations are re-sampled from current particles with probabilities proportional to their weights. This covers a broad class of sequential Monte Carlo methods, widely used in applied…
We study the continuous-time evolution of the recombination equation of population genetics. This evolution is given by a differential equation that acts on a product probability space, and its solution can be described by a Markov chain on…
While recent work has established divergence as a key framework for understanding evenness, there is currently no research exploring how the families of measures within the divergence-based framework relate to each other. This paper uses…
In this work, we first show that the properly rescaled height process of the genealogical tree of a continuous time branching process converges to the height process of the genealogy of a (possibly discontinuous) continuous state branching…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Combinatorial trees can be used to represent genealogies of asexual individuals. These individuals can be endowed with birth and death times, to obtain a so-called `chronological tree'. In this work, we are interested in the continuum…
We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large…
When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…
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…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Among the evolutionary methods, one that is quite prominent is Genetic Programming, and, in recent years, a variant called Geometric Semantic Genetic Programming (GSGP) has shown to be successfully applicable to many real-world problems.…
We investigate the evolutionary dynamics of a population structured in phenotype, subjected to trait dependent selection with a linearly moving optimum and an asexual mode of reproduction. Our model consists of a non-local and non-linear…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
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…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…