Related papers: Multiple-merger genealogies -- models, consequence…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
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…
We introduce a generalization of Kingman's coalescent on $[n]$ that we call the Kingman coalescent on a graph $G = ([n],E)$. Specifically, we generalize a forest valued representation of the coalescent introduced in Addario-Berry and Eslava…
We study a class of coalescents derived from a sampling procedure out of N i.i.d. Pareto(alpha) random variables, normalized by their sum, including beta-size-biasing on total length effects (beta < alpha). Depending on the range of alpha,…
We introduce a general diploid population model with self-fertilization and possible overlapping generations, and study the genealogy of a sample of $n$ genes as the population size $N$ tends to infinity. Unlike traditional approach in…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
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…
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…
A density-dependent branching process is a particle system in which individuals reproduce independently, but in a way that depends on the current population size. This feature can model a wide range of ecological interactions at the cost of…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…
The evolving Kingman coalescent is the tree-valued process which records the time evolution undergone by the genealogies of Moran populations. We consider the associated process of total external tree length of the evolving Kingman…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
We introduce a colored coalescent process which recovers random colored genealogical trees. Here a colored genealogical tree has its vertices colored black or white. Moving backward along the colored genealogical tree, the color of vertices…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
Evolutionary models for populations of constant size are frequently studied using the Moran model, the Wright-Fisher model, or their diffusion limits. When evolution is neutral, a random genealogy given through Kingman's coalescent is used…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…