Related papers: Multiple-merger genealogies -- models, consequence…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…
Kingman's coalescent is one of the most popular models in population genetics. It describes the genealogy of a population whose genetic composition evolves in time according to the Wright-Fisher model, or suitable approximations of it…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct…
For $\Lambda$-$n$-coalescents with mutation, we analyse the size $O_n$ of the partition block of $i\in\{1,\ldots,n\}$ at the time where the first mutation appears on the tree that affects $i$ and is shared with any other…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
Coalescents with multiple collisions, also known as $\Lambda$-coalescents, were introduced by Pitman and Sagitov in 1999. These processes describe the evolution of particles that undergo stochastic coagulation in such a way that several…
We consider a stochastic model, called the replicator coalescent, describing a system of blocks of $k$ different types which undergo pairwise mergers at rates depending on the block types: with rate $C_{i,j}$ blocks of type $i$ and $j$…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
We study a model of selection acting on a diploid population (one in which each individual carries two copies of each gene) living in one spatial dimension. We suppose a particular gene appears in two forms (alleles) $A$ and $a$, and that…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Recent statistical and computational analyses have shown that a genealogical most recent common ancestor (MRCA) may have lived in the recent past. However, coalescent-based approaches show that genetic most recent common ancestors for a…
To most mathematicians and computer scientists the word ``tree'' conjures up, in addition to the usual image, the image of a connected graph with no circuits. In the last few years various types of trees have been the subject of much…