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In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
Given a gene tree topology and a species tree topology, a coalescent history represents a possible mapping of the list of gene tree coalescences to associated branches of a species tree on which those coalescences take place. Enumerative…
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…
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…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
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…
We consider the problem of testing properties of graphs underlying high-dimensional graphical models. We adopt the model of covariance queries introduced by Lugosi, Truszkowski, Velona, and Zwiernik (2021). We study the case when the…
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
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…
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 introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the…
For a fixed set $X$ containing $n$ taxon labels, an ordered pair consisting of a gene tree topology $G$ and a species tree $S$ bijectively labeled with the labels of $X$ possesses a set of coalescent histories -- mappings from the set of…
Consider a tree $T=(V,E)$ with root $\circ$ and edge length function $\ell:E\to\mathbb{R}_+$. The phylogenetic covariance matrix of $T$ is the matrix $C$ with rows and columns indexed by $L$, the leaf set of $T$, with entries…
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…
Consider a population of fixed size that evolves over time. At each time, the genealogical structure of the population can be described by a coalescent tree whose branches are traced back to the most recent common ancestor of the…
Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
The classical model for the genealogies of a neutrally evolving population in a fixed environment is due to Kingman. Kingman's coalescent process, which produces a binary tree, universally emerges from many microscopic models in which the…