Related papers: Random ultrametric trees and applications
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
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,…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
We consider unimodular random rooted trees (URTs) and invariant forests in Cayley graphs. We show that URTs of bounded degree are the same as the law of the component of the root in an invariant percolation on a regular tree. We use this to…
We present a graph theoretical approach to the configurational statistics of random tree-like objects, such as randomly branching polymers. In particular, for ideal trees we show that Pr\"ufer labelling provides: (i) direct access to the…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
In this paper, we address the question of comparison between populations of trees. We study an statistical test based on the distance between empirical mean trees, as an analog of the two sample z statistic for comparing two means. Despite…
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…
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…
We introduce a continuous-time quantum walk on an ultrametric space corresponding to the set of p-adic integers and compute its time-averaged probability distribution. It is shown that localization occurs for any location of the ultrametric…
We extend classical results on simple varieties of trees (asymptotic enumeration, average behavior of tree parameters) to trees counted by their number of leaves. Motivated by genome comparison of related species, we then apply these…
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…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…
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…
The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices $M^{\alpha \beta ; \gamma \delta}$, is shown to be dramatically simplified through the introduction of properly chosen…
When considering the number of subtrees of trees, the extremal structures which maximize this number among binary trees and trees with a given maximum degree lead to some interesting facts that correlate to other graphical indices in…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…