Related papers: Phase transitions in Phylogeny
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Phylogenetic trees capture evolutionary relationships among species and reflect the forces that shaped them. While many studies rely on branch length information, the topology of phylogenetic trees (particularly their degree of imbalance)…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
We study a configuration model on bipartite planar maps in which, given $n$ even integers, one samples a planar map with $n$ faces uniformly at random with these face degrees. We prove that when suitably rescaled, such maps always admit…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
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…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
The mother-dependent neutral mutations model describes the evolution of a population across discrete generations, where neutral mutations occur among a finite set of possible alleles. In this model, each mutant child acquires a type…
We study random trees which are invariant in law under the operation of contracting each edge independently with probability $p\in(0,1)$. We show that all such trees can be constructed through Poissonian sampling from a certain class of…
We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree…
For a set $P$ of $n$ points in the plane in general position, a non-crossing spanning tree is a spanning tree of the points where every edge is a straight-line segment between a pair of points and no two edges intersect except at a common…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
Consider an information source generating a symbol at the root of a tree network whose links correspond to noisy communication channels, and broadcasting it through the network. We study the problem of reconstructing the transmitted symbol…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
Phylogenetic trees constitute an interesting class of objects for stochastic processes due to the non-standard nature of the space they inhabit. In particular, many statistical applications require the construction of Markov processes on…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA…
In this work, we study a family of non-Markovian trees modeling populations where individuals live and reproduce independently with possibly time-dependent birth-rate and lifetime distribution. To this end, we use the coding process…