Related papers: On the existence of infinitely many universal tree…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
We provide an $\Omega(n\log n) $ lower bound and an $O(n^2)$ upper bound for the smallest size of rooted binary trees (a.k.a. phylogenetic tree shapes), which are universal for rooted binary trees with $n$ leaves, i.e., contain all of them…
We show that there exists an outerplanar graph on $O(n^{c})$ vertices for $c = \log_2(3+\sqrt{10}) \approx 2.623$ that contains every tree on $n$ vertices as a subgraph. This extends a result of Chung and Graham from 1983 who showed that…
Geometry of networks endowed with a causal structure is discussed using the conventional framework of equilibrium statistical mechanics. The popular growing network models appear as particular causal models. We focus on a class of tree…
While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
We show that a graph $G$ has a normal spanning tree if and only if its vertex set is the union of countably many sets each separated from any subdivided infinite clique in $G$ by a finite set of vertices. This proves a conjecture by Brochet…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general,…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
We demonstrate that a tree-based theory for various dynamical processes yields extremely accurate results for several networks with high levels of clustering. We find that such a theory works well as long as the mean intervertex distance…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We prove that in both the free and the wired uniform spanning forest (FUSF and WUSF) of any unimodular random rooted network (in particular, of any Cayley graph), it is impossible to distinguish the connected components of the forest from…
The Pathwidth Theorem states that if a class of graphs has unbounded pathwidth, then it contains all trees as graph minors. We prove a similar result for dense graphs. More precisely, we give a finite family of tree-like patterns and prove…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
We answer three questions posed by Bubeck and Linial on the limit densities of subtrees in trees. We prove there exist positive $\varepsilon_1$ and $\varepsilon_2$ such that every tree that is neither a path nor a star has inducibility at…
We prove that, if $m$ is sufficiently large, every graph on $m+1$ vertices that has a universal vertex and minimum degree at least $\lfloor \frac{2m}{3} \rfloor$ contains each tree $T$ with $m$ edges as a subgraph. Our result confirms, for…