Related papers: Generalized Fitch Graphs II: Sets of Binary Relati…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Arboreal networks are a generalization of rooted trees, defined by keeping the tree-like structure, but dropping the requirement for a single root. Just as the class of cographs is precisely the class of undirected graphs that can be…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
A network $N$ on a finite set $X$, $|X|\geq 2$, is a connected directed acyclic graph with leaf set $X$ in which every root in $N$ has outdegree at least 2 and no vertex in $N$ has indegree and outdegree equal to 1; $N$ is arboreal if the…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The modular decomposition of a graph $G$ is a natural construction to capture key features of $G$ in terms of a labeled tree $(T,t)$ whose vertices are labeled as "series" ($1$), "parallel" ($0$) or "prime". However, full information of $G$…
Given a finite group $G$ and its representation $\rho$, the corresponding McKay graph is a graph $\Gamma(G,\rho)$ whose vertices are the irreducible representations of $G$; the number of edges between two vertices $\pi,\tau$ of…
We show that the class of finite rooted binary plane trees is a Ramsey class (with respect to topological embeddings that map leaves to leaves). That is, for all such trees P,H and every natural number k there exists a tree T such that for…
In this paper we study graphs which admit acyclic orientations that contain a pair of arc-disjoint out-branching and in-branching (such an orientation is called good) and we focus on edge-minimal such graphs. A 2T-graph is a graph whose…
A subgraph $H$ of an edge-colored graph $G$ is rainbow if all the edges of $H$ receive different colors. If $G$ does not contain a rainbow subgraph isomorphic to $H$, we say that $G$ is rainbow $H$-free. For connected graphs $H_1$ and…
Given a tree and a set ${\cal P}$ of non-trivial simple paths on it, $VPT({\cal P})$ is the VPT graph (i.e. the vertex intersection graph) of the paths ${\cal P}$ of the tree $T$, and $EPT({\cal P})$ is the EPT graph (i.e. the edge…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
The betweenness structure of a finite metric space $M = (X, d)$ is a pair $\mathcal{B}(M) = (X,\beta_M)$ where $\beta_M$ is the so-called betweenness relation of $M$ that consists of point triplets $(x, y, z)$ such that $d(x, z) = d(x, y) +…
In the literature, the notion of discrepancy is used in several contexts, even in the theory of graphs. Here, for a graph $G$, $\{-1, 1\}$ labels are assigned to the edges, and we consider a family $\mathcal{S}_G$ of (spanning) subgraphs of…
Let ${\cal G}=(G,w)$ be a weighted simple finite connected graph, that is, let $G$ be a simple finite connected graph endowed with a function $w$ from the set of the edges of $G$ to the set of real numbers. For any subgraph $G'$ of $G$, we…
A biased graph consists of a graph $G$ together with a collection of distinguished cycles of $G$, called balanced cycles, with the property that no theta subgraph contains exactly two balanced cycles. Perhaps the most natural biased graphs…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Let $\mathcal{G}$ be the set of simple graphs (or multigraphs) $G$ such that for each $G \in \mathcal{G}$ there exists at least two non-empty disjoint proper subsets $V_{1},V_{2}\subseteq V(G)$ satisfying $V(G)\setminus(V_{1} \cup…
Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…