Related papers: On the Subnet Prune and Regraft Distance
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
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…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Head moves are a type of rearrangement moves for phylogenetic networks. They have mostly been studied as part of more encompassing types of moves, such as rSPR moves. Here, we study head moves as a type of moves on themselves. We show that…
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…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
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…
In evolutionary biology, phylogenetic networks are now widely used to represent the historical relationships between species and population, when this history includes reticulation events such as hybridization, gene flow and admixture…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…