Related papers: Comparing and simplifying distinct-cluster phyloge…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

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…

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…

It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…

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…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

The recursive removal of leaves (dead end vertices) and their neighbors from an undirected network results, when this pruning algorithm stops, in a so-called core of the network. This specific subgraph should be distinguished from…

Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…

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…

In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…

A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…

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…

Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…