Related papers: On Tree Based Phylogenetic Networks

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…

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…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

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 evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…

In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…

In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…

Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…

Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…

A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…

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…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

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…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…