Related papers: All that Glisters is not Galled
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 networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
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…
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 bicombining tree-child networks in which…
Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
We describe Galois connections which arise between two kinds of combinatorial structures, both of which generalize trees with labelled leaves, and then apply those connections to a family of polytopes. The graphs we study can be imbued with…
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…
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…
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…
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character…
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…
Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…
A genus one labeled circle tree is a tree with its vertices on a circle, such that together they can be embedded in a surface of genus one, but not of genus zero. We define an e-reduction process whereby a special type of subtree, called an…
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…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We…
Many real complex systems cannot be represented by a single network, but due to multiple sub-systems and types of interactions, must be represented as a multiplex network. This is a set of nodes which exist in several layers, with each…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…