Related papers: Which phylogenetic networks are merely trees with …
Phylogenetic networks provide a framework for representing evolutionary histories involving reticulate events such as hybridization or horizontal gene transfer. A central problem is to infer such networks from local structural information.…
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…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
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 used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
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…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
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}…
Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Various real-life applications, for example, Internet of Things, wireless sensor networks, smart grids, transportation networks, communication networks, social networks, and computer grid systems, are always modeled as network structures.…
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…
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…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…