Related papers: All that Glisters is not Galled

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…

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…

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…

A normal (phylogenetic) network with $k$ reticulations displays $2^k$ phylogenetic trees. In this paper, we establish an analogous result for tree-child (phylogenetic) networks with no underlying $3$-cycles. In particular, we show that a…

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…

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…

We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model. In particular, every cycle of size at least 4 and every…

Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…

Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…

Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…

Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…

Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…

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…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

The Sackin index is an important measure for the balance of phylogenetic trees. We investigate two extensions of the Sackin index to the class of galled trees and two of its subclasses (simplex galled trees and normal galled trees) where we…

Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…