Related papers: Constructing the Simplest Possible Phylogenetic Ne…
Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…
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…
Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…
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…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
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…
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer.…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
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,…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
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 trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
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…
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 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}…
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…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…