Related papers: On Cherry-picking and Network Containment
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Among all characteristics exhibited by natural and man-made networks the small-world phenomenon is surely the most relevant and popular. But despite its significance, a reliable and comparable quantification of the question `how small is a…
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…
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 provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
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…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…
A challenging problem in complex networks is the network reconstruction problem from data. This work deals with a class of networks denoted as conserved networks, in which a flow associated with every edge and the flows are conserved at all…