Related papers: On Tree Based Phylogenetic Networks
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Bayesian networks can be used to extract explanations about the observed state of a subset of variables. In this paper, we explicate the desiderata of an explanation and confront them with the concept of explanation proposed by existing…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
We present a link-by-link rule-based method for constructing all members of the ensemble of spanning trees for any recursively generated, finitely articulated graph, such as the DGM net. The recursions allow for many large-scale properties…
Interest in the inference of evolutionary networks relating species or populations has grown with the increasing recognition of the importance of hybridization, gene flow and admixture, and the availability of large-scale genomic data.…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
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…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…