Related papers: Distinguishing Phylogenetic Networks
Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…
Semi-directed networks provide a graphical structure for describing the evolutionary history of organisms in the presence of hybridization. We introduce two algorithms for reconstructing semi-directed level-1 phylogenetic networks from…
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 networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is…
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…
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…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
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.…
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…
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…
For decades, complex networks, such as social networks, biological networks, chemical networks, technological networks, have been used to study the evolution and dynamics of different kinds of complex systems. These complex systems can be…
Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks as they contain both directed as well as undirected edges. While…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…