Related papers: All that Glisters is not Galled
Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network…
We consider so-called simple families of labelled trees, which contain, e.g., ordered, unordered, binary and cyclic labelled trees as special instances, and study the global and local behaviour of the number of inversions. In particular we…
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…
We present a new definition of non-ambiguous trees (NATs) as labelled binary trees. We thus get a differential equation whose solution can be described combinatorially. This yields a new formula for the number of NATs. We also obtain…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
We give a precise description of combed trees in terms of Kelly-Mac Lane graphs. We show that any combed tree is uniquely expressed as an allowable Kelly-Mac Lane graph of a certain shape. Conversely, we show that any such Kelly-Mac Lane…
The mathematical analysis of random phylogenetic networks via analytic and algorithmic methods has received increasing attention in the past years. In the present work we introduce branching process methods to their study. This approach…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
A fragmented landscape reduces the impact of interspecies connectivity, leading to higher diversity levels than otherwise possible in a connected landscape. Reconnecting a previously fragmented landscape initiates an extinction event,…
Network fluids are structured fluids consisting of chains and branches. They are characterized by unusual physical properties, such as, exotic bulk phase diagrams, interfacial roughening and wetting transitions, and equilibrium and…
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…
The generation of trees with a specified tree edit distance has significant applications across various fields, including computational biology, structured data analysis, and image processing. Recently, generative networks have been…
Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…
Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by…
A staged tree model is a discrete statistical model encoding relationships between events. These models are realised by directed trees with coloured vertices. In algebro-geometric terms, the model consists of points inside a toric variety.…
Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function.…
In evolutionary biology, phylogenetic networks are now widely used to represent the historical relationships between species and population, when this history includes reticulation events such as hybridization, gene flow and admixture…
We study varieties that contain unranked tree languages over all alphabets. Trees are labeled with symbols from two alphabets, an unranked operator alphabet and an alphabet used for leaves only. Syntactic algebras of unranked tree languages…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…