Related papers: Rank conditions on phylogenetic networks
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
Many complex systems have natural representations as multi-layer networks. While these formulations retain more information than standard single-layer network models, there is not yet a fully developed theory for computing network metrics…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation-theoretic…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
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…
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not accurately reflect the true underlying ancestral history of…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
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…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these…
This paper introduces how human languages can be studied in light of recent development of network theories. There are two directions of exploration. One is to study networks existing in the language system. Various lexical networks can be…
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,…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…