Related papers: Phylogenetic Networks
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously…
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…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
We provide precise asymptotic estimates for the number of general phylogenetic networks by using analytic combinatorial methods. Recently, this approach is studied by Fuchs, Gittenberger, and the author himself (Australasian Journal of…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
We describe Galois connections which arise between two kinds of combinatorial structures, both of which generalize trees with labelled leaves, and then apply those connections to a family of polytopes. The graphs we study can be imbued with…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
This study proposes an effective method to predict technology development from an evolutionary perspective. Product evolution is the result of technological evolution and market selection. A phylogenetic network is the main method to study…
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…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…