As the availability of whole genome sequences has increased over the past decade, the data has provided unprecedented insight into evolutionary relationships. Recent sequencing of complete genomes has led to an explosion of phylogenomics studies addressing evolutionary problems by considering entire genomes as compared individual genes. Analyzing rare genetic changes in whole genomes has the po...

Abstract. A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree in which multiple parallel edges signify divergence. A geometric space of such networks is introduced, forming a natural extension of the work by ...

Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion of level was recently introduced as a parameter on realistic kinds of phylogenetic networks to express their complexity and tree-likeness. We study the structure of level-k networks, and how they c...

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from see...

The gene composition of present-day genomes has been shaped by a complicated evolutionary history, resulting in diverse distributions of genes across genomes. The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile. It has been shown that proteins whose encoding genes have highly similar profiles tend to be functionally related: As these genes were ...

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 collection of trees, each having leaf-set some subset of $X$. In the 1980's characterizations, certain inference rules were given for when a collection of 4-l...

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For the purpose of validating evolutionary models, biologists check whether or not a phylogenetic tree is contained in a phylogenetic network on the same taxa. ...

* Correspondence: [email protected]; [email protected] † Contributed equally Physiologie de la Reproduction et des Comportements, UMR 6175 INRACNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France Full list of author information is available at the end of the article Figure 1 Phylogenetic analysis of the GPR50/MT1/MT2/Mel1c genes. (A) Overall phylogenetic tre...

A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications in predicting a species tree from a set of gene trees. This paper focuses on two of the most well-known and widely used consensus tree methods: the greedy co...