The Biogeography of Deep Time Phylogenetic Reticulation

Quantifying Reticulation in Phylogenetic Complexes Using Homology

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show c...

Locating a Phylogenetic Tree in a Reticulation-Visible Network in Quadratic Time

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. ...

T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks

UNLABELLED T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. The application includes a number of tree fitting methods like NJ, UNJ or ADDTREE which have been very popular in phylogenetic analysis. At the same time, the software comprises several new methods of phylogenetic analysis such as: tree re...

Phylogenetic Systematics and Biogeography: Using Cladograms in Historical Biogeography Methods

Genetic and phylogenetic consequences of island biogeography.

Island biogeography theory predicts that the number of species on an island should increase with island size and decrease with island distance to the mainland. These predictions are generally well supported in comparative and experimental studies. These ecological, equilibrium predictions arise as a result of colonization and extinction processes. Because colonization and extinction are also im...