A Framework for Representing Reticulate Evolution

A Framework for Representing Reticulate Evolution

Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this paper, we develop a framework for the analysis of these graphs which we call hybrid phylogenies. We are particularly interested in the problem whereby one is given a set of phylogenetic trees and wishes to deter...

Phylogenetic analysis under reticulate evolution.

The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of...

SPECTRE: a suite of phylogenetic tools for reticulate evolution

Summary Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend th...

Network (Reticulate) Evolution: Biology, Models, and Algorithms

A Framework for Representing Tutorial Discourse

We set forth general techniques for managing discourse in an intelligent tutor. These techniques are being implemented in a structure that dynamically reasons about the discourse, a student's response, and the tutor's move. The structure is flexible, domain-independent, and designed to be rebuilt-decision points and machine actions are modifiable through a visual editor. We discuss this formal ...