Beyond Galled Trees - Decomposition and Computation of Galled Networks

摘要

Reticulate networks are a type of phylogenetic network that are used to represent reticulate evolution involving hybridization, horizontal gene transfer or recombination. The simplest form of these networks are galled trees, in which all reticulations are independent of each other. This paper introduces a more general class of reticulate networks, that we call galled networks, in which reticulations are not necessarily independent, but may overlap in a tree-like manner. We prove a Decomposition Theorem for these networks that has important consequences for their computation, and present a fixed-parameter-tractable algorithm for computing such networks from trees or binary sequences. We provide a robust implementation of the algorithm and illustrate its use on two biological datasets, one based on a set of three gene-trees and the other based on a set of binary characters obtained from a restriction site map.