The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Daniel H. Huson is Professor of Algorithms in Bioinformatics at Tubingen University. He has authored numerous papers in bioinformatics, biology and mathematics, and is the main author of the widely-used computer programs Dendroscope, MEGAN and SplitsTree. Regula Rupp received her PhD in Mathematics from Bern University in 2006. Between 2007 and 2009 she held a postdoctoral research position at Tubingen University, working with Daniel H. Huson in developing robust methods for computing phylogenetic networks from real biological data. Celine Scornavacca is a postdoctoral researcher working on algorithms for phylogenetic networks with Daniel H. Huson at Tubingen University. She received her PhD in Computer Science from Montpellier University in 2009.
Part I. Introduction: 1. Basics; 2. Sequence alignment; 3. Phylogenetic trees; 4. Phylogenetic networks; Part II. Theory: 5. Clusters and rooted phylogenetic networks; 6. Splits and unrooted phylogenetic networks; Part III. Algorithms and Applications: 7. Phylogenetic networks from clusters; 8. Phylogenetic networks from splits; 9. Phylogenetic networks from sequences; 10. Phylogenetic networks from distances; 11. Phylogenetic networks from trees; 12. Phylogenetic networks from triplets or quartets; 13. Drawing phylogenetic networks; 14. Software; Glossary; Index.