Book on Phylogenetic Networks

This is the official website (www.phylogenetic-networks.org) for our book entitled "Phylogenetic Networks" by Daniel H. Huson, Regula Rupp and Celine Scornavacca, to be published by Cambridge University Press in 2011 (available November 2010).

Although many biologists believe that reticulate events such as hybridization, horizontal gene transfer, recombination and reassortment play an important role in evolution, most published studies use trees to represent the evolutionary history for the set of species studied. One reason for this is the lack of robust and accepted methods for inferring non-tree histories or phylogenetic networks. A lot of work has been done in recent years to address this problem.  Our work in this area was originally focused on developing methods for inferring unrooted phylogenetic networks and our computer program, SplitsTree, is currently the most widely-used software for the construction of phylogenetic networks. More recently, we have focused on developing methods for rooted phylogenetic networks, which we make available via our popular Dendroscope tree- and network drawing program.

Phylogenetic networks were one of the main topics of the four month research programme on Phylogenetics held at the Newton Institute of Cambridge University in 2007. There we formed the impression that the field of phylogenetic networks had advanced to a point where there was enough material to warrant a book that gives an introduction to the field and attempts to present the different questions and approaches in a unified manner. Our goal was to write a book that covers the field in a style that is accessible to bioinformatics, biologists that are interested in methods and algorithms and computer scientists that are interested in evolution. This book is the ideal companion to our SplitsTree4 and Dendroscope2 programs.

Table of contents:

Contents
Preface
Part I Introduction
1 Basics
1.1 Overview
1.2 Undirected and directed graphs
1.3 Trees
1.4 Rooted DAGs
1.5 Traversals of trees and DAGs
1.6 Taxa, clusters, clades and splits
2 Sequence Alignment
2.1 Overview
2.2 Pairwise sequence alignment
2.3 Multiple sequence alignment
3 Phylogenetic Trees
3.1 Overview
3.2 Phylogenetic trees
3.3 The number of phylogenetic trees
3.4 Models of DNA evolution
3.5 The phylogenetic tree reconstruction problem
3.6 Sequence-based methods
3.7 Maximum parsimony
3.8 Branch-swapping methods
3.9 Maximum likelihood estimation
3.10 Bootstrap analysis
3.11 Bayesian methods
3.12 Distance-based methods
3.13 UPGMA
3.14 Neighbor-joining
3.15 Balanced Minimum Evolution
3.16 Comparing trees
3.17 Consensus trees
3.18 The Newick format
4 Introduction to Phylogenetic Networks
4.1 Overview
4.2 What is a phylogenetic network?
4.3 Unrooted phylogenetic networks
4.4 Rooted phylogenetic networks
4.5 The extended Newick format
4.6 Which types of networks are currently used in practice?
Part II Theory
5 Splits and Unrooted Phylogenetic Networks
5.1 Overview
5.2 Splits
5.3 Compatibility and incompatibility
5.4 Splits and clusters
5.5 Split networks
5.6 The canonical split network
5.7 Circular splits and planar split networks
5.8 Weak compatibility
5.9 The split decomposition
5.10 Representing trees in a split network
5.11 Comparing split networks
5.12 T-Theory
6 Clusters and Rooted Phylogenetic Networks
6.1 Overview
6.2 Clusters, compatibility and incompatibility
6.3 Hasse diagrams
6.4 Cluster networks
6.5 Rooted phylogenetic networks
6.6 The lowest stable ancestor
6.7 Representing trees in rooted networks
6.8 Hardwired and softwired clusters
6.9 Minimum rooted phylogenetic networks
6.10 Decomposability
6.11 Topological constraints on rooted networks 148
6.12 Cluster containment in rooted networks
6.13 Tree containment
6.14 Comparing rooted networks
Part III Algorithms and Applications
7 Phylogenetic Networks from Splits
7.1 The convex hull algorithm
7.2 The circular network algorithm
8 Phylogenetic Networks from Clusters
8.1 Cluster networks
8.2 Divide-and-conquer using decomposition
8.3 Galled trees
8.4 Galled networks
8.5 Level-k networks from clusters
9 Phylogenetic Networks from Sequences
9.1 Condensed alignments
9.2 Binary sequences and splits
9.3 Parsimony splits
9.4 Median networks
9.5 Quasi-median networks
9.6 Median-joining
9.7 Pruned quasi-median network
9.8 Recombination networks
9.9 Galled trees
10 Phylogenetic Networks from Distances
10.1 Distances and splits
10.2 Minimum spanning network
10.3 Split decomposition
10.4 Neighbor-net
10.5 T-rex
11 Phylogenetic Networks from Trees
11.1 Consensus split networks
11.2 Consensus super split networks for unrooted trees
11.3 Distortion-filtered super split networks for unrooted trees
11.4 Consensus cluster networks for rooted trees
11.5 Minimum hybridization networks
11.6 Minimum hybridization networks and galled trees
11.7 Networks from multi-labeled trees
11.8 DLT reconciliation of gene- and species trees
12 Phylogenetic Networks from Triples or Quartets
12.1 Trees from rooted triples 272
12.2 Level-k networks from rooted triples
12.3 The quartet-net method
13 Drawing Phylogenetic Networks
13.1 Overview
13.2 Cladograms for rooted phylogenetic trees
13.3 Cladograms for rooted phylogenetic networks
13.4 Phylograms for rooted phylogenetic trees
13.5 Phylograms for rooted phylogenetic networks
13.6 Drawing rooted phylogenetic networks with transfer edges
13.7 Radial diagrams for unrooted trees
13.8 Radial diagrams for split networks
14 Software
14.1 SplitsTree
14.2 Network
14.3 TCS
14.4 Dendroscope
14.5 Other programs
Glossary
Bibliography
Index

 

Approx. 360 pages, 190 figures, 80 exercises

Datasets, links and errata will be made available on this website.