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Phylogenetic Networks
Concepts, Algorithms and Applications

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  • 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.

    • The first book to be published on phylogenetic networks
    • Describes the most important algorithms and provides examples of the applications
    • All datasets and examples discussed in the book are available from the book's companion website at www.phylogenetic-networks.org
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    Reviews & endorsements

    "Networks - rather than just trees - are fast becoming the essential tool for making sense of the complexities of evolution, and conflicting signal in genomic data. Phylogenetic Networks provides a long-overdue exposition of network-based methods, their possible uses, and details on practical software. A detailed and unified treatment of the many different types of networks is complemented by a crisp synopsis of the underlying theory. Numerous example and illustrations make the text easy to follow. This book will further transform the way biologists use genomic data to study evolution. The Tübingen group has led the development of phylogenetic network algorithms, and this book delivers a clear exposition for biologists bewildered by a plethora of recent methods, as well as for bioinformaticians aiming to develop the field further. It is essential reading for any scientist or student seeking to understand how genomic data can be used to represent and study the intricate ‘web of life’."
    Mike Steel, University of Canterbury

    "This textbook, by one of the leaders of the field (Daniel Huson) and his co-authors, provides a mathematically rigorous introduction to one of the most exciting and beautiful research areas in computational biology: phylogenetic networks. The text is clear and provides all the necessary biology background; it should be accessible to graduate students (or upper-division undergraduates) in mathematics, computer science, or statistics."
    Tandy Warnow, The University of Texas

    "This wonderfully accessible book is by far the most thorough and up to date treatment of phylgenetic networks about. Many evolutionary processes in nature do not conform to the simple model of phylogenetic trees; examples are hybridizations, symbioses, and lateral gene transfer. The more we probe nature with genomics, the more significant and numerous these examples become, so there is a real need for using networks in phylogenetics. This volume is a must for researchers working with phylogenetic networks. It is for an advanced college audience. Beautifully organized and clearly written, it really fills a void."
    Bill Martin, University of Duesseldorf

    "...a technical monograph that will be of great interest to those working in this field..."
    Paul Cull, Computing Reviews

    "What has been lacking until now is a full in-depth treatment of phylogenetic networks as they are currently used in the evolutionary literature. The new book by Huson and coworkers nicely fills this niche. The book is a tour de force of explication, making clear, in some cases for the first time, how phylogenetic networks of various sorts are actually formulated, calculated and interpreted. We have needed a comprehensive review of phylogenetic networks like this for some time now, and the authors are to be congratulated for creating a review that is clearly written and attractively presented."
    James Whitfield, University of Illinois at Urbana for Systematic Biology

    "This book is a brave and ambitious attempt to describe the field of phylogenetic networks anno 2010 from a motivated algorithmic perspective. It will deservedly become essential reading for both mathematically inclined researchers already working in the field and those looking for an easy way to enter the field. Part reference text, part introductory text, the book brings into sharp relief what we do - and do not - know about phylogenetic networks and as such will become an important milestone in the development of the field."
    Steven Kalk, Maastricht University for Systematic Biology

    "This is an excellent book for readers who know the topic well and also for those who have some knowledge of the area."
    Idalia Flores, Computing Reviews

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    Product details

    • Date Published: November 2010
    • format: Adobe eBook Reader
    • isbn: 9780511922428
    • contains: 189 b/w illus. 80 exercises
    • availability: Adobe Reader ebooks available from eBooks.com
  • Table of Contents

    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.

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    These resources are provided free of charge by Cambridge University Press with permission of the author of the corresponding work, but are subject to copyright. You are permitted to view, print and download these resources for your own personal use only, provided any copyright lines on the resources are not removed or altered in any way. Any other use, including but not limited to distribution of the resources in modified form, or via electronic or other media, is strictly prohibited unless you have permission from the author of the corresponding work and provided you give appropriate acknowledgement of the source.

    If you are having problems accessing these resources please email cflack@cambridge.org

  • Authors

    Daniel H. Huson, Eberhard-Karls-Universität Tübingen, Germany

    Regula Rupp, Eberhard-Karls-Universität Tübingen, Germany

    Celine Scornavacca, Centre National de la Recherche Scientifique (CNRS), Paris

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