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The Phylogenetic Handbook

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  • 57 b/w illus. 18 tables
  • Page extent: 750 pages
  • Size: 247 x 174 mm
  • Weight: 1.45 kg

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 (ISBN-13: 9780521730716)

The Phylogenetic Handbook
Cambridge University Press
9780521877107 - The Phylogenetic Handbook - A Practical Approach to Phylogenetic Analysis and Hypothesis Testing - Edited by Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme
Frontmatter/Prelims

The Phylogenetic Handbook

The Phylogenetic Handbook provides a comprehensive introduction to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes seven new chapters, covering topics such as Bayesian inference, tree topology testing, and the impact of recombination on phylogenies. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including Blast, FastA, Clustal, T-coffee, Muscle, Dambe, Tree-Puzzle, Phylip, Mega4, Paup∗, Iqpnni, Consel, ModelTest, ProtTest, Paml, HyPhy, MrBayes, Beast, Lamarc, SplitsTree, and Rdp3. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.

PHILIPPE LEMEY is a FWO postdoctoral researcher at the Rega Institute, Katholieke Universiteit Leuven, Belgium, where he completed his Ph.D. in Medical Sciences. He has been an EMBO Fellow and a Marie-Curie Fellow in the Evolutionary Biology Group at the Department of Zoology, University of Oxford. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches.

MARCO SALEMI is Assistant Professor at the Department of Pathology, Immunology and Laboratory Medicine of the University of Florida School of Medicine, Gainesville, USA. His research interests include molecular epidemiology, intra-host virus evolution, and the application of phylogenetic and population genetic methods to the study of human and simian pathogenic viruses.

ANNE-MIEKE VANDAMME is a Full Professor in the Medical Faculty at the Katholieke Universiteit, Belgium, working in the field of clinical and epidemiological virology. Her laboratory investigates treatment responses in HIV-infected patients and is respected for its scientific and clinical contributions to virus–drug resistance. Her laboratory also studies the evolution and molecular epidemiology of human viruses such as HIV and HTLV.


The Phylogenetic Handbook

A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

Second Edition

Edited by

Philippe Lemey

Katholieke Universiteit Leuven, Belgium

Marco Salemi

University of Florida, Gainesville, USA

Anne-Mieke Vandamme

Katholieke Universiteit Leuven, Belgium


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Published in the United States of America by Cambridge University Press, New York

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Information on this title: www.cambridge.org/9780521877107

© Cambridge University Press 2009

This publication is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press.

First published 2009

Printed in the United Kingdom at the University Press, Cambridge

A catalog record for this publication is available from the British Library

ISBN 978-0-521-87710-7 hardback
ISBN 978-0-521-73071-6 paperback

Cambridge University Press has no responsibility for the persistence or accuracy of URLs for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate.


Contents

List of contributors
xix
Foreword
xxiii
Preface
xxv
Section I:Introduction
1
1         Basic concepts of molecular evolution
Anne-Mieke Vandamme
3
1.1       Genetic information
3
1.2       Population dynamics
9
1.3       Evolution and speciation
14
1.4       Data used for molecular phylogenetics
16
1.5       What is a phylogenetic tree?
19
1.6       Methods for inferring phylogenetic trees
23
1.7       Is evolution always tree-like?
28
Section II:Data preparation
31
2         Sequence databases and database searching
33
3         Multiple sequence alignment
68
Section III:Phylogenetic inference
109
4         Genetic distances and nucleotide substitution models
111
5         Phylogenetic inference based on distance methods
142
6         Phylogenetic inference using maximum likelihood methods
181
7         Bayesian phylogenetic analysis using MRBAYES
210
8         Phylogeny inference based on parsimony and other methods using Paup*
267
9         Phylogenetic analysis using protein sequences
313
Section IV:Testing models and trees
343
10        Selecting models of evolution
345
11        Molecular clock analysis
362
12        Testing tree topologies
381
Section V:Molecular adaptation
405
13        Natural selection and adaptation of molecular sequences
Oliver G. Pybus and Beth Shapiro
407
13.1      Basic concepts
407
13.2      The molecular footprint of selection
412
13.2.1    Summary statistic methods
413
13.2.2    dN/dS methods
415
13.2.3    Codon volatility
417
13.3      Conclusion
418
14        Estimating selection pressures on alignments of coding sequences
419
Section VI:Recombination
491
15        Introduction to recombination detection
Philippe Lemey and David Posada
492
15.1      Introduction
492
15.2      Mechanisms of recombination
493
15.3      Linkage disequilibrium, substitution patterns, and evolutionary inference
495
15.4      Evolutionary implications of recombination
496
15.5      Impact on phylogenetic analyses
498
15.6      Recombination analysis as a multifaceted discipline
506
15.6.1    Detecting recombination
506
15.6.2    Recombinant identification and breakpoint detection
507
15.6.3    Recombination rate
507
15.7      Overview of recombination detection tools
509
15.8      Performance of recombination detection tools
517
16        Detecting and characterizing individual recombination events
519
Section VII:Population genetics
550
17        The coalescent: population genetic inference using genealogies
Allen Rodrigo
551
17.1      Introduction
551
17.2      The Kingman coalescent
552
17.3      Effective population size
554
17.4      The mutation clock
555
17.5      Demographic history and the coalescent
556
17.6      Coalescent-based inference
558
17.7      The serial coalescent
559
17.8      Advanced topics
561
18        Bayesian evolutionary analysis by sampling trees
564
19         Lamarc: Estimating population genetic parameters from molecular data
592
Section VIII:Additional topics
613
20        Assessing substitution saturation with Dambe
615
21        Split networks. A tool for exploring complex evolutionary relationships in molecular data
631
Glossary
654
References
672
Index
709



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