Techniques in Molecular Systematics and Evolution
The amount of information that can be obtained by using molecular techniques in evolution, systematics and ecology has increased exponentially over the last ten years. The need for more rapid and efficient methods of data acquisition and analysis is growi
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Techniques in Molecular Systematics and Evolution Edited by Rob DeSalle Gonzalo Giribet Ward Wheeler
Springer Basel AG
Editors: Dr. Rob DeSalle Dr. Gonzalo Giribet Dr. Ward C. Wbeeler American Museum of Natural History Department of Entomology Central Park West at 79 th Street New York, NY 10024-5192
USA
Library of Congress Cataloging-in-Publication Data Techniques in molecular systematics and evolution / edited by Rob DeSalle, Gonzalo Giribet, Ward Wheeler. p. ; cm. - (Methods and tools in biosciences and medicine)
ISBN 978-3-7643-6257-7 ISBN 978-3-0348-8125-8 (eBook) DOI 10.1007/978-3-0348-8125-8 1. Molecular evolution-Methodology. 1. DSalle, Rob. II. Giribet, Gonzalo. III. Wbeeler, Ward. IV. Series. [DNLM: 1. Evolution, Molecular. 2. Data Interpretation, Statistic al. 3. Genomics-methods. 4. Phylogeny. QH 367.5 T255 2001] QH506.T435 2001 572.8'38-d21 2001035041 Deutsche Bibliothek Cataloging-in-Publication Data Techniques in molecular systematics and evolution / ed. by Rob DeSalie .... - Basel ; Boston; Berlin: Birkhăuser, 2001 (Methods and tools in biosciences and medicine)
ISBN 978-3-7643-6257-7 The publisher and editor can give no guarantee for the information on drug dosage and administration contained in this publication. The respective user must check its accuracy by consulting other sources ofreference in each individual case. The use ofregistered names, trademarks etc. in this publication, even ifnot identified as such, does not imply that they are exempt from the relevant protective laws and regulations or free for general use. This work is subject to copyright. AlI rights are reserved, whether the whole or part of the material is concerned, specifically the rights oftranslation, reprinting, re-use ofillustrations, recitation, broadcasting, reproduction on microfilms or in other ways, and storage in data banks. For any kind of use permission of the copyright owner must be obtained. © 2002 Springer Basel AG Originally published by Birkhăuser Verlag, Basel in 2002 Softcover reprint of the hardcover Ist edition 2002 Printed on acid-free paper produced from chlorine-free pulp. TCF
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ISBN 978-3-7643-6257-7 987654321
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Contents List of Contributors General Introduction
_ _
VII IX
I Analytical Methods Introduction to Part I Rob DeSalle, Gonzalo Giribet and Ward C. Wheeler
3
1 Phylogenetic Analysis: The Basic Method John W. Wenzel
4
2 Parsimony Analysis Mark E. Siddall
31
3 Optimization Alignment: Down, Up, Error, and Improvements_ Ward C. Wheeler
55
4 Techniques for Analyzing Large Data Sets Pablo A. GolobofT
70
5 Measures of Support Mark E. Siddall
80
6 Partitioning of Multiple Data Sets in Phylogenetic Analysis Patrick M. O'Grady, James Remsen and John E. Gatesy
102
7 Complex Model Organism Genome Databases Charles G. Wray
120
8 Comparative Phylogenomics: A Strategy for High-throughput Large-scale Sub-genomic Sequencing Projects for Phylogenetic Analysis Aloysius J. Phillips 9 Comparative Methods Richard H. Baker
132 146
10 Analyzing Data at the
