Techniques in Molecular Systematics and Evolution

by Desalle, Rob; Giribet, Gonzalo; Wheeler, Ward

• ISBN13: 9783764362577
• ISBN10: 376436257X
• Format: Paperback
• Copyright: 2002-08-01
• Publisher: Birkhauser

Summary

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 growing accordingly. This manual presents some of the most important techniques for data acquisition developed over the last years. The choice and justification of data analysis techniques is also an important and critical aspect of modern phylogenetic and evolutionary analysis and so a considerable part of this volume addresses this important subject. The book is mainly written for students and researchers from evolutionary biology in search for methods to acquire data, but also from molecular biology who might be looking for information on how data are analyzed in an evolutionary context. To aid the user, information on web-located sites is included wherever possible. Approaches that will push the amount of information which systematics will gather in the

Table of Contents

List of Contributors	vii
General Introduction	ix
I Analytical Methods
Introduction to Part I	3	(1)
Rob DeSalle
Gonzalo Giribet
Ward C. Wheeler
Phylogenetic Analysis: The Basic Method	4	(27)
John W. Wenzel
Parsimony Analysis	31	(24)
Mark E. Siddall
Optimization Alignment: Down, Up, Error, and Improvements	55	(15)
Ward C. Wheeler
Techniques for Analyzing Large Data Sets	70	(10)
Pablo A. Goloboff
Measures of Support	80	(22)
Mark E. Siddall
Partitioning of Multiple Data Sets in Phylogenetic Analysis	102	(18)
Patrick M. O'Grady
James Remsen
John E. Gatesy
Complex Model Organism Genome Databases	120	(12)
Charles G. Wray
Comparative Phylogenomics: A Strategy for High-throughput Large-scale Sub-genomic Sequencing Projects for Phylogenetic Analysis	132	(14)
Aloysius J. Phillips
Comparative Methods	146	(16)
Richard H. Baker
Analyzing Data at the Population Level	162	(14)
Phaedra Doukakis
Kenneth D. Birnbaum
Howard C. Rosenbaum
II Laboratory Methods
Introduction to Part II	175	(1)
Rob DeSalle
Gonzalo Giribet
Ward C. Wheeler
Obtaining, Storing and Archiving Specimens and Tissue Samples for Use in Molecular Studies	176	(73)
Lorenzo Prendini
Robert Hanner
Rob DeSalle
DNA Isolation Procedures	249	(39)
Michele K. Nishiguchi
Phaedra Doukakis
Mary Egan
David Kizirian
Aloysius Phillips
Lorenzo Prendini
Howard C. Rosenbaum
Elizabeth Torres
Yael Wyner
Rob DeSalle
Gonzalo Giribet
Late Pleistocene DNA Extraction and Analysis	288	(14)
Alex D. Greenwood
PCR Methods and Approaches	302	(26)
James Bonacum
Julian Stark
Elizabeth Bonwich
High-Throughput DNA Sequencing for Systematics	328	(23)
Michael F. Whiting
A Practical Guide for Microsatellite Analysis	351	(14)
Kenneth D. Birnbaum
Howard C. Rosenbaum
Determining the Spatial and Temporal Patterns of Developmental Gene Expression in Vertebrates and Invertebrates Using in situ Hybridization Techniques	365	(30)
Ruth D. Gates
Thorsten Hadrys
Cesar Arenas-Mena
David K. Jacobs
Guide to Solutions	395	(2)
Guide to protocols	397	(2)
Troubleshooting Guide	399	(2)
Index	401