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