Techniques in Molecular Systematics and Evolution

1. Front Matter

   Pages I-IX

   PDF

2. Analytical Methods

   1. Front Matter

      Pages 1-3

      PDF

   2. Phylogenetic Analysis: The Basic Method

      • John W. Wenzel

      Pages 4-30

   3. Parsimony Analysis

      • Mark E. Siddall

      Pages 31-54

   4. Optimization Alignment:Down,Up,Error,and Improvements

      • Ward C. Wheeler

      Pages 55-69

   5. Techniques for Analyzing Large Data Sets

      • Pablo A. Goloboff

      Pages 70-79

   6. Measures of Support

      • Mark E. Siddall

      Pages 80-101

   7. Partitioning of Multiple Data, Sets Phylogenetic Analysis

      • Patrick M. O’Grady, James Remsen, John E. Gatesy

      Pages 102-119

   8. Complex Model Organism Genome Databases

      • Charles G. Wray

      Pages 120-131

   9. Comparative Phylogenomics: A Strategy for High-throughput Large-scale Sub-genomic Sequencing Projects for Phylogenetic Analysis

      • Aloysius J. Phillips

      Pages 132-145

   10. Compartive Methods

       • Richard H. Baker

       Pages 146-161

   11. Analyzing Data at the Population Level

       • Phaedra Doukakis, Kenneth D. Birnbaum, Howard C. Rosenbaum

       Pages 162-172

3. Laboratory Methods

   1. Front Matter

      Pages 173-175

      PDF

   2. Obtaining, Storing and Archiving Specimens and Tissue Samples for Use in Molecular Studies

      • Lorenzo Prendini, Robert Hanner, Rob DeSalle

      Pages 176-248

   3. DNA Isolation Procedures

      • Michele K. Nishiguchi, Phaedra Doukakis, Mary Egan, David Kizirian, Aloysius Phillips, Lorenzo Prendini et al.

      Pages 249-287

   4. Late Pleistocene DNA Extraction and Analysis

      • Alex D. Greenwood

      Pages 288-301

   5. PCR Methods and Approaches

      • James Bonacum, Julian Stark, Elizabeth Bonwich

      Pages 302-327

   6. High-Throughput DNA Sequencing for Systematics

      • Michael F. Whiting

      Pages 328-350

   7. A Practical Guide for Microsatellite Analysis

      • Kenneth D. Birnbaum, Howard C. Rosenbaum

      Pages 351-364

   8. 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, David K. Jacobs

      Pages 365-394

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

• biology
• development
• ecology
• evolution
• evolutionary biology
• genes
• genomics
• invertebrates
• molecular biology
• population
• systematics
• Tempo
• tissue
• vertebrates

• Department of Entomology, American Museum of Natural History, New York, USA

  Rob DeSalle, Gonzalo Giribet, Ward Wheeler

Policies and ethics