Techniques in Molecular Systematics and Evolution
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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
List of ContributorsGeneral IntroductionIAnalytical MethodsIntroduction to Part I31Phylogenetic Analysis: The Basic Method42Parsimony Analysis313Optimization Alignment: Down, Up, Error, and Improvements554Techniques for Analyzing Large Data Sets705Measures of Support806Partitioning of Multiple Data Sets in Phylogenetic Analysis1027Complex Model Organism Genome Databases1208Comparative Phylogenomics: A Strategy for High-throughput Large-scale Sub-genomic Sequencing Projects for Phylogenetic Analysis1329Comparative Methods14610Analyzing Data at the Population Level162IILaboratory MethodsIntroduction to Part II17511Obtaining, Storing and Archiving Specimens and Tissue Samples for Use in Molecular Studies17612DNA Isolation Procedures24913Late Pleistocene DNA Extraction and Analysis28814PCR Methods and Approaches30215High-Throughput DNA Sequencing for Systematics32816A Practical Guide for Microsatellite Analysis35117Determining the Spatial and Temporal Patterns of Developmental Gene Expression in Vertebrates and Invertebrates Using in situ Hybridization Techniques365Guide to Solutions395Guide to protocols397Troubleshooting Guide399Index401
