Molecular systematics

목차 (Table of Contents)

• CONTENTS
• 1. Molecular Systematics : Context and Controversies = 1
• Part 1. Sampling
• 2. Project Design = 17
• 3. Collection and Storage of Tissues = 29
• Part 2. Molecular Techniques
• 4. Proteins : Isozyme Electrophoresis = 51
• 5. Chromosomes : Molecular Cytogenetics = 121
• 6. Nucleic Acids Ⅰ : DNA－DNA Hybridization = 169
• 7. Nucleic Acids Ⅱ : The Polymerase Chain Reaction = 205
• 8. Nucleic Acids Ⅲ : Analysis of Fragments and Restriction Sites = 249
• 9. Nucleic Acids Ⅳ : Sequencing and Cloning = 321
• Part 3. Analysis
• 10. Intraspecific Differentiation = 385
• 11. Phylogenetic Infeence = 407
• 12. Applications of Molecular Systematics : The State of the Field and a Look to the Future = 515
• Chapter 1 Molecular Systematics : Context and Controversies / Craig Moritz ; David M. Hillis = 1
• THE EVOLUTION OF MOLECULAR SYSTEMATICS = 1
• The Link Between Molecular Evolution and Systematics = 3
• The Link Between Molecular Population Genetics and Phylogenetics = 4
• CONTROVERSIES IN MOLECULAR SYSTEMATICS = 5
• Molecules versus Morphology = 5
• Types of Characters and Methods of Analysis = 6
• Homology and Similarity in Molecular Systematics = 7
• Gene Trees and Organismal Phylogeny = 9
• Constancy of Evolutionary Rates = 10
• Neutrality of Molecular Variants = 11
• Data Quality and Presentation = 11
• SCOPE AND USE OF THIS BOOK = 12
• FOR FURTHER STUDY = 12
• Part 1 Sampling
• Chapter 2 Project Design / Peter R. Baverstock ; Craig Moritz = 17
• INTRODUCTION = 17
• STATISTICAL CONSIDERATIONS = 18
• MOLECULAR SYSTEMATICS = 18
• Studies of Population Structure = 19
• Studies of Species Boundaries and Hybridization = 22
• Phylogenetic Relationships = 25
• CONCLUDING REMARKS = 27
• Chapter 3 Collection and Storage of Tissues / Herbert C. Dessauer ; Charles J. Cole ; Mark S. Hafner = 29
• INTRODUCTION = 29
• REGULATIONS GOVERNING ACQUISITION OF SPECIMENS = 30
• REMOVING AND PRESERVING TISSUES IN THE FIELD = 30
• General Procedures = 30
• Procedures Unique to Animal Tissue Collection = 33
• Procedures Unique to Plant Tissue Collection = 35
• Collecting Cell Lines = 35
• TRANSPORT OF TISSUES FROM FIELD TO LABORATORY OR BETWEEN LABORATORIES = 36
• Shipping Regulation = 36
• Sources of Liquid Nitrogen and Dry Ice = 36
• STORAGE OF TISSUES ON RETURN FROM THE FIELD = 37
• STABILITY OF MACROMOLECULES DURING LONG－TERM STORAGE = 37
• DEVELOPMENT AND SUPPORT OF SYNOPTIC TISSUE COLLECTIONS = 39
• Disposition of Tissues for Long－Term Preservation = 40
• Curatorial Problems Unique to Tissue Collections = 40
• EXISTING COLLECTIONS = 41
• Appendix : Synoptic Tissue Collctions = 42
• Part 2 Molecular Techniques
• Chapter 4 Proteins : Isozyme Electrophoresis / Robert W. Murphy ; Jack W. Sites, Jr. ; Donald G. Buth ; Christopher H. Haufler = 51
• INTRODUCTION = 51
• PRINCIPLES AND COMPARISON OF METHODS = 52
• General Principles = 52
• Assumptions = 53
• Comparison of the Primary Methods = 54
• APPLICATIONS AND LIMITATIONS = 56
• Intraspecific Applications = 56
• Interspecific Applications = 58
• Gene Expression and Gene Duplication = 62
• Limitations = 63
• LABORATORY SETUP = 67
• PROJECT PLANNING = 69
• Protocols
• Protocol 1 : Tissue Homogenization = 73
• Protocol 2 : Preparaion of Starch Gels = 79
• Protocol 3 : Gel Loading = 81
• Protocol 4 : Electrophoresis = 82
• Protocol 5 : Gel Slicing = 84
• Protocol 6 : Histochemical Staining = 86
• Protocol 7 : Drying of Agar Overlays = 88
• Protocol 8 : Documentation of Results = 89
• INTERPRETATION AND TROUBLESHOOTING = 89
• ENZYME AND LOCUS NOMENCLATURE = 94
• Appendix 1 : Enzyme Staining Formulas = 96
• Appendix 2 : Buffers and Tracking Dye for Isozyme Electrotrophoresis = 116
• Chapter 5 Chromosomes : Molecular Cytogenetics / Stanley K. Sessions = 121
• PRINCIPLES AND COMPARISON OF METHODS = 121
• General Principles = 121
• Assumptions = 126
• Comparison of the Primary Methods = 127
• APPLICATIONS AND LIMITATIONS = 142
• Applications = 142
• Limitations = 146
• LABORATORY SETUP = 148
• Protocols
• Protocol 1 : Subbed Slides = 149
• Protocol 2 : Mitotic Chromosomes from Gut epithelium = 149
• Protocol 3 : Mitotic Chromosomes from Plant Root Tips = 149
• Protocol 4 : Squash Technique for Mitotic and Meiotic Chromosomes = 150
• Protocol 5 : Yeast Method for Mitotic Chromosomes from Small Vertebrates = 151
• Protocol 6 : Splash Technique for Slide Preparations of Mitotic Chromosomes = 151
• Protocol 7 : Mitotic Chromosomes from Peripheral Blood in Vertebrates = 152
• Protocol 8 : Mitotic Chromosomes from Fibroblast Cultures （Reptiles） = 153
• Protocol 9 : Mitotic Chromosomes from Corneal Epithelium of Vertebrates = 153
• Protocol 10 : Mitotic Chromosomes from Insect Embryos = 154
• Protocol 11 : Polytene Chromosomes from Dipteran Salivary Glands = 155
• Protocol 12 : Lampbrush Chromosomes = 155
• Protocol 13 : C－Banding = 156
• Protocol 14 : Q－Banding = 157
• Protocol 15 : G－banding = 157
• Protocol 16 : Fluorochrome R－Banding with Chromomycin A3 = 157
• Protocol 17 : AgNOR Banding = 157
• Protocol 18 : Differential Replication Banding with BrdU = 158
• Protocol 19 : Modification of BrdU Banding for Salamander Embryos = 158
• Protocol 20 : Labeling Probes for ISH via Nick Translation = 159
• Protocol 21 : Radioisotopic ISH for Reiterated Sequences Using a DNA Probe = 160
• Protocol 22 : Radioisotopic ISH Using an RNA Probe = 161
• Protocol 23 : Radioisotopic Localization of Single－Copy Sequences = 161
• Protocol 24 : Autoradiography for Detection of Radioisotopic ISH = 162
• Protocol 25 : Chromosome Painting Using FISH = 163
• Protocol 26 : FISH with Single－Copy Genomic Probe = 164
• INTERPRETATION AND TROUBLESHOOTING = 165
• Chromosome Bands = 165
• In Situ Hybridization = 165
• Appendix : Stock Solutions = 166
• Chapter 6 Nucleic Acids Ⅰ : DNA－DNA Hybridization / Steven D. Werman ; Mark S. Springer ; Roy J. Britten = 169
• INTRODUCTION = 169
• PRINCIPLES AND COMPARISON OF METHODS = 170
• General Principles = 170
• Summary of the DNA Hybridization Techniques and Data Analysis = 171
• Properties of Hybridization Data = 172
• Factors Affecting DNA Hybridization = 172
• The Criterion and Precision of Reassociation = 173
• Comparison of the Primary Methods = 174
• APPLICATIONS AND LIMITATIONS = 176
• LABORATORY SETUP = 178
• Protocols
• Protocol 1 : DNA Isolation and Purification = 179
• Protocol 2 : Preparing Sheared Drivers From Long Native DNA = 180
• Protocol 3 : Tracer Preparation with 32P or 3H = 181
• Protocol 4 : Tracer Self－Reaction and repeat Removal = 182
• Protocol 5 : Fractionation of Single－Copy Tracer over Hydroxyapatite = 183
• Protocol 6 : Estimation of Tracer Fragment Length = 184
• Protocol 7 : Preparing Tracers by Iodination = 184
• Protocol 8 : DNA Hybridization with Hydroxyapatite and Phophate Buffer = 185
• Protocol 9 : Hydroxyapatite Column Preparation = 186
• Protocol 10 : Phenol Emulsion Reassociation Technique （PERT） = 187
• Protocol 11 : Analysis of Hybrid Thermal Stability Using the S1 Nuclease－TEACL Assay = 188
• INTERPRETATION AND TROUBLESHOOTING = 189
• Calculation of Melting Curves from Raw Counts : An Example = 189
• Problematic Melting Curves = 192
• Characteristics of Distance Estimates Derived from Raw Melting Curve Data = 194
• Hybridization Data in Phylogenetic Reconstruction = 197
• Appendix : Stock Solutions = 201
• Chapter 7 Nucleic Acids Ⅱ : The Polymerase Chain Reaction / Stephen R. Palumbi = 205
• INTRODUCTION = 205
• PRINCIPLES AND COMPARISON OF METHODS = 206
• General Principles = 206
• The Cycle = 207
• Choosing Reaction Conditions = 209
• PCR Components = 210
• The Thermal Cycler = 211
• Primers and Primer Design = 212
• ASSUMPTIONS = 214
• APPLICATIONS AND LIMITATIONS = 215
• Types of Amplifications and Types of Data = 215
• LABORATORY SETUP = 221
• Protocols
• Protocol 1 : DNA isolation for PCR = 222
• Protocol 2 : The Polymerase Chain Reaction = 225
• Protocol 3 : PCR From RNA = 229
• TROUBLESHOOTING = 230
• Avoiding PCR Problems : PCR Hygiene = 230
• Some Common Problems with PCR = 230
• Problems with Single－Strand Amplification = 231
• USEFUL PRIMERS = 232
• Nuclear Ribosomal Gene Primers = 232
• Animal Mitochondrial Gene Primers = 235
• Chloroplast DNA Primers = 239
• Intron Primers = 240
• More Information about PCR = 245
• Appendix : Stock Soltions = 246
• Chapter 8 Nucleic Acids Ⅲ : Analysis of Fragments and Restriction Sites / Thomas E. Dowling ; Craig Moritz ; Jeffrey D. Palmer ; Loren H. Rieseberg = 249
• PRINCIPLES AND COMPARISON OF METHODS = 249
• General Principles = 249
• Assumptions = 255
• Comparison of the Primary Methods = 257
• APPLICATIONS AND LIMITATIONS = 266
• Choice of Sequence = 266
• Population－Level Comparisons = 268
• Species－Level Comparisons = 276
• Higher－Level Systematics = 279
• LABORATORY SETUP = 282
• Protocols
• Protocol 1 : Isolation of Animal mtDNA Using CsCl－PI Gradients = 283
• Protocol 2 : Isolation of cpDNA Using Sucrose Step and CsCl－EB Gradients = 289
• Protocol 3 : Digestion of DNA with Restriction Endonucleases = 290
• Protocol 4 : Agarose and Polyacrylamide Electrophoresis = 291
• Protocol 5 : Staining with Ethidium Bromide = 297
• Protocol 6 : α32P3'End－Labeling of Restriction Fragments = 297
• Protocol 7 : Primer Labeling for Microsatellite Analysis = 298
• Protocol 8 : Transfer Hybridizatioh = 299
• Protocol 9 : Mapping Restriction Sites = 302
• INTERPRETATION AND TROUBLESHOOTING = 308
• RFLP Analysis = 308
• Troubleshooting = 314
• Microsatellites = 317
• Appendix : Stock Solutions = 319
• Chapter 9 Nucleic Acids Ⅳ : Sequencing and Cloning / David M. Hillis ; Barbara K. Mable ; Allan Larson ; Scott K. Davis ; Elizabeth A. Zimmer = 321
• PRINCIPLES AND COMPARISON OF METHODS = 321
• Isolating Target Sequences = 323
• Nucleic Acid Sequencing = 326
• Assumptions = 330
• Comparison of the Primary Techniques = 332
• APPLICATIONS AND LIMITATIONS = 335
• Evolution of Genes = 335
• Intraspecific Diversity = 336
• Interspecific Diversity = 337
• SUMMARY = 339
• LABORATORY SETUP = 339
• Protocols
• Protocol 1 : DNA Isolation from Animals, Protists, and Prokaryotes = 342
• Protocol 2 : DNA Isolation from Plants, Fungi, and Algae = 343
• Protocol 3 : Isolation of DNA from Minute Quantities of Tissue = 344
• Protocol 4 : Isolation of RNA from Animals = 345
• Protocol 5 : Isolation of RNA from Plants = 346
• Protocol 6 : Preparation of Partial Gene Libraries in λ Bacterophage Vectors = 347
• Protocol 7 : Growing Bacteriophage = 347
• Protocol 8 : Screening Bacteriophage Libraries = 348
• Protocol 9 : Miniprep Isolation of λDNA = 349
• Protocol 10 : Subcloning into Plasmids or M13 = 351
• Protocol 11 : Preparation of Frozen Competent Cells for Transformation = 351
• Protocol 12 : Transformation of E. coli with Plasmid DNA = 352
• Protocol 13 : Transformation of M13 Bacteriophage DNA = 352
• Protocol 14 : Isolation of Plasmid DNA = 353
• Protocol 15 : Miniprep Isolation of M13 DNA = 354
• Protocol 16 : Preparing Permanent Frozen Stocks of Plasmid Clones = 354
• Protocol 17 : Isolation of PCR Products for Sequencing = 355
• Protocol 18 : Cloning Methods for PCR Products = 356
• Protocol 19 : Purification of PCR Products for Sequencing = 359
• Protocol 20 : Screening Methods for Detecting Variation in DNA Sequences = 361
• Protocol 21 : Preparing a Sequencing Gel = 362
• Protocol 22 : DNA Sequencing Reactions = 363
• Protocol 23 : RNA Sequencing Reactions = 366
• Protocol 24 : Thermal Cycle Sequencing = 367
• Protocol 25 : Running a Sequencing Gel = 368
• Protocol 26 : Microsatellites = 370
• INTERPRETATION AND TROUBLESHOOTING = 371
• Autoradiograph Interpretation = 371
• Sequence Comparison and Alignment = 374
• Appendix : Stock Solutions = 378
• Part 3 : Analysis
• Chapter 10 Intraspecific Differentiation / Bruce S. Weir = 385
• BIOLOGICAL CONTEXT = 385
• General and Statistical Sampling = 387
• Fixed and Random Models = 388
• STATISTICAL METHODS = 389
• Fixed Populations = 389
• Random Populations = 394
• APPLICATIONS = 401
• Conditional Genotypic Frequencies = 401
• IMPLEMENTATION = 402
• Sampling = 402
• Analysis = 403
• AN EXAMPLE = 403
• CONCLUSION = 405
• Chapter 11 Phylogenetic Inference / David L. Swofford ; Gary J. Olsen ; Peter J. Waddell ; David M. Hillis = 407
• INTRODUCTION = 407
• Algorithms versus Optimality Criteria = 408
• Use of Models and Assumptions in Phylogenetics = 409
• Definitions of Terms = 410
• TYPES OF DATA = 410
• Sequence Data = 412
• Restriction Endonuclease Data = 412
• Isozyme Data = 413
• Gene Order Data = 414
• OPTIMALITY CRITERIA Ⅰ : PARSIMONY METHODS = 415
• Fitch and Wagner Parsimony = 416
• Other Parsimony Variants = 419
• Generalized Parsimony = 422
• Parsimony on Protein Sequences = 424
• Parsimony on Allozyme Data = 425
• OPTIMALITY CRITERIA Ⅱ : METHODS BASED ON MODELS OF EVOLUTIONARY CHANGE = 426
• The Utility of Models = 426
• Maximum Likelihood Methods = 430
• Pairwise Distance Methods = 446
• Model－Based Corrections for Character Data : Hadamard Conjugation = 464
• Lake's Methods of Invariants = 474
• Rooting Revisited = 477
• SEARCHING FOR OPTIMAL TREES = 478
• Exact Algorithms = 478
• Heuristic Approaches = 482
• Algorithmic and Other Methods = 486
• RELIABILITY OF INFERRED TREES = 493
• Systematic versus Random Error = 493
• Systematic Error = 494
• Random Error = 503
• Appendix Programs and Software = 510
• Chapter 12 Applications of Molecular Systematics / David M. Hillis ; Barbara K. Mable ; Craig Moritz = 515
• INTRODUCTION = 515
• CHOOSING A TECHNIQUE FOR A PARTICULAR PROBLEM = 516
• DATA ANALYSIS : ISSUES AND CONTROVERSIES = 521
• Trees versus Networks = 521
• Combined versus Separate Analyses of Multiple Data Sets = 522
• Hypothesis Testing and the Parametric Bootstrap = 523
• Phylogenetic Accuracy = 526
• Predictions of Time from Molecular Data = 531
• APPLICATION OF PHYLOGENIES FOR ANALYZING MACRO－EVOLUTIONARY PATTERNS : COMPARATIVE METHODS = 540
• THE FUTURE OF MOLECULAR SYSTEMATICS = 543
• Acknowledgments = 545
• Measurement Symbols = 548
• Glossary and Abbreviations = 549
• Literature Cited = 560
• Index = 636