Molecular Tools for Screening Biodiversity: Plants and Animals

Front Matter....Pages i-xxiv
Front Matter....Pages 1-1
Isolation of Animal Cellular Total DNA....Pages 5-9
Plant Total DNA Extraction....Pages 10-14
Chloroplast DNA Extraction Procedure for Species High in Phenolics and Polysaccharides....Pages 15-17
Quantification of DNA....Pages 18-21
Miniprep Procedures for the Isolation of Plant DNA....Pages 22-24
Special DNA Extraction Methods for Some Animal Species....Pages 27-31
Methods for Difficult Plant Species/Tissues....Pages 32-35
DNA Maxipreparations: A Comparison of Protocols for Rapid Extraction of Good Quality DNA from Recalcitrant Species....Pages 36-37
Isolation of DNA from Preserved Specimens....Pages 41-45
Field Collection: Animals....Pages 46-48
Field Collection: Plants....Pages 49-50
DNA Extraction Using Anion-Exchange Chromatography and Silica-Gel Based Membranes....Pages 53-54
Isolation of Nucleic Acids Using Anion-Exchange Chromatography: QIAGEN-tip Based Methods....Pages 54-59
Isolation of Nucleic Acids Using Silica-Gel Based Membranes: Methods Based on the Use of QIAamp Spin Columns....Pages 59-63
Isolation of Total RNA from Animal Tissue Using Anion-Exchange Chromatography (QIAGEN-tips)....Pages 64-66
Isolation of Total RNA Using Silica-Gel Based Membranes....Pages 67-70
Front Matter....Pages 71-71
Isozymes....Pages 75-81
RFLP Analysis....Pages 85-95
Nonradioactive Probes....Pages 96-97
DNA Fingerprinting with VNTR Sequences....Pages 101-108
Front Matter....Pages 71-71
Polymerase Chain Reaction....Pages 111-118
PCR Sequencing....Pages 119-124
Routes to DNA Sequencing....Pages 125-130
Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLPs)....Pages 131-134
TGGE and DGGE....Pages 135-143
Theoretical Aspects of Thermal Denaturation of Nucleic Acids....Pages 144-146
Modifications for the Improvement of TGGE and DGGE....Pages 147-148
Temporal TGGE....Pages 149-149
TGGE and SSCP....Pages 150-151
Single-Strand Conformation Polymorphism (SSCP) Analysis....Pages 152-156
A Rapid Screening Procedure for Detecting mtDNA Haplotypes in Humpback Whales ( Megaptera novaeangliae )....Pages 157-163
Modifications to SSCP Analysis Conditions....Pages 164-164
Automation and the Polymerase Chain Reaction....Pages 165-167
Randomly Amplified Polymorphic DNAs (RAPDs)....Pages 171-175
Reproducibility Testing of RAPDs by a Network of European Laboratories....Pages 176-179
Amplified Fragment Length Polymorphism (AFLP)....Pages 183-190
Reproducibility Testing of AFLPs by a Network of European Laboratories....Pages 191-192
Genotyping with Microsatellite Markers....Pages 195-201
Characteristics of Microsatellites....Pages 202-205
PCR Analysis of SSR Polymorphisms in Plants Using Agarose Gels....Pages 206-207
Front Matter....Pages 71-71
Fluorescent Labelling of SSRS and Automated Detection....Pages 208-208
Reproducibility Testing of SSRs by a Network of European Laboratories....Pages 209-211
Front Matter....Pages 213-213
Cloning of Random Amplified Polymorphic DNA (RAPD) to Generate Codominant Genetic Markers....Pages 217-222
cpDNA....Pages 223-228
RFLP Markers....Pages 229-236
Nuclear DNA Primers....Pages 239-248
Primers for Animal Mitochondrial DNA: The Importance of Species-Specific Primers....Pages 249-255
cpDNA and mtDNA Primers in Plants....Pages 256-261
Variations on a Theme....Pages 262-264
Ribosomal DNA Probes and Primers....Pages 267-276
Isolation of Microsatellite Markers in Animals....Pages 279-285
VNTR Probes....Pages 286-286
Designing SSR Primer Pairs Using Macvector Software....Pages 287-287
Isolation of Microsatellite Markers in Plants....Pages 288-296
Front Matter....Pages 297-297
Definitions....Pages 301-303
Diversity and Differentiation at the Allelic Level....Pages 303-306
Diversity and Differentiation at the Nucleotide Level....Pages 306-311
Measuring Genetic Distance....Pages 315-325
Binary Data Analysis....Pages 329-331
Reading DNA Sequences....Pages 332-333
Front Matter....Pages 297-297
Multiple Alignment....Pages 334-340
Selected Software Packages for Personal Computers....Pages 341-343
Constructing Phylogenies from Discrete Data — Parsimony Methods....Pages 344-352
Constructing Phylogenies from Discrete Data — Maximum Likelihood....Pages 353-355
Molecules vs Morphology....Pages 359-364
Gene Trees vs Species Trees....Pages 365-365
Front Matter....Pages 367-367
Comparison of Molecular Marker Assays in Inbreeding (Barley) and Outbreeding (Potato) Species....Pages 371-381
The Use of Molecular Markers for the Identification of Tomato Cultivars....Pages 382-387
Molecular Analysis of Variation in Lactuca ....Pages 388-393
Evaluation of the AFLP and RAPD Molecular Marker Technologies with Regard to the Genetic Diversity of Commercial Wheat Cultivars....Pages 394-397
Screening Germplasm Collections....Pages 398-400
PCR-RFLP Analysis of Chloroplast DNA of Various Gymnosperms: A Rapid Tool for Assessing Genetic Variation at the Above-Species Level....Pages 403-406
Analysis of Hypervariable Chloroplast Microsatellites in Pinus Halepensis Reveals a Dramatic Genetic Bottleneck....Pages 407-412
Genetic Variation of Mitochondrial DNA Reveals Subdivision of Norway Spruce ( Picea Abies (L.) Karst.)....Pages 413-417
Diversity in Insect Species Using DNA Sequences....Pages 418-425
The Usefulness of Parallel Analysis of Uni- and Bi-Parental Markers: The North Atlantic Humpback Whale....Pages 426-430
Partitioning of Genetic Diversity in the House Mouse....Pages 431-434
Molecular Studies on the Phylogeny of the Genus Barley ( Hordeum ; Poaceae)....Pages 437-440
The Genus Rhododendron : A Case Study to Test the Value of Various Molecular Techniques as Measures of Biodiversity....Pages 441-448
Rapd Fingerprinting as a Tool for Taxonomic Studies in the Genus Populus ....Pages 449-455
Front Matter....Pages 367-367
Screening for ‘Useful Variation’ Using Rapd Markers....Pages 459-463
Application of Stress Responsive Genes RFLP Analysis to the Evaluation of Genetic Diversity in Plants....Pages 464-470
Exploiting Genome Plasticity for the Detection of Hypervariable Sequences....Pages 471-484
Back Matter....Pages 485-498