Wildlife DNA Analysis (eBook)

Applications in Forensic Science

Adrian Linacre, Shanan Tobe (Autoren)

eBook Download: PDF

2013
John Wiley & Sons (Verlag)
978-1-118-49655-8 (ISBN)

Infos

WILDLIFE DNA ANALYSIS Applications in Forensic Science

DNA typing of non-human DNA is a fast developing area of research and professional practice. The application of DNA typing in wildlife forensic science is one of these prime uses of DNA typing and is gaining increasing profile. The use of DNA profiling in wildlife forensic science falls into two broad areas: species testing and genetic linkage. Species testing answers the question 'what species is this?' and genetic linkage answers the question 'did these two samples come from the same organism or population?' Wildlife DNA Analysis: Applications in Forensic Science provides an accessible introduction to both of these key areas.

Clearly structured throughout, the introduction highlights the different types of crime where these techniques are regularly used. This chapter includes a discussion as to who performs forensic wildlife examinations, the standardisation and validation of methods, and the role of the expert witness in this type of alleged crime. This is followed by a detailed section on the science behind DNA typing including the problems in isolating DNA from trace material and subsequent genetic analysis are also covered. The book then undertakes a comprehensive review of species testing using DNA, including a step-by-step guide to sequence comparisons. A comparison of the different markers used in species testing highlights the criteria for a genetic marker. A full set of case histories illustrates the use of the different markers used. The book details the use of genetic markers to link two or more hairs/feathers/leaves/needles to the same individual organism and the software used in population assignment. The problems and possibilities in isolating markers, along with the construction of allele databases are discussed. The book concludes with evaluation and reporting of genetic evidence in wildlife forensic science illustrated by examples of witness statements.

• An accessible introduction to this fast developing area of research within forensic science.
• Case studies throughout to link theory and practice and to highlight the use of DNA testing in species testing.
• Covers both crimes against wildlife and offences where wildlife can provide vital evidence.
• Assumes only a basic background knowledge of DNA.
• Includes a comprehensive review of species testing using DNA, including a step-by-step guide to sequence comparisons.

Adrian M. T. Linacre, Flinders University, Adelaide, Australia

Shanan S. Tobe, University of Strathclyde, Glasgow, UK

Inhalt

Wildlife DNA Analysis 3
Contents 7
Foreword 11
Preface 13
About the Authors 15
Acknowledgements 17
1 Introduction 19
1.1 Importance of wildlife forensic science investigations 19
1.2 Role of forensic science in wildlife crimes 21
1.3 Legislation covering wildlife crime 22
1.4 Role of non-human DNA in forensic science 26
1.5 Development of wildlife DNA testing 27
1.5.1 History and current state of wildlife DNA forensic science 28
1.5.2 Wildlife forensic science testing 29
1.5.3 Performing DNA typing in wildlife investigations 31
1.6 Accreditation and certification 32
1.7 Standardisation and validation 38
1.8 Collection of evidential material, continuity of evidence and transportation to the laboratory 42
1.9 Note taking and maintenance of a casefile 47
1.10 Case assessment and initial testing 48
1.11 Scope of book 50
Useful websites 50
References 51
2 DNA, Genomes and Genetic Variation 55
2.1 Introduction 55
2.2 The DNA molecule 55
2.3 Chromosomes and nuclear DNA 57
2.4 Genomes 59
2.4.1 Nuclear DNA 59
2.4.2 Mitochondrial and chloroplast DNA 62
2.5 DNA mutation and genetic variation 65
2.5.1 Genetic variation of repetitive DNA 66
2.5.2 Single base changes leading to genetic variation 66
2.5.3 Genetic loci used in species testing 68
2.6 DNA polymorphisms leading to speciation 71
2.6.1 Genetic isolation 72
2.6.2 Other processes leading to speciation 74
2.7 What is a species? 74
2.7.1 Subspecies 78
2.7.2 Genus to Kingdom 79
2.8 Summary 81
References 82
3 Methods in Wildlife Forensic DNA Analysis 87
3.1 Introduction 87
3.2 Protein polymorphisms 87
3.3 DNA isolation, purification and concentration 88
3.3.1 Generic aspects of DNA isolation 88
3.3.2 Lysis step 89
3.3.3 DNA purification: silica-based extraction 90
3.3.4 DNA purification: Chelex R 100 resin 91
3.3.5 DNA purification: organic extraction 92
3.3.6 Microconcentration 94
3.4 DNA quantification 94
3.5 Restriction fragment length polymorphisms (RFLP) 96
3.6 Methods based on the polymerase chain reaction 99
3.6.1 Factors affecting PCR efficiency and optimisation of PCR 102
3.6.2 PCR-based methods of DNA quantification 106
3.6.3 Random amplification of polymorphic DNA 109
3.6.4 Amplification of fragment length polymorphisms (AFLP) 111
3.7 PCR set-up 113
3.8 PCR clean-up 116
3.9 DNA sequencing 117
3.10 SNP typing 118
3.11 New generation of DNA sequence methods 120
Suggested reading 122
4 Species Testing 123
4.1 Introduction 123
4.2 Species 124
4.2.1 Genetic variation and correspondence with taxonomy 124
4.3 Attributes of a species testing locus 124
4.4 Application of a locus to a species 128
4.5 Tests available and how they are performed 128
4.5.1 Sequencing 129
4.5.2 Species-specific primers 142
4.6 Developing a species test 145
4.6.1 Use of data on GenBank and sequence alignment 146
4.6.2 Designing primers 153
4.6.3 Validation 174
4.7 Interpretation and reporting of results 177
4.7.1 Interpretation and reporting sequencing results 178
4.7.2 Interpretation and reporting species-specific testing results 187
4.8 Other limitations: hybrids and wild/captive bred 189
4.9 Future methodologies 191
References 191
5 Genetic Linkage 195
5.1 Introduction 195
5.2 Whole genome testing 195
5.3 Types of individualisation testing 196
5.3.1 Short Tandem Repeats 197
5.4 Identifying STR loci 200
5.4.1 DNA libraries 201
5.4.2 Locating novel microsatellite motifs using Next Generation Sequencing 202
5.5 Allele databases 208
5.5.1 Number of theoretical genotypes 210
5.5.2 Allelic ladders 210
5.6 Hardy-Weinberg equilibrium 211
5.7 Kinship factors and accounting for shared alleles 217
5.7.1 Rare or absent alleles on the database 220
5.8 Assessing the suitability of STR loci 221
5.8.1 The Genetic Data Analysis software (GDA) 223
5.8.2 The Excel Microsatellite Toolkit 232
5.8.3 Arlequin 238
5.8.4 API-Calc 246
5.8.5 Genepop 248
5.8.6 FSTAT 253
5.8.7 Structure 254
5.8.8 Summary 260
5.9 Genetic assignment: paternity testing 262
5.9.1 Genetic assignment: paternity testing if one parent is not available 267
5.9.2 Genetic assignment in paternity testing, incorporating kinship factor 269
5.10 Concluding comments 271
References 272
6 Interpretation, Evaluation and Reporting of Results 277
6.1 Introduction 277
6.2 Case assessment 278
6.3 Hierarchies of propositions 279
6.4 DNA evidence evaluation 280
6.4.1 The frequentist approach 281
6.4.2 Likelihood ratios 282
6.4.3 The Bayesian approach 284
6.4.4 Comparison of the three approaches 285
6.5 Evaluation of DNA evidence in wildlife cases 287
6.5.1 Case scenario 1 287
6.5.2 Case scenario 2 289
6.5.3 Case scenario 3 290
6.6 Role of the expert witness 291
6.7 Report writing 293
6.8 Summary and comments 295
Statement of witness 296
References 317
Measurements 321
Glossary 323
Appendix A Simulated Sample Populations 329
Appendix B Useful websites 341
Index 343
Supplemental Images 353

Produkt-Details

• Erscheint lt. Verlag: 27.3.2013
• Reihe/Serie: Essential Forensic Science
• Reihe/Serie: Essentials of Forensic Science
• Sprache: englisch
• Themenwelt: Informatik ► Weitere Themen ► Bioinformatik
• Themenwelt: Medizin / Pharmazie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zoologie
• Themenwelt: Naturwissenschaften ► Chemie
• Schlagworte: Analytische Chemie / Forensik • Biowissenschaften • Chemie • Chemistry • Conservation Science • Forensics • Forensic Science • Forensik • Life Sciences • Naturschutzbiologie
• ISBN-10: 1-118-49655-8 / 1118496558
• ISBN-13: 978-1-118-49655-8 / 9781118496558