Adrian Linacre, Shanan Tobe

Wildlife DNA Analysis (eBook, ePUB)

Applications in Forensic Science

• Format: ePub

Produktbeschreibung

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/feather/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 in this chapter. The book concludes with evaluation and reporting of genetic evidence in wildlife forensic science illustrated by examples of witness statements.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 352
• Erscheinungstermin: 27. März 2013
• Englisch
• ISBN-13: 9781118496527
• Artikelnr.: 38047063

Autorenporträt

Adrian M. T. Linacre, Flinders University, Adelaide, Australia Shanan S. Tobe, University of Strathclyde, Glasgow, UK

Inhaltsangabe

Foreword ix Preface xi About the Authors xiii Acknowledgements xv 1
Introduction 1 1.1 Importance of wildlife forensic science investigations 1
1.2 Role of forensic science in wildlife crimes 3 1.3 Legislation covering
wildlife crime 4 1.4 Role of non-human DNA in forensic science 8 1.5
Development of wildlife DNA testing 9 1.5.1 History and current state of
wildlife DNA forensic science 10 1.5.2 Wildlife forensic science testing 11
1.5.3 Performing DNA typing in wildlife investigations 13 1.6 Accreditation
and certification 14 1.7 Standardisation and validation 20 1.8 Collection
of evidential material, continuity of evidence and transportation to the
laboratory 24 1.9 Note taking and maintenance of a casefile 29 1.10 Case
assessment and initial testing 30 1.11 Scope of book 32 Useful websites 32
References 33 2 DNA, Genomes and Genetic Variation 37 2.1 Introduction 37
2.2 The DNA molecule 37 2.3 Chromosomes and nuclear DNA 39 2.4 Genomes 41
2.4.1 Nuclear DNA 41 2.4.2 Mitochondrial and chloroplast DNA 44 2.5 DNA
mutation and genetic variation 47 2.5.1 Genetic variation of repetitive DNA
48 2.5.2 Single base changes leading to genetic variation 48 2.5.3 Genetic
loci used in species testing 50 2.6 DNA polymorphisms leading to speciation
53 2.6.1 Genetic isolation 54 2.6.2 Other processes leading to speciation
56 2.7 What is a species? 56 2.7.1 Subspecies 60 2.7.2 Genus to Kingdom 61
2.8 Summary 63 References 64 3 Methods in Wildlife Forensic DNA Analysis 69
3.1 Introduction 69 3.2 Protein polymorphisms 69 3.3 DNA isolation,
purification and concentration 70 3.3.1 Generic aspects of DNA isolation 70
3.3.2 Lysis step 71 3.3.3 DNA purification: silica-based extraction 72
3.3.4 DNA purification: Chelex R 100 resin 73 3.3.5 DNA purification:
organic extraction 74 3.3.6 Microconcentration 76 3.4 DNA quantification 76
3.5 Restriction fragment length polymorphisms (RFLP) 78 3.6 Methods based
on the polymerase chain reaction 81 3.6.1 Factors affecting PCR efficiency
and optimisation of PCR 84 3.6.2 PCR-based methods of DNA quantification 88
3.6.3 Random amplification of polymorphic DNA 91 3.6.4 Amplification of
fragment length polymorphisms (AFLP) 93 3.7 PCR set-up 95 3.8 PCR clean-up
98 3.9 DNA sequencing 99 3.10 SNP typing 100 3.11 New generation of DNA
sequence methods 102 Suggested reading 104 4 Species Testing 105 4.1
Introduction 105 4.2 Species 106 4.2.1 Genetic variation and correspondence
with taxonomy 106 4.3 Attributes of a species testing locus 106 4.4
Application of a locus to a species 110 4.5 Tests available and how they
are performed 110 4.5.1 Sequencing 111 4.5.2 Species-specific primers 124
4.6 Developing a species test 127 4.6.1 Use of data on GenBank and sequence
alignment 128 4.6.2 Designing primers 135 4.6.3 Validation 156 4.7
Interpretation and reporting of results 159 4.7.1 Interpretation and
reporting sequencing results 160 4.7.2 Interpretation and reporting
species-specific testing results 169 4.8 Other limitations: hybrids and
wild/captive bred 171 4.9 Future methodologies 173 References 173 5 Genetic
Linkage 177 5.1 Introduction 177 5.2 Whole genome testing 177 5.3 Types of
individualisation testing 178 5.3.1 Short Tandem Repeats 179 5.4
Identifying STR loci 182 5.4.1 DNA libraries 183 5.4.2 Locating novel
microsatellite motifs using Next Generation Sequencing 184 5.5 Allele
databases 190 5.5.1 Number of theoretical genotypes 192 5.5.2 Allelic
ladders 192 5.6 Hardy-Weinberg equilibrium 193 5.7 Kinship factors and
accounting for shared alleles 199 5.7.1 Rare or absent alleles on the
database 202 5.8 Assessing the suitability of STR loci 203 5.8.1 The
Genetic Data Analysis software (GDA) 205 5.8.2 The Excel Microsatellite
Toolkit 214 5.8.3 Arlequin 220 5.8.4 API-Calc 228 5.8.5 Genepop 230 5.8.6
FSTAT 235 5.8.7 Structure 236 5.8.8 Summary 242 5.9 Genetic assignment:
paternity testing 244 5.9.1 Genetic assignment: paternity testing if one
parent is not available 249 5.9.2 Genetic assignment in paternity testing,
incorporating kinship factor 251 5.10 Concluding comments 253 References
254 6 Interpretation, Evaluation and Reporting of Results 259 6.1
Introduction 259 6.2 Case assessment 260 6.3 Hierarchies of propositions
261 6.4 DNA evidence evaluation 262 6.4.1 The frequentist approach 263
6.4.2 Likelihood ratios 264 6.4.3 The Bayesian approach 266 6.4.4
Comparison of the three approaches 267 6.5 Evaluation of DNA evidence in
wildlife cases 269 6.5.1 Case scenario 1 269 6.5.2 Case scenario 2 271
6.5.3 Case scenario 3 272 6.6 Role of the expert witness 273 6.7 Report
writing 275 6.8 Summary and comments 277 Statement of witness 278
References 299 Measurements 303 Glossary 305 Appendix A Simulated Sample
Populations 311 Appendix B Useful websites 323 Index 325