Wildlife DNA Analysis E-Book

Adrian Linacre

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Essential Forensic Science
• Sprache: Englisch

Seitenzahl: 545

Veröffentlichungsjahr: 2013

Beschreibung

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.

Leseprobe

Contents

Cover

Title Page

Copyright

Foreword

Preface

About the Authors

Acknowledgements

Chapter 1: Introduction

1.1 Importance of wildlife forensic science investigations

1.2 Role of forensic science in wildlife crimes

1.3 Legislation covering wildlife crime

1.4 Role of non-human DNA in forensic science

1.5 Development of wildlife DNA testing

1.6 Accreditation and certification

1.7 Standardisation and validation

1.8 Collection of evidential material, continuity of evidence and transportation to the laboratory

1.9 Note taking and maintenance of a casefile

1.10 Case assessment and initial testing

1.11 Scope of book

Useful websites

References

Chapter 2: DNA, Genomes and Genetic Variation

2.1 Introduction

2.2 The DNA molecule

2.3 Chromosomes and nuclear DNA

2.4 Genomes

2.5 DNA mutation and genetic variation

2.6 DNA polymorphisms leading to speciation

2.7 What is a species?

2.8 Summary

References

Chapter 3: Methods in Wildlife Forensic DNA Analysis

3.1 Introduction

3.2 Protein polymorphisms

3.3 DNA isolation, purification and concentration

3.4 DNA quantification

3.5 Restriction fragment length polymorphisms (RFLP)

3.6 Methods based on the polymerase chain reaction

3.7 PCR set-up

3.8 PCR clean-up

3.9 DNA sequencing

3.10 SNP typing

3.11 New generation of DNA sequence methods

Suggested reading

Chapter 4: Species Testing

4.1 Introduction

4.2 Species

4.3 Attributes of a species testing locus

4.4 Application of a locus to a species

4.5 Tests available and how they are performed

4.6 Developing a species test

4.7 Interpretation and reporting of results

4.8 Other limitations: hybrids and wild/captive bred

4.9 Future methodologies

References

Chapter 5: Genetic Linkage

5.1 Introduction

5.2 Whole genome testing

5.3 Types of individualisation testing

5.4 Identifying STR loci

5.5 Allele databases

5.6 Hardy–Weinberg equilibrium

5.7 Kinship factors and accounting for shared alleles

5.8 Assessing the suitability of STR loci

5.9 Genetic assignment: paternity testing

5.10 Concluding comments

References

Chapter 6: Interpretation, Evaluation and Reporting of Results

6.1 Introduction

6.2 Case assessment

6.3 Hierarchies of propositions

6.4 DNA evidence evaluation

6.5 Evaluation of DNA evidence in wildlife cases

6.6 Role of the expert witness

6.7 Report writing

6.8 Summary and comments

Appendix 1 Explanation of the DNA test

Appendix 1 Explanation for DNA test (human identification)

Appendix 2 Explanation of Beaver Test

Appendix 3 Blood pattern interpretation

Appendix 1

Appendix 1 Species-specific test

Appendix 2 Genetic assignment

References

Measurements

Glossary

Appendix A: Simulated Sample Populations

Appendix B: Useful websites

Society, NGO and legal websites

Software

Resources and databases

Index

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Foreword

On 3 March 2013, in Bangkok, the 176 Parties to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) will start their 16th meeting of the Conference of the Parties with a celebration of the fact that the Convention was signed 40 years ago.

One of the main difficulties in the global fight against illegal trade in wild animals and plants is – and always has been – the identification of the multitude of products derived from the 5000 animal and some 30 000 plant species covered by the Convention. The (sub-)species or products indicated on CITES permits and certificates may be completely different from the shipment they cover.

In quite a number of cases, commercial trade is prohibited when specimens are taken from the wild in certain countries but not in other range states. Also, trade in captive-bred animals may be allowed while specimens taken from the wild cannot be traded. In these cases it is necessary to be able to identify an individual as originating in a given wild or captive population, which requires a more complicated in depth analysis.

Fortunately, more robust methods than those relying on the morphological characteristics of particular species are being developed to assist wildlife trade controls. Methods such as those described in this book are crucial to identify specimens of species in international trade in contravention of CITES and of national conservation legislation.

Any identification method must be rapid, easy and most importantly accurate. It is vital that tests developed be so at the highest standards to ensure that any evidential analysis is beyond reproach. Error rates acceptable in other disciplines of science are not acceptable in criminal investigations and so comprehensive validation must be undertaken for any test used, something that is discussed in detail in this book.

Wildlife DNA Analysis: Applications in Forensic Science is a major contribution to more effective and reliable wildlife trade controls.

There is great interest in wildlife crime and interest in non-human DNA analysis is on the rise, which makes Wildlife DNA Analysis: Applications in Forensic Science a much needed book. It fills a gap, bringing together the relevant aspects of wildlife analysis and introducing the rigor required in forensic science.

This book is a must for all those involved in wildlife trade controls.

Willem WijnstekersFormer Secretary-General of CITES

Preface

Wildlife forensic science is a relatively new field in both research and its use in criminal investigations. It should be acknowledged from the outset that wildlife forensic science encompasses many areas of the analytical sciences and each plays a potentially crucial role. This book is focused on the use of DNA in wildlife forensic science while noting the importance of other areas of biological and chemical testing. It is also focused primarily on mammalian and avian DNA typing, again noting the importance and relevance of other species.

The book is aimed at those with an interest in DNA for human identification who are considering developing a wildlife forensic science capability. It is also aimed at those with little DNA knowledge but share an interest in wildlife criminal investigations. Only a scant knowledge of DNA is assumed in reading this book and every effort is made to explain terms and concepts.

While the application of DNA to wildlife forensic science investigations is relatively new, requests for assistance with such investigations are only likely to increase as the availability and appreciation of the technology also increases. It is paramount that all work conducted in the criminal justice system is to the highest standards expected and that there is no reduction in the quality of the work performed because the crime is against wildlife. It only takes one poor example of work presented in court to tarnish the rest of the members of the wildlife forensic science community. On a very positive note, there is such interest among forensic practitioners to become involved in wildlife forensic science investigations; this can only be beneficial.

The six chapters that comprise this book are designed to take the reader sequentially through the process of wildlife DNA typing, starting with introducing the rationale for the book and why we have become so passionate about our research and professional work in the investigation of alleged crimes involving wildlife. There are recurring questions in wildlife forensic science: what species is this? and from what individual or population did this sample originate? These questions can be addressed by DNA typing and the science behind the analysis to address these questions is the subject for the rest of the book. Chapters 2 and 3 describe aspects of the science behind the use of DNA in wildlife forensic science. These chapters are written with the assumption that the reader has little grounding in DNA and gives a historical context for the methods in current use. The use of DNA sequence databases to determine the probability that an unknown sample is from a particular species is illustrated in Chapter 4. This chapter is also designed to show step-by-step how different software programs are used in wildlife forensic investigations. Chapter 5 addresses the other main issues with wildlife DNA forensic science such an assigning a sample to an individual or a population. This type of sample assignment requires the use of software programs and equations, which will be explained to those unfamiliar with them. The final stage in forensic science is the evaluation and reporting of the results. This is described in Chapter 6 and draws on the experience of the authors. The need for high quality standards and best practice are common throughout the book.

The authors come from a forensic science background working in the area of human identification but developed an interest in wildlife investigation and scientific research. This profile led to requests and instructions to assist with criminal cases requiring the application of non-human DNA. We do not profess to have an in-depth knowledge of conservation genetics but wrote this book from a forensic science perspective. We very much hope that this book will lead to others gaining the same interest in this rapidly developing aspect of forensic science. We also very much hope that our work plays some part in the conservation of protected species and in the successful investigation of alleged crimes against wildlife.

About the Authors

Adrian M.T. Linacre is currently the South Australia Justice Chair in Forensic Science at Flinders University in Adelaide. His first degree was in Zoology at Edinburgh University before undertaking a PhD and three Research Fellowships at Sussex University, UK. Prior to moving to Australia he worked at the Centre for Forensic Science at the University of Strathclyde, UK for 16 years.

He has published over 90 papers in international journals with a wide range of these publications being related to wildlife research. He was chair of the International Society for Forensic Genetics Commission on the use of non-human DNA and has played a role in recommending standards and best practice in the forensic science.

He is co-author of the text An Introduction to Forensic Genetics, which is now in its second edition and is editor of the book Forensic Science in Wildlife Investigations. He has presented at a number of international conferences, is the President of the 25th Congress of the International Society of Forensic Genetics, and is Associate Editor of Forensic Science International: Genetics, handling non-human DNA publications. He is also on the editorial board of Investigative Genetics. His research is on trace DNA from both human and non-human sources.

Shanan S. Tobe is currently a Vice Chancellor's Post-Doctoral Fellow at Flinders University. He has studied forensic science for over 10 years specialising in forensic biology, genetics and in wildlife forensic science. He obtained his BSc Honours degree in Forensic Biology from Laurentian University in Canada followed by a MSc and PhD from the University of Strathclyde in Glasgow, UK.

Shanan is widely published in the area of wildlife forensic genetics and regularly presents at international scientific symposia. He holds membership with the American Academy of Forensic Sciences, the International Society for Forensic Genetics and holds professional membership with the Forensic Science Society.

His research focus is currently on the identification and individualisation of endangered species, and also on improving techniques for the recovery of DNA, both human and non-human, in relation to wildlife crime. Previously, Shanan developed a multiplex reaction capable of simultaneously identifying 18 different mammalian species common to the UK that were often associated with crime scenes.

Acknowledgements

We express special thanks to those who have helped with the development of this book.

The following all assisted with critical reading of the text: Sherryn Ciavaglia, Elaine Kellett, and Eleanor Tobe.

We are indebted to colleagues at the University of Strathclyde and Flinders University, both past and present, for their mentoring, encouragement, and access to equipment to conduct research and casework.

Our research could not be conducted without access to samples and in this regard we are grateful to Andrew Kitchener at the National Museum of Scotland and Rebecca Johnson at the Australian National Museum.

Financial support for Adrian Linacre has been provided by the Leverhulme Trust and the Department of Justice South Australia. Shanan Tobe has been provided with financial assistance from the Leverhulme Trust, University of Strathclyde and Flinders University.

1

Introduction

1.1 Importance of wildlife forensic science investigations

The scale of wildlife crime is difficult to judge accurately as so much may go undiscovered, unreported or unrecorded. The poaching of protected species by its very nature can occur in remote and isolated areas where there is little surveillance. As such, wildlife crime is more likely to be identified when samples are transported through border controls or other checkpoints.

Poaching of any kind can result in high financial rewards, a low chance of prosecution and penalties associated with convictions for wildlife crime are generally low. For these reasons there is an often quoted figure of something like:

‘The illegal trade in wildlife is a US$20 billion a year industry, second only to trade in illegal drugs’ (Zhang et al., 2008; Alacs et al., 2010).

The monetary figure will range between US$6 and 40 billion a year and is often attributed to Interpol, World Wide Fund for Nature (WWF) or another non-governmental organisation (NGO); however, Interpol have confirmed that they have never issued any statement to this effect (Christy, 2010). This figure, although believable (considering the cost of individual animal components), is difficult to estimate as monitoring the amount of illegal trade is itself the problem. It is at best an estimate as there are not the same international surveillance methods used in other areas of international criminal activity, such as drug enforcement or the trade in firearms, to investigate and prosecute offences involving wildlife. Organised crime has not been proven to be linked to wildlife crime, but there are indications that this could be the case (Sellar, 2009). Another influencing factor in wildlife crime is that there is a high financial return with little chance of capture, and even if captured, the penalties are light. Rarely does the maximum penalty for the alleged event meet the potential financial gains (Li et al., 2000).

These financial gains can be highlighted by a number of examples of the illegal trade in wildlife or products derived from protected species. These examples include the illegal trade in the ultra-fine fabric to make a shawl called a shahtoosh, which requires between three to five killed Tibetan antelope (Pantholops hodgsonii) to make one shawl and a single shawl can retail at between US$8000 and $10 000. Single Australian parrot eggs could fetch as much as US$30 000 on the international market (Alacs and Georges, 2008). The cost of ivory on the black market remains high with ivory being marketed as from mammoth. Mammoth, since extinct, are exempt from international regulations and so can be imported, exported and sold legally. The cost of mammoth ivory is currently on average US$350 per kilogram (different ‘grades’ of ivory sell for different amounts and the highest grade can retail for over US$500 per kg), equivalent to US$350 000 per tonne, and worth US$21 million per year to the Russian economy (Martin and Martin, 2010). A clear issue is to be able to distinguish between mammoth and elephant ivory to ensure that ivory sold as mammoth is not actually from an elephant, but more importantly the need to ensure that the growing trade in what is described as ‘mammoth’ ivory does not lead to the increased poaching of elephants in Africa.