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DNA markers for forensic identification of non-human biological traces

Wesselink, M.

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Citation for published version (APA):Wesselink, M. (2018). DNA markers for forensic identification of non-human biological traces.

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Download date: 05 Oct 2020

DNA markers for forensic identification

of non-human biological traces

Monique Wesselink

DNA markers for forensic identification

of non-human biological traces

ACADEMISCH PROEFSCHRIFT

ter verkrijging van de graad van doctor

aan de Universiteit van Amsterdam

op gezag van de Rector Magnificus

prof. dr. ir. K.I.J. Maex

ten overstaan van een door het College voor Promoties ingestelde commissie,

in het openbaar te verdedigen in de Agnietenkapel

op donderdag 26 april 2018, te 12:00 uur

door

Monique Wesselink

geboren te Zwolle

Promotiecommissie:

Promotor: Prof. dr. A.D. Kloosterman

Institute for Biodiversity and Ecosystem Dynamics

Universiteit van Amsterdam

Copromotor: Dr. I. Kuiper

Niet-Humane Biologische Sporen

Nederlands Forensisch Instituut

Overige leden: Prof. dr. A.M.T. Linacre

Biological Sciences

Flinders University

Prof. dr. mr. M.E. de Meijer

Amsterdam Centre on the Legal Professions

Universiteit van Amsterdam

Prof. dr. M. Schilthuizen

Institute of Biology Leiden

Universiteit Leiden

Prof. dr. M.J. Sjerps

Korteweg-de Vries Institute for Mathematics

Universiteit van Amsterdam

Prof. dr. P.H. van Tienderen

Institute for Biodiversity and Ecosystem Dynamics

Universiteit van Amsterdam

Faculteit : Faculteit der Natuurwetenschappen, Wiskunde en Informatica

The research described in this thesis was performed within the

Non-Human Biological Traces group of the Netherlands Forensic

Institute.

Printing of this thesis was financially supported by the Netherlands

Forensic Institute, the Co van Ledden Hulsebosch Centrum (CLHC),

Amsterdam Center for Forensic Sciences and Medicine and the

Institute for Biodiversity and Ecosystem Dynamics (IBED), University

of Amsterdam.

DNA markers for forensic identification of non-human biological traces

Copyright © 2018 Monique Wesselink

PhD thesis, University of Amsterdam (IBED), The Netherlands

ISBN/EAN 978-94-91407-58-1

Cover design the author

Cover image Vikpit

Printing GildePrint

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Table of contents

Outline of this thesis 9

Chapter 1 13

Molecular species identification of “Magic Mushrooms”

Chapter 2 39

Forensic utility of the feline mitochondrial control region - A Dutch perspective

Chapter 3 53

Forensic analysis of mitochondrial control region DNA from single cat hairs

Chapter 4 57

Local populations and inaccuracies: Determining the relevant mitochondrial haplotype

distributions for North West European cats

Chapter 5 75

DNA typing of birch: Development of a forensic STR system for Betula pendula

and Betula pubescens

Chapter 6 103

The forensic potential of DNA typing of birch (Betula) seeds

Chapter 7 115

General discussion

Epilogue 127

Summary 129

Samenvatting 133

Overview of author contributions 137

Acknowledgements 141

9

Outline of this thesis

M. Wesselink and I. Kuiper

The majority of investigative questions encountered in forensic case work involve a certain level of classification, often referred to as ‘source level’ questions. Such questions can seem quite trivial, examples being “Is this blood human?”, “Is this white powder cocaine?” and “Are

these wounds caused by a baseball bat?”. However answering such questions is generally far

from a trivial matter. Apart from the specific biological, chemical or physical knowledge that is required to answer such questions, additional knowledge of for example the relevant classes, within and between class variation, and reliability of the measurements and features under investigation are always needed to reliably provide an answer that may be used in a criminal proceeding. After addressing the questions of classification, additional knowledge of how traces or specific features are transferred from one object to another, and how these persist after transfer has occurred, can further influence the certainty with which forensic questions such as ‘activity level’ questions may be answered. One of the first steps in providing an answer that may be used in a criminal proceeding, is to determine the relevant and reliable level of classification, where relevant and reliable often are far from identical. Relevant classes may be very narrow, in which cases the relevance of such investigative questions is readily seen (one specific chemical compound in “Is this white

powder cocaine?”). Alternatively the classes may be broader, in which cases additional (case)

information may be required to correctly see the relevance (the biological species human in “Is

this blood human?” and the group of bats designed to play baseball in “Are these wounds

caused by a baseball bat?”). Independent of whether the defined groups are narrow or broad,

once the desired level of classification has been determined, the next challenge to define whether class specific characteristics are expected to exist. Biological groups that have a common ancestor (monophyletic groups such as all individuals of a species) or chemical compounds that are derived from a certain precursor (such as certain opiates) are more likely

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to exhibit readily recognizable class specific features, than paraphyletic groups that are better described by use (such as bats used to play a specific ball game; remains from wooden (baseball/softball/cricket) bats may be easier to discriminate from remains from metal bats than distinguishing between remains from baseball bats in general and remains from all other bats). When class specific characteristics are expected to exist or can theoretically be distinguished, irrespective of whether these are based on usage or origin, the next effort will be to determine whether identification of these characteristics is practically possible in the relevant groups, more specifically whether the identified characteristics can reliably be measured in forensic case samples. If again this question can be answered affirmatively, analyzing test samples, creating databases, and sharing this data with the forensic community for review and comparison are generally the final steps that precede application of the identified characteristics in case work. When biological traces are under investigation, morphological traits and DNA characteristics are generally utilized. Although morphological classification has many benefits, its application is limited in cases when often only small or poorly conserved traces are available. Additionally, the number of species for which classification at the level of a single organism is possible based solely on morphological features is limited, even when relative large samples are available. Since analysis of DNA markers has become common practice, identification of individuals of at least one species (Homo sapiens) is well known in forensics, illustrating the forensic potential of such markers. Comparable methods may be designed for other species, but biological factors such as reproductive strategies (e.g. sexual, self-fertilizing or clonal) may influence their application. Another biological factor that influences both the technical applicability of DNA markers as well as the interpretation of results, is the (cellular) origin of the DNA markers. The different types of DNA present in cells (i.e. autosomal, mitochondrial, chloroplast) have their own potentials and pitfalls that should be taken into account when determining whether a marker should be pursued for a forensic application. As the history and relatedness of the DNA of relevant classes can often be studied theoretically, the existence of characteristics that are relatively constant within a class (the intraclass variation) but differ between classes (interclass variation), can often be predicted. From a biological point of view, if a certain species is the class of interest, a valuable characteristic for identification would display a small intraspecies variation and a larger interspecies variation, enabling one species to be distinguished from other species. In this thesis, DNA markers are described that enable forensically relevant classification of three groups of non-human biological traces: (A) fungi (chapter 1), (B) domestic cats (chapters 2, 3 an d 4) and (C) birch trees (chapters 5 and 6). Because the forensic questions associated with these traces require different levels of classification and the theoretical availability of class specific characteristics varies between the groups studied in these chapters, the different chapters of this thesis illustrate the variation in levels of classification. Additionally, the inheritance of the DNA available for forensic investigations and the reproductive strategies

Outline of this thesis

11

differ between the studied species, thereby influencing the value of being included as member of a certain class. Determining the forensic value of inclusion into a class is therefore included in all chapters and varies considerably. Chapter 1 of this thesis describes the search for a DNA marker that is capable of discriminating between species of mushrooms that are controlled by law and their neighbor species that are not controlled by law. Although from a legal point of view these are distinct classes, these groups are not necessarily biologically distinguishable due to the paraphyletic nature of the classes (comparable to the group of bats designed to play one specific ball game). Chapter 1 focusses on the search for class specific DNA markers for the relevant species, after which the testing of these markers is described and an ideal marker is proposed. The DNA markers studied in chapter 2 have the potential to discriminate between groups of individuals within the species Felis catus (domestic cat). Identification of only the species Felis catus is not often of forensic interest as such. However when cat hairs are encountered as trace evidence, distinguishing between for example the victim’s cat and the suspect’s cat can be

highly relevant, potentially providing a link to a crime scene. In chapter 2, the value of several potentially distinguishing characteristics within the domestic Dutch cat population are described, and a marker is proposed for forensic use. Due to apparent differences between the Dutch cat population and other cat populations described in literature, testing of additional samples from other origins is advised. Adaption of the laboratory procedures used to reliably characterize the DNA markers proposed in chapter 2 not only on high quality samples, but also in forensic case samples such as single shed undercoat hairs is described in the technical note included as chapter 3. Chapter 4 addresses the testing of Belgian, German and additional Dutch cat samples with the DNA markers proposed in chapter 2, through the improved method described in chapter 3, and incorporates published data from the United States of America, Canada, the United Kingdom and Poland. The DNA marker proposed in chapter 2 is considered sufficient for the desired discrimination in North West continental European cats and superior to other described markers. However, major differences between the North West continental European cat population and cats from the United Kingdom, Canada and parts of the United States of America are recognized, leading to the conclusion that although a suitable marker has been found, case specific testing of relevant cat populations may be necessary prior to application in case work especially in regions and localities not covered by the present studies. Additional analysis of the large combined dataset gave rise to certain technical recommendations to improve the nature of the data recorded and published. Analogous to the forensic relevance of distinguishing between cat hairs, indicating that certain botanical traces may have originated from a specific tree can provide information about

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someone’s prior whereabouts. Chapter 5 describes the identification and technical validation of DNA markers suitable to distinguish between individual birch (Betula) trees. Testing these DNA markers on larger numbers of individuals of the two species of birch naturally occurring in the Netherlands, showed greater differences between these two species than between the different locations in which the trees had been sampled, calling for the recording of population data in two different databases. As one of the two species is a diploid species, and the other a tetraploid species, different models to estimate the evidential value of a DNA profile are considered for these two species of trees. Apart from this genetic influence on the estimation of the evidential value, the natural versus human influenced propagation of trees is found to be a factor that needs consideration. Refinement of the method developed in chapter 5 to enable application not only to botanical debris as leaves and twigs but also to seeds is described in chapter 6. Although the DNA markers advised for the DNA typing of birch are no different than the markers described in chapter 5, all technical components involved in obtaining and interpreting a DNA profile have been reconsidered and altered to enable efficient typing of birch seeds allow comparison to profiles from reference trees. The application of this method to an actual forensic case is described. In chapter 7, the findings described in chapters 1-6 are discussed both from an applied forensic biological perspective, but also integrated with perceptions from molecular biology, taxonomy and ecology on one hand, and law, policy making and criminalistics on the other. The scientific advances described in this thesis, and how these could influence court proceedings will also be touched upon.