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Genetic Investigations Into the Black Death Genetic Investigations into the Black Death Ph D. Thesis K. Bos; McMaster University Anthropology Genetic Investigations into the Black Death By KIRSTEN BOS, B.Sc. Hon, M.A. A Thesis Submitted to the School of Graduate Studies in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by Kirsten Bos, December 2011 i Ph D. Thesis K. Bos; McMaster University Anthropology McMaster University DOCTOR OF PHILOSOPHY (2011) Hamilton, Ontario (Anthropology) TITILE: Genetic Investigations into the Black Death AUTHOR: Kirsten Bos, BSc. Hon., M.A. (McMaster University) SUPERVISOR: Professor H.N. Poinar NUMBER OF PAGES: xiv, 219 ii Ph D. Thesis K. Bos; McMaster University Anthropology Abstract This dissertation discusses molecular analyses of dental and skeletal material from victims of the Black Death with the goal of both identifying and describing the evolutionary history of the causative agent of the pandemic. Through this work, Yersinia pestis DNA was successfully identified in skeletal material from a well- documented Black Death burial ground, the East Smithfield cemetery of London, England (1348 -1350). The thesis presents two major methodological advancements in the field of ancient pathogen research: 1) it describes a protocol to confirm the authenticity of ancient pathogen DNA, thus circumventing tenuous issues relating to modern contaminants, and 2) it demonstrates the applicability of DNA capture methods to isolate ancient pathogen DNA from its complex metagenomic background common to ancient DNA extracts. The dissertation is comprised of three publications. The first, submitted to the journal BMC Systems Biology, describes a computational software program for oligo design that has applications to PCR, and capture techniques such as primer extension capture (PEC) and array-based capture. The second manuscript, published in the Proceedings of the National Academy of Sciences, presents a novel capture technique for retrieval of the pestis-specific pPCP (9.6kb) plasmid which can be used as a simple screening tool for the presence of Y. pestis DNA in ancient remains, and describes a method for authenticating ancient pathogen DNA. The third paper, published in the journal Nature, presents a draft genome of Yersinia pestis isolated from the individuals of the East Smithfield collection, thus presenting the first ancient pathogen genome in published literature. Evolutionary changes as they relate to phylogenetic placement and the evolution of virulence are discussed within an anthropological framework. iii Ph D. Thesis K. Bos; McMaster University Anthropology Acknowledgements Beyond the many years of hard work that were required of me to complete this document, it simply would not have been possible without the support of many influential people. I thank Hendrik Poinar for his years of tutelage along with his continued faith in both me and the project, for acquainting me with the adaptive and opportunistic aspects of scientific research, and for teaching me that disappointment is simply a matter of perception. I thank Ann Herring for recognising strength in me when I didn’t see it in myself, and for demonstrating that professionalism and friendship can come hand in hand. I’m grateful to all past and present members of the McMaster Ancient DNA Centre who shepherded me through the experimental design features of the project, and provided me with excellent training and scientific advice. I am indebted to Johannes Krause for recognising the potential of the project, for granting me the opportunity to work alongside him at the Max Planck Institute in Leipzig, and for his devotion to seeing the project to completion, even when the powers of Spider-Man were needed. I thank Verena Schuenemann for her impressive and infectious dedication to our shared work. I hold the contributions and comments of all coauthors of my publications in high regard, and I fully appreciate the concerted group effort that made these publications a success. I issue a special ‘thank you’ to Stephen Forrest for his hours happily spent at a computer terminal implementing design features imposed by me, and his enthusiasm for learning the intricacies of DNA capture methods necessary for writing PrimerClique source code appropriately. I thank my committee members Ann Herring, Brian Golding, and external examiner Anne Stone for constructive comments on the dissertation, and I thank Ben Evans and the late Shelley Saunders for their support in earlier phases of my PhD research. Additionally I also thank the late Bill White for granting me access to the material from the East Smithfield collection, Allison Sekuler for expediting my readmission process, and Svante Pääbo for use of his facilities at the Max Planck Institute for Evolutionary Anthropology, especially when timelines were originally optimistic. In addition to posing intellectual challenges, my years as a PhD student tested my emotional strength time and time again. Overcoming these obstacles would not have been possible without the love and unconditional support of my parents Tony and Ferne Bos, and my loving partner (and recent husband) Stephen Forrest. I thank my parents for their listening ears and for their wisdom evident in their sound advice. I thank Stephen for showing enthusiasm for my work (even on days when I did not share it!), iv Ph D. Thesis K. Bos; McMaster University Anthropology for his unyielding belief in my abilities, and for his resounding love that could make it seem like the sun was shining on even the darkest of days. For financial support I thank the Social Sciences and Humanities Research Council of Canada for three years of funding through the Canada Graduate Scholarship programme, the Department of Anthropology of McMaster University for a graduate fellowship, the School of Graduate Studies for travel support, Hendrik Poinar for research, travel, and personal funding, and Stephen Forrest for support throughout the degree, but especially for the post-thesis-submission trip to New York City and the awesome boots. v Ph D. Thesis K. Bos; McMaster University Anthropology TABLE OF CONTENTS Abstract..............................................................................................................................ii Acknowledgements...........................................................................................................iii Table of Contents.............................................................................................................................v List of Figures................................................................................................................................x List of Tables................................................................................................................................xii Declaration of Academic Achievement....................................................................................................................xiii Chapter 1 – Introduction....................................................................................................1 1.1 – History of the Black Death..............................................................................5 1.2 – Contributions of ancient DNA and other Molecular investigations.............13 1.3 – Goals of the current work............................................................................16 1.4 – Contents of the dissertation........................................................................21 Chapter 2 - PrimerClique: Open Source software for design of multiplex primers and array probes for contiguous template coverage..............................................................26 2.1 – Author contributions....................................................................................26 2.2 –Abstract.........................................................................................................27 2.3 – Background..................................................................................................28 vi Ph D. Thesis K. Bos; McMaster University Anthropology 2.4 – Implementation and Features of PrimerClique...........................................31 2.5 – Results and Discussion.................................................................................37 2.6 – Conclusion....................................................................................................41 2.7 – Availability and System Requirements.........................................................43 2.8 – Acknowledgments........................................................................................43 2.9 – References Cited..........................................................................................44 2.10 – Figures........................................................................................................47 Chapter 3 – Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death................................................................50 3.1 – Author contributions...............................................................................................51 3.2 – Abstract...................................................................................................................52 3.3 – Introduction.............................................................................................................53 3.4 – Results.....................................................................................................................55
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