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Ancient Metaproteomics: a Novel Approach for Understanding Disease And Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ................................................................................................................................ iii List of Contents ...................................................................................................................... v List of Figures ...................................................................................................................... xv List of Tables...................................................................................................................... xix Acknowledgements .......................................................................................................... xxiii Author’s Declaration .......................................................................................................... xxv Chapter 1: Research Framework and Aims ........................................................................... 1 1.1 Research Context and Significance ................................................................................... 1 1.2 Aims .................................................................................................................................. 1 1.3 Thesis Structure and Outline ............................................................................................. 3 1.3.1 Chapter Outline .......................................................................................................... 3 1.3.2 Appendices ............................................................................................................... 10 1.4 Research Network: EUROTAST .................................................................................... 11 1.5 Statement on Language ................................................................................................... 11 1.6 Data Deposition ............................................................................................................... 13 Chapter 2: Introduction to Methods ..................................................................................... 15 2.1 Introduction to Palaeopathology ..................................................................................... 15 2.1.1 Palaeomicrobiology, Infectious Diseases and the Microbiome ............................... 16 2.2 The Study of Past Diseases ............................................................................................. 18 2.2.1 Historical Records .................................................................................................... 19 v 2.2.2 Osteological Observation .......................................................................................... 19 2.2.3 Biomolecular Palaeopathology ................................................................................. 21 2.3 Ancient DNA and Ancient Genomics ............................................................................. 22 2.3.1 Introduction to DNA ................................................................................................. 23 2.3.2. Ancient DNA ........................................................................................................... 24 2.3.3 Applications of Ancient DNA .................................................................................. 26 2.3.4 Ancient DNA and Disease ........................................................................................ 26 2.3.5 Challenges of Ancient DNA Research ..................................................................... 29 2.4 Ancient Proteins and Ancient Proteomics ....................................................................... 31 2.4.1 Introduction to Proteins and the Proteome ............................................................... 31 2.4.2 The Development of Ancient Proteins ..................................................................... 34 2.4.3 Protein Mass Spectrometry ....................................................................................... 35 2.4.4 Applications of Ancient Proteins .............................................................................. 39 2.4.5 Ancient Proteins and Disease ................................................................................... 41 2.5 Dental Calculus ................................................................................................................ 43 2.5.1 Introduction to Dental Calculus ................................................................................ 44 2.5.2 Dental Calculus as an Archaeological Resource ...................................................... 46 2.5.3 Biomolecular Applications of Dental Calculus ........................................................ 47 2.5.4 Potential of Dental Calculus ..................................................................................... 49 Chapter 3: Historical Background and Introduction to Case Study .................................. 51 3.1 Introduction to the Transatlantic Slave Trade ................................................................. 51 3.1.1 The Transatlantic Slave Trade in the 19th Century and its Abolition ....................... 52 3.1.2 The West-African Squadron ..................................................................................... 55 vi 3.2 Introduction to St Helena ................................................................................................ 55 3.2.1 The “Liberated African Establishment” ................................................................... 57 3.2.2 Archaeological Excavations ..................................................................................... 58 3.3 The Study of Disease in the Transatlantic Slave Trade .................................................. 59 3.3.1 Historical Sources .................................................................................................... 61 3.3.2 Osteological Investigations ...................................................................................... 64 3.4 Rates of Mortality in the Transatlantic Slave Trade ....................................................... 68 3.5 Diseases Associated with the Transatlantic Slave Trade ................................................ 70 3.5.1 Infectious Diseases ................................................................................................... 70 3.5.2 Parasitic Diseases ..................................................................................................... 78 3.5.3 Nutritional Diseases ................................................................................................. 80 3.6 Diseases at St Helena ...................................................................................................... 82 3.6.1 Diseases Documented in Historical Sources ............................................................ 82 3.6.2 Osteologically Identified Diseases ........................................................................... 84 3.6.3 Ethical Considerations ............................................................................................. 85 3.7 Legacies of Diseases of the Transatlantic Slave Trade ................................................... 86 Chapter 4: Disease and Dental calculus: A Novel Biomolecular Perspective on the Transatlantic Slave Trade ...................................................................................................... 89 Abstract ................................................................................................................................. 89 4.1 Health and Disease in the Transatlantic Slave Trade ...................................................... 90
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