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Enhancing Archaeoparasitology By UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE DIGGING DEEPER: ENHANCING ARCHAEOPARASITOLOGY BY COMBINING MOLECULAR METHODS WITH TRADITIONAL MORPHOLOGICAL APPROACHES A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By LAUREN MARIE CLEELAND Norman, Oklahoma 2015 DIGGING DEEPER: ENHANCING ARCHAEOPARASITOLOGY BY COMBINING MOLECULAR METHODS WITH TRADITIONAL MORPHOLOGICAL APPROACHES A DISSERTATION APPROVED FOR THE DEPARTMENT OF ANTHROPOLOGY BY ______________________________ Dr. Cecil M. Lewis, Co-Chair ______________________________ Dr. Susan C. Vehik, Co-Chair ______________________________ Dr. Tassie Hirschfeld ______________________________ Dr. Patrick Livingood ______________________________ Dr. Paul Lawson © Copyright by LAUREN MARIE CLEELAND 2015 All Rights Reserved. I dedicate this dissertation to the memory of my husband, Peter Riley Cleeland (1966-2012). Acknowledgements I offer my deepest gratitude to the members of my committee, who have encouraged and supported me through the doctoral process. Especially, I thank Dr. Cecil Lewis and Dr. Susan Vehik for their guidance and the gift of their knowledge, and supporting me through the loss of my husband, which delayed this process. I thank Dr. Tassie Hirschfeld for her insight and direction in thinking about the modern implications of prehistoric parasite work. I thank Dr. Patrick Livingood for his wisdom and enthusiasm and his willingness to always discuss a variety of topics. I thank Dr. Paul Lawson for bringing a broader ecological consideration to the study of prehistoric parasitism. I thank the University of Oklahoma Graduate School for providing the opportunity for me to study and gain the experience I need to master the concepts that have culminated in this dissertation. I thank the Department of Anthropology for their support and guidance. I thank Raul Tito for all of his help in the lab and in sharing his molecular expertise. I especially thank Dr. Robert Brooks for his support and technical help. I thank the Oklahoma Department of Health and the Texas State Department of Health, specifically, Michael Lytle and Cathy Snider for donations of modern parasite material for use in the development of positive control samples and primer design. I thank Dr. Lewis A. Hassell, from the Oklahoma Health Sciences, Department of Pathology for his contributions to parasite samples. iv Finally, I thank my family, specifically my mother and siblings and my children who sacrificed much so that I might attend the university. Much thanks as well to my friends, especially, Simone Bachmai Rowe for her willingness to push and prod and advise as well as encourage and support this endeavor. Most importantly, I thank, Fr. William Ross for all of his support throughout my educational experience, and my husband, Peter Cleeland, although both are no longer with us, without their insistence and encouragement and great sacrifice this educational journey would never have found fruition. v Table of Contents Acknowledgements ............................................................................................iv List of Tables .................................................................................................... viii List of Figures .....................................................................................................ix Abstract ..............................................................................................................xi Chapter 1: Introduction ....................................................................................... 1 La Cueva de los Muertos Chiquitos, El Zape, Durango, Mexico ................... 9 DNA Sequencing: Sanger and Next-Generation Technology ..................... 18 Ancient DNA Technologies: PCR and NGS ................................................ 25 Coprolites .................................................................................................... 34 Coprolites and Parasites ............................................................................. 36 Sanger Sequencing and Paleoparasitology ................................................ 39 Coprolites: Next Generation Sequencing .................................................... 45 Human Parasitism ....................................................................................... 46 Caveat on Coprolite Identification of Origin ................................................. 52 Chapter Three: Methodology ............................................................................ 57 Preparatory Methods: Positive Controls ...................................................... 59 Alternate Positive Control Samples ............................................................. 60 Primer Choice and Design .......................................................................... 61 Sample Origin ............................................................................................. 61 Sample Preparation .................................................................................... 62 Rehydration ................................................................................................. 63 Morphological Analysis ............................................................................... 63 vi Microscope Slide Extraction ........................................................................ 64 Ancient DNA Extraction ............................................................................... 65 PCR Amplification ....................................................................................... 65 Sequencing ................................................................................................. 69 Cloning ........................................................................................................ 69 Phylogenetic Tree Building ......................................................................... 70 NGS – Whole Genome Shotgun Data Analysis .......................................... 70 Chapter Four: Results and Discussion ............................................................. 76 Discarding Zape 29 ..................................................................................... 77 Identification of Coprolite Origin .................................................................. 77 Morphological Analysis ............................................................................... 79 PCR Amplification – Microscope slide......................................................... 80 PCR Results – Ancient DNA Material ......................................................... 85 Additional Primer Design ............................................................................. 85 Phylogenetic Tree Construction .................................................................. 86 Difficulty in Diagnosis of Physaloptera Infection .......................................... 89 Importance of Physaloptera Infection in Humans ........................................ 90 Next Generation – Whole Genome Sequencing Results ............................ 93 Chapter Five: Conclusion ............................................................................... 104 References ..................................................................................................... 108 Appendix A: Timeline of aDNA and Parasites ................................................ 133 Appendix B: PCR Results for Zape 23 ........................................................... 135 Appendix C: First Contact: Archaeologists and Molecular Work .................... 139 vii List of Tables Table 1: General Criteria of Authenticity based on a version from Poinar (2003) and modifications from Kemp and Smith (2010a). ............................................ 31 Table 2: Intestinal parasites identified in prehistoric humans up to 1985. ........ 38 Table 3: Previously published Ascaris primer sets ........................................... 66 Table 4: PCR Thermocycler Parameters for Ascaris Primers ........................... 66 Table 5: Physaloptera primer set designed for this study. ................................ 66 Table 6: PCR Thermocycler Parameters for Physaloptera primers. ................. 67 Table 7: 454 pyrosequencing data sets as originally processed in the MG-Rast pipeline. Hits suggest sequence matches. ....................................................... 71 Table 8: Filtering steps and retained sequences. ............................................. 73 Table 9: NCBI database descriptions ............................................................... 75 Table 10: Taxonomy Comparison of Physaloptera spp., Ascaris spp., and Contracaecum spp. .......................................................................................... 82 Table 11: Final results of NEMBASE4 search, after filtering. ........................... 96 Table 12: Results of BLAST searches for Zape 23 NGS-WGS data. ............... 97 Table 13: Appendix A:Photos Taken During Microscopy for Zape Samples .. 133 Table 14: Appendix B: Zape 23 PCR/Sequencing Results ............................. 135 Table 15: Appendix C: Comparison of Journals Used by Archaeologists and Journals with Published Calls to Archaeologists, those in bold intersect. ....... 153 viii List of Figures Figure 1: 1400 year-old Ascarid suspect from La Cueva de los Muertos Chiquitos, sample number 29, recovered from unit B4 during 1957 Excavations. Photo Taken at 400x magnification.
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