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HOST-PARASITE INTERACTIONS: COMPARATIVE ANALYSES of POPULATION GENOMICS, DISEASE-ASSOCIATED GENOMIC REGIONS, and HOST USE a Diss

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HOST-PARASITE INTERACTIONS: COMPARATIVE ANALYSES of POPULATION GENOMICS, DISEASE-ASSOCIATED GENOMIC REGIONS, and HOST USE a Diss HOST-PARASITE INTERACTIONS: COMPARATIVE ANALYSES OF POPULATION GENOMICS, DISEASE-ASSOCIATED GENOMIC REGIONS, AND HOST USE A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy By SARA ROSE SEIBERT B.S., The Ohio State University, 2010 M.S., Wright State University, 2014 2020 Wright State University WRIGHT STATE UNIVERSITY GRADUATE SCHOOL April 22, 2020 I HEREBY RECOMMEND THAT THE DISSERTATION PREPARED UNDER MY SUPERVISION BY Sara Rose Seibert ENTITLED Host-parasite interactions: comparative analyses of population genomics, disease- associated genomic regions and host use. BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Doctor of Philosophy. __________________________ Jeffrey L. Peters, Ph.D. Dissertation Director __________________________ Mill W. Miller, Ph.D. Director, Biomedical Sciences Ph.D. Program __________________________ Barry Milligan, Ph.D. Interim Dean of the Graduate School Committee on Final Examination: ________________________________ Paula Bubulya, Ph.D. ________________________________ Quan Zhong, Ph.D. ________________________________ Michael Leffak, Ph.D. ________________________________ Oleg Paliy, Ph.D. ________________________________ Philip Lavretsky, Ph.D. (non-voting) ABSTRACT Seibert, Sara Rose Ph.D., Biomedical Sciences Ph.D. Program, Wright State University, 2020. Host-parasite interactions: comparative analyses of population genomics, disease-associated genomic regions, and host use Birds are major vectors and reservoir hosts of pathogens across our globe. Pathogens can be spread through the dispersal and seasonal movements of migratory and resident wild birds. Although biogeographic barriers have the potential to restrict completely or in part gene flow in wild birds, variation in ecological drivers of dispersal likely influences the effectiveness of these barriers amongst different species. This dissertation seeks to enhance our knowledge of Southern Hemisphere waterfowl species’ dispersal, population genomics, and disease ecology using population genomic techniques (double-digest restriction- site associated DNA sequencing (ddRADseq)) and multi-variate statistics. First, we investigated the roles of dispersal behavior and biogeographic barriers in genetically structuring populations of four species of Australasian waterfowl. Additionally, we explored host-parasite theory by comparing the genetic structure of a southern African waterfowl population and its Plasmodium parasite. Next, we identified genomic regions associated with Plasmodium infection in waterfowl using traditional and novel computational methods. Finally, we performed a meta-analysis to create a linear model to explain variation in Plasmodium infection rates in birds using host demographic variables on a global scale. The iii knowledge gained from this dissertation benefits research in the public health, agriculture, and wildlife management fields. iv TABLE OF CONTENTS PAGE Foreword ............................................................................................................. 1 Chapter 1: Southern Hemisphere waterfowl population genomics and phylogeograhy ...................................................................................................... 5 Introduction ................................................................................................ 5 Methods ................................................................................................... 10 Results ..................................................................................................... 17 Discussion ............................................................................................... 27 Conclusions ............................................................................................. 31 Appendix 1 ............................................................................................... 33 Chapter 2: Host-parasite population genomics ................................................... 62 Introduction .............................................................................................. 62 Methods ................................................................................................... 66 Results ..................................................................................................... 74 Discussion ............................................................................................... 85 Chapter 3: Identification of genomic regions associated with Plasmodium infection .............................................................................................................. 90 Introduction .............................................................................................. 90 Methods ................................................................................................... 94 Results ..................................................................................................... 97 Discussion ............................................................................................. 111 Appendix 3 ............................................................................................. 115 Chapter 4: Host demographic variables associated with avian Plasmodium ... 118 Introduction ............................................................................................ 118 Methods ................................................................................................. 121 Results ................................................................................................... 130 Discussion ............................................................................................. 141 Appendix 4 ............................................................................................. 148 Concluding Remarks ........................................................................................ 163 References ....................................................................................................... 166 v LIST OF FIGURES FIGURE PAGE Chapter 1 1.1 Biogeographical barriers in northern Australia and southern Papua New Guinea ....................................................................................................... 7 1.2 Radjah shelduck ........................................................................................... 20 1.3 Wandering Whistling-Duck ........................................................................... 22 1.4 Green Pygmy-Goose .................................................................................... 24 1.5 Pacific Black Duck ....................................................................................... 26 Appendix 1 S2 Double-digest Restriction site Associated DNA sequencing library preparation protocol ................................................................................................... 36 S3 Double-digest Restiction site Associated DNA sequencing bioinformatic pipeline .................................................................................................... 41 S4.1 Heat map for kinship and inbreeding coefficients in Radjah shelduck ........ 44 S4.2 Heat map for kinship and inbreeding coefficients in Wandering Whistling- Duck......................................................................................................... 45 S4.3 Heat map for kinship and inbreeding coefficients in Green Pygmy-Goose 46 S4.4 Heat map for kinship and inbreeding coefficients in Pacific Black Duck ..... 47 S5 Principal Component Analysis R script ......................................................... 48 S6.1 Principal component analysis for Radjah shelduck with sibling groups ...... 50 vi S6.2 Principal component analysis for Wandering Whistling-Duck with sibling groups ...................................................................................................... 51 S7 Non-metric multidimensional scaling R script ................................................ 55 S10.1 Non-metric multidimensional scaling plot for Radjah shelduck ................. 58 S10.2 Non-metric multidimensional scaling plot for Wandering Whistling-Duck . 59 S10.3 Non-metric multidimensional scaling plot for Green Pygmy-Goose ......... 60 S10.4 Non-metric multidimensional scaling plot for Pacific Black Duck .............. 61 Chapter 2 2.1 Range map of Red-billed Duck ..................................................................... 65 2.2 Principal component analysis of Red-billed Duck ......................................... 77 2.3 Maximum likelihood phylogeny of Red-billed Duck nuclear loci .................... 79 2.4 Maximum likelihood phylogeny of Red-billed Duck mitochondrial control region ....................................................................................................... 80 2.5 Maximum likelihood phylogeny of Plasmodium cytochrome b gene ............ 84 Chapter 3 3.1 Host-parasite disease triangle ...................................................................... 91 3.2 ΦST distribution plot for Red-billed Duck ...................................................... 98 3.3 Principal component analysis of Red-billed Duck Plasmodium infected vs. non-infected ............................................................................................ 99 3.4 BayeScan plot for Red-billed Duck for Plasmodium infected vs. non-infected ..............................................................................................................
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