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(SNP) Resources for Black Bass (Micropterus Spp.) Conservation and Management

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(SNP) Resources for Black Bass (Micropterus Spp.) Conservation and Management Utility of Single Nucleotide Polymorphism (SNP) Resources for Black Bass (Micropterus spp.) Conservation and Management by Lauren E. Davis A thesis submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Master of Science Auburn, Alabama May 6, 2018 Keywords: Single Nucleotide Polymorphism, hybridization, Micropterus Copyright 2018 by Lauren E. Davis Approved by Eric Peatman, Associate Professor; School of Fisheries Aquaculture and Aquatic Sciences Matt Catalano, Assistant Professor; School of Fisheries Aquaculture and Aquatic Sciences Steven Sammons, Research Fellow; School of Fisheries Aquaculture and Aquatic Sciences Benjamin Beck, Research Leader; USDA-ARS, Auburn AL Abstract The black basses (Micropterus spp.) are a genus of apex predators and important game fishes in North American freshwater ecosystems. Efforts to improve recreational bass fisheries have led to the widespread stocking of black bass species, often facilitating introgressive hybridization between endemic and non-native species. Phenotypic differentiation of black bass species and their hybrids is notoriously unreliable. Molecular tools are needed to rapidly and accurately assess bass populations, whether they are intensively managed in a reservoir or the target for conservation in un-impacted streams. My thesis describes the development and application of practical tools to better integrate molecular analyses with black bass conservation and management. Following a review of pertinent literature in Chapter I, in Chapter II I detail the development, validation, and field-testing of a methodology to collect bass DNA through buccal swabbing. This method is simple, robust, and cost-effective, allowing angler involvement in genetic sample collection from bass populations otherwise difficult to obtain. In Chapter III, I utilize recently developed diagnostic black bass single nucleotide polymorphism (SNP) marker panels to provide one of the first genetic analyses of black bass populations in the Altamaha River Basin (ARB). My results, from over 500 individuals, shed light on the status of introduced Spotted Bass (M. punctulatus) in the basin, hybridization patterns of introduced Shoal Bass (M. cataractae), and provide an important revision to the accepted intergrade status of native Largemouth Bass in the drainage. I also provide evidence pointing to the presence of a genetically distinct bass in the ARB Coastal Plain, deserving of closer scrutiny in the future. ii Acknowledgments I would like to thank my advisor and mentor, Dr. Eric Peatman, for giving me the opportunity to pursue a master’s degree and for his guidance and support during the process. I would also like to thank my committee members, Dr. Matt Catalano, Dr. Steven Sammons, and Dr. Benjamin Beck for their time and assistance on this project. I would like to thank my lab members, Wilawan Thongda and Honggang Zhao, for their guidance in the lab and helping me to perform the genetic analyses for my work. I also would like to thank the rest of my lab members, Dr. Haitham Mohammed, Taylor Brown, James Mazzola, Dongdong Zhang, Sarah Johnson, and Megan Roberts for their support over the course of my time here. I would like to thank the ADCNR for providing funding for my project, which gave me the opportunity to study at Auburn University. Thank you to Graves Lovell, for helping me to collect samples for the second chapter of my project. Thank you as well to the GADNR biologists for providing samples for the third chapter of my project. Lastly, I would like to thank my parents, Jane Burns, Craig Davis, and Ivey Burns for their love and continued support during this process. iii Table of Contents Abstract ......................................................................................................................................... ii Acknowledgments........................................................................................................................ iii List of Tables ............................................................................................................................... vi List of Figures ............................................................................................................................. vii List of Abbreviations ................................................................................................................. viii Chapter I: Literature Review ...................................................................................................... 1 Black Basses ................................................................................................................... 2 Conservation Concerns ................................................................................................. 10 Molecular Mark Tools and Approaches for Black Basses ............................................ 13 Chapter Overviews ........................................................................................................ 22 References ..................................................................................................................... 24 Chapter II: Development of a Swab Protocol for an Angler-Driven Program to Promote the Genetic Assessment of Black Bass Populations ....................................................................... 34 Introduction ................................................................................................................... 35 Materials and Methods .................................................................................................. 37 Results ........................................................................................................................... 46 Discussion ..................................................................................................................... 56 References ..................................................................................................................... 59 iv Chapter III: Evaluation of Black Bass Purity and Hybridization in the Altamaha River Basin Using Species-Diagnostic SNP Markers ................................................................................. 61 Introduction ................................................................................................................... 62 Materials and Methods .................................................................................................. 65 Results ........................................................................................................................... 72 Discussion ..................................................................................................................... 87 References ..................................................................................................................... 93 Appendix I ................................................................................................................................ 96 Appendix II ............................................................................................................................. 115 Appendix III ............................................................................................................................ 130 Appendix IV ............................................................................................................................. 135 Appendix V .............................................................................................................................. 136 v List of Tables Table 1 ....................................................................................................................................... 44 Table 2 ....................................................................................................................................... 47 Table 3 ....................................................................................................................................... 48 Table 4 ....................................................................................................................................... 50 Table 5 ....................................................................................................................................... 51 Table 6 ....................................................................................................................................... 52 Table 7 ....................................................................................................................................... 54 Table 8 ....................................................................................................................................... 55 Table 9 ....................................................................................................................................... 69 Table 10 ..................................................................................................................................... 71 Table 11 ..................................................................................................................................... 73 Table 12 ..................................................................................................................................... 74 Table 13 ..................................................................................................................................... 76 Table 14 ....................................................................................................................................
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