Georgia Southern University Digital Commons@Georgia Southern Electronic Theses and Dissertations Graduate Studies, Jack N. Averitt College of Fall 2017 A Population Genetic Investigation of the Reticulated Flatwoods Salamander (Ambystoma bishopi) on Eglin Air Force Base Alexander S. Wendt Follow this and additional works at: https://digitalcommons.georgiasouthern.edu/etd Part of the Other Animal Sciences Commons, Other Genetics and Genomics Commons, and the Population Biology Commons Recommended Citation Wendt, Alexander S., "A Population Genetic Investigation of the Reticulated Flatwoods Salamander (Ambystoma bishopi) on Eglin Air Force Base" (2017). Electronic Theses and Dissertations. 1693. https://digitalcommons.georgiasouthern.edu/etd/1693 This thesis (open access) is brought to you for free and open access by the Graduate Studies, Jack N. Averitt College of at Digital Commons@Georgia Southern. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons@Georgia Southern. For more information, please contact [email protected]. A POPULATION GENETIC INVESTIGATION OF THE RETICULATED FLATWOODS SALAMANDER (AMBYSTOMA BISHOPI) ON EGLIN AIR FORCE BASE by ALEXANDER WENDT (Under the Direction of James H. Roberts) ABSTRACT The reticulated flatwoods salamander (RFS) is an endangered salamander with a unique life history. One of the largest known, best studied refuges for RFS is found on Eglin Air Force Base, and these RFS have been sampled and managed extensively since 2010. My thesis seeks to better understand RFS by using genetic techniques to address several unknowns, including: 1) determining the population structuring of RFS and the manageable units for species conservation, 2) estimating the size and status of populations, 3) understanding dispersal of RFS and factors that influence this, 4) exploring the breeding biology and recruitment patterns of RFS and how they affect population sizes, and 5) drawing general conclusions about RFS population biology and recommendations for future management. The first, second, and third objectives are addressed in Chapter 1, by analyzing variation at nuclear microsatellite genetic markers within and among known, extant breeding populations on Eglin to determine the genetic structuring of RFS as well as landscape factors that would influence dispersal between the breeding ponds. The fourth objective is addressed in Chapter 2 and utilizes the same microsatellite markers but focuses on two ponds and two years in which extensive sampling of adult and larval RFS was conducted. The fifth objective is addressed in the General Conclusion section in which I use data from both chapters to provide management suggestions that can be utilized both on Eglin and elsewhere. INDEX WORDS: Reticulated flatwoods salamanders, Ambystoma bishopi, Population genetics, Landscape genetics, Wildlife management A POPULATION GENETIC INVESTIGATION OF THE RETICULATED FLATWOODS SALAMANDER (AMBYSTOMA BISHOPI) ON EGLIN AIR FORCE BASE by ALEXANDER WENDT B.S. Iowa State University, 2013 A Thesis Submitted to the Graduate Faculty of Georgia Southern University in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE STATESBORO, GEORGIA © 2017 ALEXANDER WENDT All Rights Reserved 1 A POPULATION GENETIC INVESTIGATION OF THE RETICULATED FLATWOODS SALAMANDER (AMBYSTOMA BISHOPI) ON EGLIN AIR FORCE BASE by ALEXANDER WENDT Major Professor: James H. Roberts Committee: John S. Harrison Lance D. McBrayer Carola A. Haas Electronic Version Approved: December 2017 2 ACKNOWLEDGMENTS Many thanks to my fellow colleagues, friends, and family that through their assistance and support made my work a possibility. I am grateful to my advisor, Dr. Jamie Roberts, who has taught me so much and helped me grow in my understanding of conservation genetics and given me the tools to be successful in my future career. Thank you for your guidance, patience, and persistence for your students to be the best they can. I would also like to thank Dr. Scott Harrison and Dr. Lance McBrayer of Georgia Southern University, and Dr. Carola Haas of Virginia Tech for serving as members on my thesis committee. Their comments and insight helped with my research and to develop my thesis. Additional thanks to Dr. Harrison for allowing me to use the equipment in his lab and for providing assistance and advice with genetic aspects in my thesis. An additional thank you to Dr. Carola Haas along with Thomas Gorman for spearheading the management and sampling of reticulated flatwoods salamanders on Eglin. The collection of samples from Eglin and management of data was made possible through the assistance of George Brooks, Kelly Jones, Brandon Rincon, Vivian Porter, Houston Chandler, Steve Goodman, A. Hillman, J. Newman, K. Erwin, J. Newton, S. Konkolics, T. Abeles, A. Perez-Umphrey, T. Williams, J. Da Silva Neto, J. Hefner, T. Mammone, B. Moore, A. Saenger, and many others. Without their hard work on Eglin, none of this would have been possible. Over the time I have spent at Georgia Southern, I have had the pleasure of working with lab mates that have helped me and supported me. Many thanks to Jackman Eschenroeder, Garret Strickland, and Rebecca Scott for their help both within the lab and outside of it. From software 3 programs and concepts to labeling tubes you have been a tremendous help and made the Roberts lab a great place to work in. A big thanks to my family and friends who supported me during my time working on my thesis. Thanks to my mother Pam, father Scott, and little (but taller) brother Sam who believed in me and pushed me to finish. 4 TABLE OF CONTENTS ACKNOWLEDGMENTS .............................................................................................................. 2 LIST OF TABLES .......................................................................................................................... 8 LIST OF FIGURES ...................................................................................................................... 11 GENERAL INTRODUCTION ..................................................................................................... 14 Amphibian Global Patterns of Diversity ................................................................................... 14 A Fauna in Decline .................................................................................................................... 16 Diversity and Imperilment of Amphibians in the Southeast United States............................... 20 Pond Breeding Salamanders in the Southeastern United States ............................................... 21 Flatwoods Salamander .............................................................................................................. 23 Eglin Air Force Base Overview ................................................................................................ 25 Purpose of this Study................................................................................................................. 27 References ................................................................................................................................. 29 CHAPTER 1: FACTORS INFLUENCING POPULATION STRUCTURE AND GENE FLOW OF RETICULATED FLATWOODS SALAMANDERS (AMBYSTOMA BISHOPI) ON EGLIN AIR FORCE BASE....................................................................................................................... 47 Abstract ..................................................................................................................................... 47 Introduction ............................................................................................................................... 48 Methods ..................................................................................................................................... 54 Sample Collection.................................................................................................................. 54 5 Laboratory Methods .............................................................................................................. 55 Evaluation of Markers ........................................................................................................... 56 Delineation of Population Structure ...................................................................................... 57 Determining Dispersal between Ponds .................................................................................. 58 Estimation of Effective Population Size and Genetic Diversity ............................................ 59 Landscape Influences on Gene Flow ..................................................................................... 60 Results ....................................................................................................................................... 62 Microsatellite Markers Evaluation ........................................................................................ 62 Delineation of Population Structure ...................................................................................... 63 Dispersal between Ponds ....................................................................................................... 65 Estimation of Population Size and Assessment of Genetic Diversity ................................... 66 Landscape Influences on Gene Flow ....................................................................................