Georgia Southern University Digital Commons@Georgia Southern Electronic Theses and Dissertations Graduate Studies, Jack N. Averitt College of Spring 2017 Assessing the Genetic Status and Factors Leading to the Decline of the Roanoke Bass (Ambloplites Cavifrons) Jackman C. Eschenroeder Follow this and additional works at: https://digitalcommons.georgiasouthern.edu/etd Part of the Ecology and Evolutionary Biology Commons Recommended Citation Eschenroeder, J.C. Assessing the genetic status and factors leading to the decline of the Roanoke bass (Ambloplites cavifrons). MS thesis. Georgia Southern University, 2017. 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]. ASSESSING THE GENETIC STATUS AND FACTORS LEADING TO THE DECLINE OF THE ROANOKE BASS (AMBLOPLITES CAVIFRONS) by JACKMAN ESCHENROEDER (Under the direction of James H. Roberts) ABSTRACT Although numerous factors have led to the staggering declines in freshwater biodiversity throughout the United States and the world, habitat alteration and introduced species pose some of the greatest challenges to conservation efforts. Learning more about how these two factors lead to the decline of an endemic organism could help prevent the future loss of unique species and the premature conclusion of evolutionary trajectories. Roanoke bass (Ambloplites cavifrons) is a sport fish endemic to portions of the Roanoke, Chowan, Tar, and Neuse river basins of North Carolina and Virginia. This species has been in decline for many years, and it is believed that their continued existence is threatened by competition, and potentially hybridization and introgression with their introduced relative, the rock bass (Ambloplites rupestris). In addition to interactions with this invasive species, significant alteration of habitat is likely also a contributing factor in the decline of A. cavifrons. This study seeks to evaluate the relative contributions of these various factors to the decline of A. cavifrons. I utilized a combination of nuclear markers and mitochondrial sequence data to address the question of whether or not the two species are hybridizing in areas of syntopy, and furthermore to determine whether hybrids are fertile and able to breed back with the parental species. In addition, I identified extant populations of A. cavifrons throughout their historic range, and evaluated the genetic diversity of these populations and correlated these values with changes to the landscape in the form of alterations to watershed land use and the construction of impoundments. My results indicate large portions of the historic range of A. cavifrons no longer contain the species, and that remaining populations occur at the stream level and exist in isolation from one another. Obtaining this information allows for a better understanding of the current state of this unique species, provides information that may help managers prevent its disappearance from its native range, and affords insight into the interactions of an introduced and a native species in a landscape that has been heavily altered by human activity. INDEX WORDS: Hybridization, Conservation genetics, Invasive species ASSESSING THE GENETIC STATUS AND FACTORS LEADING TO THE DECLINE OF THE ROANOKE BASS (AMBLOPLITES CAVIFRONS) by JACKMAN ESCHENROEDER B.S. University of Missouri, 2014 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 JACKMAN ESCHENROEDER All Rights Reserved 1 ASSESSING THE GENETIC STATUS AND FACTORS LEADING TO THE DECLINE OF THE ROANOKE BASS (AMBLOPLITES CAVIFRONS) by JACKMAN ESCHENROEDER Major Professor: James H. Roberts Committee: Stephen P. Vives John S. Harrison Electronic Version Approved: May 2017 2 ACKNOWLEDGEMENTS My work would not have been possible without the support and assistance of numerous colleagues, friends, and family members. I am proud of the work I have conducted in my time as a master’s student, but my thesis is truly an accomplishment to be shared with everyone who helped me along the way. Many thanks are owed to the people who helped bring this project to fruition before I even became a part of it. Mike Pinder was instrumental to the realization of this project, and provided invaluable assistance with field work and logistics. The collection of samples from Virginia was also made possible through the cheerful assistance of Rob Adams, Eric Brittle, Preston Chrisman, Nicole Kmetz, Brian Parks, Brandon Plunkett, Scott Smith, and Derek Wheaton. Paul Angermeier kindly provided equipment resources for field studies. Obtaining North Carolina samples was made possible through the hard work of Corey Oakley, who also has the distinction of being the fishing guide who helped me catch my very first Roanoke bass. Over the course of my two years at Georgia Southern, I have had the good fortune of working with excellent lab mates. Many thanks to Alex Wendt, Garrett Strickland, and Becky Scott for the numerous times they helped me to struggle my way through troubleshooting software programs and molecular techniques, and also for providing a wonderful lab community in which to work. I am glad to have had the opportunity to work and learn with each of them. I would also like to thank Scott Harrison and Stephen Vives for serving as members on my thesis committee. Their insightful comments and suggestions aided my research and in the creation of a meaningful and scientifically sound thesis. Additional thanks are due to Scott Harrison for allowing me use of the equipment in his laboratory to process my samples and for providing assistance and advice that greatly contributed to the achievement of genetic objectives. 3 I cannot over emphasize the thanks owed to my advisor, Jamie Roberts. Under his mentorship I have learned more about molecular analysis, conservation genetics, and fish ecology than I thought possible. His guidance has allowed me to develop into the scientist I want to be, and my current and future success as a biologist I largely attribute to him. I am proud to have been his first graduate student, and I will always consider him not only a colleague but also a friend. My most profound thanks to my family and friends, who tirelessly provided me with the support (and occasional prodding) necessary to help me accomplish my goals. Thanks to my mother Kelly, father Richard, and sisters Corinne and Grace who believe me to be much smarter than I am, and who never doubted my capability. Finally, a special thanks to my partner Shelby Rudolph, whose continuous love, encouragement, and patience gave me the strength I needed to persevere and succeed. 4 TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................................ 2 LIST OF TABLES .......................................................................................................................... 6 GENERAL INTRODUCTION ..................................................................................................... 12 REFERENCES ............................................................................................................................. 17 CHAPTER 1 ................................................................................................................................. 20 ABSTRACT .................................................................................................................................. 20 INTRODUCTION ........................................................................................................................ 21 METHODS ................................................................................................................................... 28 Sample Collection ................................................................................................................................................... 28 Laboratory Methods ............................................................................................................................................... 29 Data Analysis .......................................................................................................................................................... 29 RESULTS ..................................................................................................................................... 33 DISCUSSION ............................................................................................................................... 38 REFERENCES ............................................................................................................................. 47 CHAPTER 2 ................................................................................................................................. 64 ABSTRACT .................................................................................................................................. 64 INTRODUCTION ........................................................................................................................ 65 METHODS ..................................................................................................................................