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Under the Direction of Dr ABSTRACT COPE, WILLIAM ROBERT. Status, Trends, Habitat, and Genetics of the Endemic Carolina Madtom. (Under the direction of Dr. Thomas J. Kwak) Nongame fishes contribute to diversity and important ecological functions in freshwater ecosystems, but many are imperiled, and their status and ecology are poorly understood. Instream habitat loss and degradation are major threats among nongame species as degraded and fragmented habitat affects fish directly, but also divides species into multiple small populations, which may be at greater risk for loss of genetic variation or extirpation. One such imperiled, nongame species is the Carolina Madtom (Noturus furiosus), a small catfish endemic to the Tar and Neuse river basins of North Carolina. Systematic surveying has shown declines in Carolina Madtom populations, and as such, the species is listed as State Threatened. Although populations are declining, the Carolina Madtom has been sparsely studied, with only three major surveying events describing and assessing extant population status, and no genetic research has been conducted on the remaining populations. The objectives of this research were to assess the population status, microhabitat use, and genetic structure of the Carolina Madtom to inform protective listing and management decisions for this understudied species. We snorkel surveyed for Carolina Madtoms at 75 sites in the Tar and Neuse river basins during 2016 and 2017. Microhabitat data were collected at all surveyed sites and at points-of-capture for all Carolina Madtoms. Additionally, artificial cover units were constructed and deployed at 8 sites to determine if they could be an effective passive sampling technique for Carolina Madtoms. All captured Carolina Madtoms were fin-clipped for genetic structure and diversity analyses. We collected 59 Carolina Madtoms during snorkel surveys in the Tar River basin, whereas no fish were collected from the Neuse River basin. Occupancy modeling estimated Carolina Madtom occupancy probability at 0.35 and detection probability at 0.81, with dominant substrate particle size affecting occupancy and mean-column water velocity affecting detection probability. Analysis of microhabitat use and available microhabitat among sites found that Carolina Madtoms nonrandomly select microhabitat. Habitat suitability functions were developed, and we determined the most suitable ranges of microhabitat parameters for Carolina Madtom occupancy. Comparison of available suitable habitat in the Tar and Neuse river basins determined that adequate suitable habitat was available in the Neuse River basin. Thirty Carolina Madtoms were collected from artificial cover units at 2 sites in the Tar River basin. Occupancy modeling estimated Carolina Madtom detection probability using artificial cover units at 0.92. Compared to other standardized survey methods, artificial cover units were found to be an efficient, passive sampling technique for detecting Carolina Madtoms. Observations also revealed that artificial cover units were used in reproduction by Carolina Madtoms. Using 10 microsatellite primers developed for the related Yellowfin Madtom (Noturus flavipinnis), we successfully identified genetic structure of the Carolina Madtom. Resulting analyses quantified low genetic diversity in the species. Mean M-ratios for the Tar and Neuse river basin populations indicated that both populations have experienced demographic bottlenecks, and effective population size (Ne) estimates for the respective populations were small, indicating low genetic diversity within populations. However, multilocus population differentiation metrics G’EST and DEST were significantly different from zero indicating significant genetic variation between the Tar and Neuse river basin populations. The application of these results may inform natural resource managers on the status of the extant populations, habitat use, and genetic structure of the Carolina Madtom and guide planning toward informed protective listing and management decisions to maintain the viability of this important endemic species. © Copyright 2018 by William Robert Cope All Rights Reserved Status, Trends, Habitat, and Genetics of the Endemic Carolina Madtom by William Robert Cope A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Master of Science Fisheries, Wildlife, and Conservation Biology Raleigh, North Carolina 2018 APPROVED BY: _____________________________ _____________________________ Dr. Thomas J. Kwak Dr. Tyler R. Black Chair of Advisory Committee _____________________________ Dr. Krishna Pacifici DEDICATION To my parents and family. Thank you for the support, encouragement, and love — I wouldn’t be where I am without you. ii BIOGRAPHY I was born in La Crosse, Wisconsin, in 1993, but I moved to North Carolina at the age of four and have lived here ever since. My interests in aquatic fauna began long ago, as I grew up fishing with my family all over the place, in ponds, lakes, and rivers. As I grew older, my love for fish and other aquatic life only became stronger. With the aid of my father, I had numerous opportunities to explore the field. At the age of 14, I was already working with freshwater mollusks as part of a North Carolina Wildlife Resource Commission research project. From there, my experience only grew. I participated in summer research internships with Dr. Damian Shea and Dr. Tom Kwak at North Carolina State University, assisting graduate students and fellow researchers on a variety of freshwater fish and mollusk ecology and toxicology projects while attending Apex High School. I graduated from Apex High School in 2011 and was accepted into the Honors College at East Carolina University. I already knew fisheries science was my passion, but my time at East Carolina was invaluable in furthering my knowledge of aquatic systems and helping prepare me for a future in fisheries. A requirement of the Honors College was the completion of an undergraduate thesis, and with the help of Dr. Joe Luczkovich, I researched and wrote a report on the diet composition of two co-occurring, closely-related Silverside species in the Pamlico and Albemarle sounds of North Carolina. This project also gave me a chance to get a glimpse into the professional fisheries world, as I was able to present this research at an annual Tidewater Chapter of the American Fisheries Society meeting. I graduated from East Carolina in 2015 with a B.S. in Biology, and I accepted this M.S. position with Dr. Kwak at NC State. My time here has been an amazing experience. I have spent the past three years learning much about fisheries science and how to achieve as a fisheries iii professional through taking classes, conducting research, and presenting research at multiple American Fisheries Society meetings, as well as serving as President of the NC State Student Fisheries Society. I hope to continue my education after completing this degree and am positive my experiences at NC State have helped me become a better researcher and scientist so that I may pursue a professional career in aquatic sciences after I finish my academic career. iv ACKNOWLEDGEMENTS First, I would like to thank my advisor, Dr. Tom Kwak, for his continuous guidance and support. I have grown as a person and a biologist as a result of your teachings and encouragement over the many years of working and researching with you. I would also like to thank Dr. Krishna Pacifici and Dr. Tyler Black who have been fantastic mentors and committee members. Thank you both for the guidance and assistance in the background research, long field work hours, methodology, and analyses to ensure we completed the most accurate research possible. All your mentorship and advice has been invaluable and has helped me become a better fisheries researcher. I would also like to acknowledge numerous individuals who provided immense support on this project. Thanks to Dr. Eric Hallerman and his students, Shelia Harris and Caitlin Miller, at Virginia Tech University for their support with the genetic analyses and guiding me through the murky waters of conservation genetics. Thanks also to the North Carolina Wildlife Resources Commission biologists who assisted in making this project successful. I am grateful to Chris Wood for the insight and prior knowledge on the Carolina Madtom, ensuring I had all the necessary information to successfully survey the species and to Tom Fox and his field technicians who spent many long hours on the river with me searching for a seemingly invisible fish. Thank you to my two awesome field technicians, Will Wood and Joseph McIver, for putting up with my nonsense for months on end and keeping a positive attitude and hardworking mentality even with the long hours, uncooperative weather, and a lack of fish that would drive anybody insane. Thanks to Ruby Valeton for the support and for keeping things moving smoothly on the administrative front, and also to Spencer Gardner, Tiffany Penland, Gus Engman, Sean Buczek, Jennifer Archambault, and the rest of the NC State University professors, staff, graduate, and undergraduate students that helped and supported me throughout my time here at NC State. A v special thanks to Stephen Parker and Emilee Briggs for being the best friends and colleagues a person could want and for supporting and challenging me to be the best researcher possible, while keeping me sane during the arduous process of writing a thesis — you two are the best. I would like to thank my family for being a constant source of support, encouragement, and love. Having a support group just a short drive away has been a blessing during the trying times during research and writing and I would not be the person I am today without your guidance. I thank you all for always pushing me to do my best, be the best person possible, and encouraging me to take risks and shoot for the stars. Finally, I would like to acknowledge the various agencies that made this project possible. I would like to thank the North Carolina Wildlife Resources Commission for funding the project under the State Wildlife Grants program and specifically Todd Ewing for grant administration.
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