ESTIMATING POPULATION DISTRIBUTION AND ABUDANCE USING OCCUPANCY AND DETECTION MODELS A Thesis by CHANTELLE LEIGH RONDEL Submitted to the Graduate School at Appalachian State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2019 Department of Biology ESTIMATING APPALACHIAN ELKTOE DISTRIBUTION AND ABUNDANCE USING OCCUPANCY AND DETECTION MODELS A Thesis by CHANTELLE LEIGH RONDEL August 2019 APPROVED BY: Michael M. Gangloff, Ph.D. Chairperson, Thesis Committee Zachary J. Farris, Ph.D. Member, Thesis Committee Lynn M. Siefferman, Ph.D. Member, Thesis Committee Zack E. Murrell, Ph.D. Chairperson, Department of Biology Mike J. McKenzie, Ph.D. Dean, Cratis D. Williams School of Graduate Studies Copyright by Chantelle Leigh Rondel 2019 All Rights Reserved Abstract ESTIMATING APPALACHIAN ELKTOE DISTRIBUTION AND ABUNDANCE USING OCCUPANCY AND DETECTION MODELS Chantelle Leigh Rondel B.S., Western Carolina University M.S., Appalachian State University Chairperson: Michael M. Gangloff, Ph.D. Understanding the factors influencing the abundance, density, occupancy and detectability of endangered species is a critical component of managing at-risk species. However, to date few studies have attempted to incorporate detectability into estimates of endangered freshwater mussel population size or occupancy. The Appalachian elktoe (Alasmidonta raveneliana) is an endangered freshwater mussel endemic to the upper Tennessee River Drainage. I studied an Appalachian elktoe population in the South Toe River in Yancey County, North Carolina and used a 3-pass mark-recapture study to model mussel detectability and occupancy at long-term monitoring sites. I used models that accounted for imperfect detection and allowed me to estimate capture, recapture, occupancy, and detection probability while incorporating habitat, mussel behavior, and sampling covariates. Appalachian elktoe capture probability ranged from p = 0.582 ± 0.035 to p = 0.685 ± 0.031 and was most influenced by substrate composition whereas recapture probability ranged from c = 0.372 ± 0.019 and c = 0.376 ± 0.022 and was most influenced by mussel length and substrate composition. Probability of occupancy was influenced by iv substrate type and current velocity and detectability was influenced by depth, searcher experience and the percentage of bedrock cover. Model-averaged occupancy and detection estimates were Ψ = 0.778 ± 0.067 and p = 0.550 ± 0.063. This study represents the first large- scale, empirical estimate of Appalachian elktoe population size, detectability and occupancy and serves as a model for future distribution and status surveys for this species and with a framework for collecting robust and precise population estimates for freshwater mussel populations. Future studies of Appalachian elktoe should include habitat modeling to identify occupied habitats and improve search effectiveness while obtaining data that may be useful to long-term monitoring in dynamic headwater streams. v Acknowledgments I would first like to thank the North Carolina Department of Transportation for funding this research; the financial support helped with field expenses and labor compensation. Next, I would like to thank my advisor Dr. Mike Gangloff for taking a chance on me and accepting me into his lab with minimal prior field experience. Mike has been a patient mentor and teacher as I learn ecological concepts, aquatic systems and canoeing and has supplied endless burritos before and after long field days. I would also like to thank my committee member Dr. Zach Farris for allowing me to ask hundreds of modeling questions and for providing me with encouraging words during our morning meetings as I was running my analyses. Next, I would like to express my appreciation for Dr. Lynn Siefferman for providing helpful experimental design and thesis feedback as one of my committee members and also making me feel like a part of the family. I would like to thank Jay Mays of the U.S. Fish and Wildlife Service for helping guide this research project as well as providing a helping hand and encouragement in the field. This work could not have been possible without the prompt and reliable help I received in the field from Luke Etchison and Dylan Owensby. I will also be forever indebted to the following Aquatic Conservation Research Lab members, in no particular order: Freddy Ortega Jr., Chrissy Verdream, Sam Fritz, Hans Lohmeyer, Elizabeth Branch, Amber Olson, Jon Wells, Gretchen Bailey, and Jason Selong for their support and help in the field. Special thanks Vincent Santini for his extensive help in the field and the maps, videos, and pictures vi he has supplied for numerous reports, presentations, and this thesis. I would also like to specially thank Michael Thompson for not only his help in the field, but being voice of reason during some of the longest days. I would like to next express my gratitude to Ashley Yaun and Tori Fowler. Ashley has helped me with field and lab work, and provided an immense amount of emotional support. I am honored to have had her as a lab mate, roommate, and most importantly, a friend throughout these the past two years. Tori was a vital part of the completion of my field work, providing both a helping hand and endless entertainment during field work. She was and is a lab mate and a friend that I could count on to support me during graduate school. I would like to next thank my friends and family for supporting me, and listening to me ramble about the importance of freshwater mussels. I would also like to express my appreciation to my mom and step-dad, Darlene and Brian Asher, for always encouraging me to achieve my goals, no matter how lofty they are. Without their support and love, I wouldn’t have achieved a master’s degree. I would also like to thank my papaw, Charles Pendergrass, for taking me fishing and being the source of my love for wildlife. Finally, I would like to give infinite thanks to my fiancé, Grant Hoffner, who has provided patience throughout my time as a graduate student. His encouraging talks allowed me to achieve the seemingly impossible. vii Dedication I dedicate this thesis to Melody Ledford Pendergrass (July 6th, 1950 – December 18th, 2017) who provided me with an excellent example of hard-work and determination. viii Table of Contents Abstract .............................................................................................................................. iv Acknowledgments.............................................................................................................. vi Dedication ........................................................................................................................ viii List of Tables .......................................................................................................................x List of Figures ................................................................................................................... xii Foreword .......................................................................................................................... xiv Introduction ..........................................................................................................................1 Methods................................................................................................................................6 Results ................................................................................................................................16 Discussion ..........................................................................................................................20 References ..........................................................................................................................32 Appendix A ........................................................................................................................59 Vita .....................................................................................................................................60 ix List of Tables Table 1. Covariates for mark-recapture modeling of Appalachian elktoe historical sites in the South Toe River with corresponding definitions and units..........................................41 Table 2. Covariates for mark-recapture modeling of only historical South Toe Site 2 with corresponding definitions and units ...................................................................................42 Table 3. Covariates for occupancy modeling at historic Appalachian elktoe sites in the South Toe River with corresponding definitions and units ...............................................43 Table 4. Beta estimates from the top-ranked mark-recapture model for six historical Appalachian elktoe sites in the South Toe River; p(searcher experience + site mean substrate size), c(mussel length + microhabitat percent pebble + microhabitat percent silt) .....................................................................................................................................44 Table 5. Top-ranking models (ΔAICc ≤ 2.00) for historical site mark-recapture analysis in the South Toe River (n=6 sites) to assess broad-scale influences on detection of Appalachian elktoe.............................................................................................................45 x Table 6. Beta estimates based on the top-ranked mark-recapture model for historical Appalachian elktoe Site 2 in the South Toe River only; p(microhabitat