ABSTRACT BINION-ROCK, SAMANTHA MICHELLE. Trophic Dynamics and Ecosystem Modeling of Finfishes in Pamlico Sound, North Carolina (Under the direction of Dr. Jeffrey A. Buckel). Fisheries management is increasingly becoming more holistic and shifting from single-species to multispecies and ecosystem-based approaches. Understanding trophic dynamics is critical for these approaches; however, the quality of the food habits data used in these models can vary. I conducted a multispecies food habits study for 25 finfish species in Pamlico Sound, NC and its tributaries. Seventeen thousand predators were sampled from four fisheries-independent surveys conducted by the North Carolina Division of Marine Fisheries (NCDMF). I used spatial kernel density estimation (SKDE) to adjust for spatial dependence when estimating predator diet composition. I conducted a Monte Carlo simulation study, at a range of bandwidths (i.e. width of the kernel; smaller bandwidths represent higher levels of spatial clustering) and predator stomach sample sizes, to compare the performance of SKDE to a traditional diet estimator that does not account for spatial dependence. Mean squared error, bias, and Bhattacharyya distance were the metrics used to evaluate estimator performance. For all bandwidths and predator sample sizes, SKDE was consistently favored over the traditional diet estimator for all metrics. Agglomerative hierarchical cluster analyses and similarity profiles were used to identify significant trophic guilds. Differences in the size-selectivity of NCDMF survey gears (e.g. trawl, gill net) had a significant impact on the observed diet composition and trophic guild classification for predators. Predators sampled from a trawl survey were generally smaller, relied more heavily on invertebrate prey, and consumed less types of fish, with anchovy (Anchoa mitchilli and A. hepsetus) being the main fish prey. Predators sampled from gill net surveys were larger and exhibited higher levels of piscivory. Atlantic menhaden (Brevoortia tyrannus), spot (Leiostomus xanthurus), and Atlantic croaker (Micropogonias undulatus) were the most commonly consumed fish for larger predators. Spatial correlation and size-selectivity of sampling gears should be addressed when analyzing food habits data. I constructed a 43 compartment Ecopath model for Pamlico Sound with an emphasis on piscivores and their prey. Forage fish were identified using qualitative and quantitative metrics and consumption estimates from Ecopath. The proportion of production removed for forage fish, blue crabs, and penaeid shrimp through consumption and fisheries harvest was estimated at current predator biomasses and with the biomasses of five predators increased to meet management thresholds. Mixed trophic impacts (MTI) analysis in Ecopath identified the potential impacts of small increases in the biomass of a predator on other compartments within Pamlico Sound. MTI predicted that small increases in the biomass of predators had the potential to have indirect and direct negative impacts on commercially-important species in Pamlico Sound. Choice of metric also influenced forage fish identification. Qualitative metrics identified Atlantic menhaden, anchovy, and silversides (Atherinidae) as forage fish. Atlantic menhaden, anchovy, and spot were identified a forage fish using quantitative metrics. Based on total consumption, Atlantic menhaden, anchovy, spot, and Atlantic croaker were the top forage fish species and represented 80% of the total fish consumed in Pamlico Sound. At current biomass levels, over 75% of forage fish production is removed annually through predation and fisheries. When predator biomasses were increased to management thresholds, 90% of forage fish production was removed and removals exceeded production for spot and Atlantic croaker. Blue crabs and shrimp saw smaller increases (8 and 2%, respectively) in the amount of production removed. Based on my estimates, the forage base in Pamlico Sound is not large enough to support all predators having biomasses at their management threshold. If found to hold though independent analyses, I recommend fisheries managers focus on tradeoffs between forage fish and non-forage fish fisheries. Trophic Dynamics and Ecosystem Modeling of Finfishes in Pamlico Sound, North Carolina by Samantha Michelle Binion-Rock A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Fisheries, Wildlife, and Conservation Biology Raleigh, North Carolina 2018 APPROVED BY: Dr. Jeffrey A. Buckel Dr. Robert R. Christian Committee Chair External Member Dr. David B. Eggleston Dr. Brian J. Reich Dr. Kyle W. Shertzer DEDICATION To my dad, Mike Binion. Thank you for teaching me the value of hard work and always believing in me. I love and miss you very much. ii BIOGRAPHY I was born in Ashland, KY. My family moved to Eglin AFB, FL when I was in the third grade, then to a suburb outside of Atlanta, GA in 5th grade. My love of nature and animals developed as a little kid catching crawdads in KY, playing at the beaches in FL, and exploring the woods along the Flint River. I received my B.S. in Biology from Emory University. As an undergrad, I interned at Mote Marine Laboratory, Sarasota, FL and Marine Biological Laboratory, Woods Hole, MA. As an intern at Mote, I assisted in projects evaluating the impacts of barotrauma on reef fishes in the Gulf of Mexico. At the Marine Biological Laboratory, I studied the effects of habitat type on the foraging behavior of juvenile toadfish. After graduating from Emory, I returned to Mote as a technician and was ultimately promoted to a Staff Biologist II. While at Mote, I was the project manager for multiple projects studying the impacts of power plant impingement and entrainment on zooplankton and fish communities in Tampa Bay. I left Mote to attend East Carolina University, Greenville, NC where I obtained a M.S. in Biology under the direction of Dr. Anthony Overton. My master’s research evaluated whether larval alosines in the lower Roanoke River and Albemarle Sound were food limited. After graduating from East Carolina, I entered the doctoral program at North Carolina State University under the direction of Dr. Jeff Buckel. I am married to Jason Rock and we have a beautiful daughter, Jocelyn. iii ACKNOWLEDGEMENTS I am indebted to many people who provided invaluable support during my dissertation. First, I would like to thank my advisor Dr. Jeffrey Buckel for providing mentorship and support throughout my doctoral program. I would also like to thank my committee members Drs. Bob Christian, David Eggleston, Brian Reich, and Kyle Shertzer for their advice, feedback, and willingness to answer my numerous questions along the way. The guidance provided by my entire committee strengthened the quality of my doctoral research and pushed me to become a better scientist. I am thankful to my technician Jeffery Merrell who stuck with me through the processing of ~ 17,000 predator stomachs. I could consistently rely on Jeffery to provide reliable, high-quality assistance throughout my project. I am also thankful to my interns Ben Kornegay, Cameron Luck, and Josie Daniel, and volunteer Tim Westbrook for spending their summers sorting through fish guts with me. This project would not have been possible without the assistance of numerous biologists and technicians at the North Carolina Division of Marine Fisheries (NCDMF). Katy West, Jason Rock, and Lee Paramore were instrumental in coordinating sample collection and providing the framework to link my food habits data with data collected by NCDMF. Ashley Grandy, Beth Egbert, Carol Etheridge, Casey Knight, Chris Braddy, Fred Jarrett, Garry Wright, Greg Judy, Holly White, Joe Cox, Katharine Jarrell, Kathleen Boylan, Lee Cannady, Lele Judy, Michael Brinkly, Mike Loeffler, Ray Mroch, Shane Staples, Stan Ward, Stephen Johnson, Tyler Averett, and William Schmidt collected the predators sampled for food habits and provided otolith samples for my reference collection. George Joyner designed and created the database for my program and Jim iv Fox provided me with access to the NCDMF biological database. Dan Zapf provided data from the predator surveys and assisted with correcting data mismatches. I would like to thank all of the scientists who generously shared data with me to support the development of my Ecopath model. From NCDMF, Alan Bianchi, Dr. Drew Cathey, and Chris Wilson provided data on commercial and recreational landings. Jacob Boyd and Kevin Brown provided data on fisheries discards. Dr. Vicky Thayer shared bottlenose dolphin data from the North Carolina Marine Mammal Strandings Program. Laura Lee provided biomasses estimates for spotted seatrout and was generous in sharing her expertise in modeling fisheries data. Dr. Hans Paerl (UNC-CH Institute of Marine Science) provided chl-a data from his monitoring programs in Neuse River and Pamlico Sound. Dr. Charles Bangley (Smithsonian Environmental Research Center) shared food habits data for multiple species of sharks in North Carolina. I want to thank Dr. Paul Rudershausen for always allowing me to bounce ideas off of him and sharing insights about life in general. Thank you to Marlu Bolton, Meredith Henry, Susan Marschalk, Freha Legoas, and Dawn Newkirk for providing administrative support. I would like to thank Linda Dunn for providing IT support at CMAST. I would also like to thank Lucas Jennings (University of Florida) and Jim Culter (Mote Marine