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Using Environmental DNA and Macroinvertebrate Biotic Integrity to Inform Conservation Efforts for the Carolina Heelsplitter

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Using Environmental DNA and Macroinvertebrate Biotic Integrity to Inform Conservation Efforts for the Carolina Heelsplitter Clemson University TigerPrints All Theses Theses December 2020 Using Environmental DNA and Macroinvertebrate Biotic Integrity to Inform Conservation Efforts for the Carolina Heelsplitter Benjamin Schmidt Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Recommended Citation Schmidt, Benjamin, "Using Environmental DNA and Macroinvertebrate Biotic Integrity to Inform Conservation Efforts for the Carolina Heelsplitter" (2020). All Theses. 3441. https://tigerprints.clemson.edu/all_theses/3441 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. USING ENVIRONMENTAL DNA AND MACROINVERTEBRATE BIOTIC INTEGRITY TO INFORM CONSERVATION EFFORTS FOR THE CAROLINA HEELSPLITTER A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Science Wildlife and Fisheries Biology by Benjamin Schmidt December 2020 Accepted by: Dr. Catherine M. Bodinof Jachowski, Committee Chair Dr. Stephen F. Spear Dr. Robert F. Baldwin ABSTRACT The Carolina Heelsplitter (Lasmigona decorata) is a federally endangered freshwater mussel endemic to North and South Carolina, USA. The species has experienced dramatic range-wide declines as a result of habitat fragmentation and water quality deterioration, and the remaining populations are isolated and extremely small. Conservation efforts for the Carolina Heelsplitter have been limited by a lack of knowledge regarding distribution, life history traits, and habitat requirements. Our objectives during this project were to 1. Evaluate the efficacy of an environmental DNA (eDNA) assay to detect the Carolina Heelsplitter and a known host fish, the Bluehead Chub, from stream water samples and 2. Develop a biotic integrity index to assess habitat suitability within three ecologically important watersheds. To determine if eDNA techniques can be used to detect the Carolina Heelsplitter and the Bluehead Chub from stream water samples, we developed species specific primer pairs and probes for the target taxa and applied our assay to water samples collected from 100 randomly selected sites. While our assay validation successfully detected the Carolina Heelsplitter in stream segments where the species was known to occur, our results were highly variable, and we failed to detect the species at any new locations within the study area. Detection rates for the Bluehead Chub were high, indicating that host fish availability is relatively widespread within the study area and likely not a limiting factor in Carolina Heelsplitter recruitment. Our results suggest that ii current eDNA sampling methods may be ineffective for some extremely rare unionid taxa. To assess habitat suitability, we developed a predictive model of macroinvertebrate biotic integrity based on samples collected across 49 spatially balanced sites. We used multiple linear regression and model ranking criteria to evaluate potential drivers of biotic integrity at multiple spatial scales. We found that local stream conditions were influenced by a relatively large spatial extent, and that land use immediately adjacent to the stream edge plays a larger role in determining biological condition than land use across the entire upstream watershed. Our results can be used to identify areas of high and low habitat quality, evaluate connectivity between populations, and prioritize locations for reintroducing propagated mussels. iii ACKNOWLEDGEMENTS First and foremost, I would like to thank my advisor, Dr. Cathy Jachowski, for her mentorship, patience, and encouragement during my time at Clemson. I am incredibly grateful for your unwavering support through all the twists and turns of my graduate school journey. I would also like to thank my graduate committee, Dr. Stephen Spear and Dr. Robert Baldwin, for their guidance, advice, and insight during the formation of this thesis. I would like to extend my greatest appreciation to all those who provided support during data collection and analysis. Thank you to Jonathan Wardell at the Orangeburg National Fish Hatchery for teaching me how to identify freshwater mussels and for helping me collect control samples. Thank you to Morgan Kern at the S.C. Department of Natural Resources and Morgan Wolf at the U.S. Fish and Wildlife Service for providing expertise and technical assistance. Thank you to Rachael Hoch at the N.C. Wildlife Resources Commission for providing supplies and assistance in the pilot study. Thank you to the technicians at the Wilds Conservation Center, Amelia Tomi, Sophie Aller, Molly Garrett, and Kristina Black for spending countless hours processing water samples. Thank you to Dr. John Morse, Matthew Green, and Nathan Arey for collecting, sorting, and identifying macroinvertebrate samples. I would like to thank my fellow graduate students whose friendship became the highlight of my time spent at Clemson. To Ellie Johnson in particular, thank you for believing in me and helping me stay focused whenever I was discouraged. Finally, I iv would like to thank my parents, Anne and John Schmidt, for their love, continuous encouragement and emotional support. Thank you for inspiring me to follow my dreams. This research was funded by the National Fish and Wildlife Foundation through the Southeast Aquatics Fund (project ID: 1906.17.058597), with additional support provided by Clemson University and The Wilds Conservation Center. v TABLE OF CONTENTS PAGE TITLE PAGE ....................................................................................................................... i ABSTRACT ....................................................................................................................... ii ACKNOWLEDGEMENTS ................................................................................................... iv LIST OF TABLES ............................................................................................................. viii LIST OF FIGURES ............................................................................................................. ix CHAPTER I. EVALUATING THE EFFICACY OF ENVIRONMENTAL DNA (eDNA) TO DETECT AN ENDANGERED FRESHWATER MUSSEL LASMIGONA DECORATA (BIVALVIA: UNIONIDAE) .......................................................... 1 Abstract ............................................................................................... 1 Introduction ......................................................................................... 2 Methods .............................................................................................. 5 Results ............................................................................................... 15 Discussion .......................................................................................... 17 References ......................................................................................... 23 II. USING ENVIRONMENTAL DNA (eDNA) TO PREDICT HOST FISH DISTRIBUTION FOR AN ENDANGERED FRESHWATER MUSSEL LASMIGONA DECORATA ........................................................................ 38 Abstract ............................................................................................. 38 Introduction ....................................................................................... 39 Methods ............................................................................................ 41 Results ............................................................................................... 50 Discussion .......................................................................................... 52 References ......................................................................................... 55 vi TABLE OF CONTENTS (CONTINUED) PAGE III. PREDICTING BIOLOGICAL INTEGRITY IN STREAMS: THE IMPORTANCE OF SCALE AND VARIABLE SELECTION .................................................... 70 Abstract ............................................................................................. 70 Introduction ....................................................................................... 71 Methods ............................................................................................ 74 Results ............................................................................................... 83 Discussion .......................................................................................... 85 References ......................................................................................... 93 vii LIST OF TABLES TABLE PAGE 1.1 Estimated detection probability for Lasmigona decorata based on sample replicates and volume ........................................... 32 1.2 List of covariates used to model sample inhibition in the upper Lynches River Sub-basin ........................................................... 33 1.3 Candidate models used to investigate the probability of sample inhibition in stream water samples ....................................... 34 1.4 Coefficient estimates for the top-ranked models used to describe sample inhibition in stream water samples ........................ 35 2.1 List of covariates used to model occupancy and detection probability of Nocomis leptocephalus ............................................... 62 2.2 Candidate models used to investigate
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