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Effects of Impoundments on the Community Assemblage and Gene Flow of Stream Crayfishes

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Effects of Impoundments on the Community Assemblage and Gene Flow of Stream Crayfishes University of Mississippi eGrove Electronic Theses and Dissertations Graduate School 2019 Effects of Impoundments on the Community Assemblage and Gene Flow of Stream Crayfishes Zanethia Choice Barnett University of Mississippi Follow this and additional works at: https://egrove.olemiss.edu/etd Part of the Biology Commons Recommended Citation Barnett, Zanethia Choice, "Effects of Impoundments on the Community Assemblage and Gene Flow of Stream Crayfishes" (2019). Electronic Theses and Dissertations. 1548. https://egrove.olemiss.edu/etd/1548 This Dissertation is brought to you for free and open access by the Graduate School at eGrove. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of eGrove. For more information, please contact [email protected]. EFFECTS OF IMPOUNDMENTS ON THE COMMUNITY ASSEMBLAGE AND GENE FLOW OF STREAM CRAYFISHES A Dissertation Presented in partial fulfillment of requirements for the degree of Doctor of Philosophy in the Department of Biological Sciences The University of Mississippi By ZANETHIA CHOICE BARNETT May 2019 ABSTRACT Dams and their impoundments block movement of stream organism and change stream physiochemical properties, which subsequently changes biological assemblages and creates barriers to gene flow. While changes in species assemblages and gene flow have been assessed for numerous impoundments and stream organisms, no study has assessed the effects of large impoundments on crayfish assemblages and population genetic diversity and connectivity. I examined the physiochemical, biological, and genetic effects of impoundments on crayfishes. Between May 2015 and August 2017, I sampled multiple sites up- and downstream of three impounded streams, and along the lengths of two unimpounded streams, in the Bear Creek and Cahaba River drainages in Alabama, USA. First, I assessed the most effective sampling methods for collecting crayfishes in high gradient southern Appalachian streams. A combination of kick seining and electroshocking were most effective at collecting crayfishes, with higher species richness and decreased sampling biases when using both methods. Once effective methods were established, I assessed the effects of impoundments and their subsequent changes to crayfish assemblages and their habitats. Impoundments altered crayfish assemblages up- and downstream of impoundments. Crayfish abundances and species diversity were lower in impounded than unimpounded streams. Assemblages up- and downstream of impoundments were similar, but in unimpounded streams, gradual shifts in dominant species occurred from up- to downstream. Assemblage differences between impounded and unimpounded streams were associated with more stable temperature and flow regimes, decreases in crayfish refuge habitats (i.e., aquatic vegetation, interstitial space), and increased abundances of predatory fishes in impounded ii streams. Nonetheless, with distance downstream of impoundments, crayfish assemblages began to recover and resemble unimpounded stream assemblages. Impoundments also impacted gene flow and genetic structure of crayfishes. Impounded streams’ crayfish populations were genetically isolated, and unidirectional downstream gene flow, or no gene flow, was detected between up- and downstream populations. The degree of impact of impoundments on gene flow was species-specific, with intrinsic biological and life history characteristics, such as dispersal ability and physiological tolerance, determining the degree of impact. With already declining crayfish populations, decreases in species and genetic diversity due to impoundments can decrease the persistence of hundreds of crayfish species in thousands of impounded streams. These changes in crayfish populations can cause cascading effects throughout stream ecosystems by altering the numerous ecosystem services provided by crayfishes. iii DEDICATION This work is dedicated to my grandmothers, Regenia Peterson and Mary Choice, who were two of the most tenacious women I knew. They showed me what it meant to work your hardest and strive for excellence despite all adversity. Their motivation to defeat the odds was passed on to me, and because of them, I can take advantage of opportunities that they didn’t even dare to dream. Thus, this dissertation is a product of their struggles to pursue their dreams when there were little to no opportunities for African Americans or women. iv LIST OF ABBREVIATIONS AND SYMBOLS µ Mutation rate π Nucleotide diversity θ Mutation-scaled effective population size AFS American Fisheries Society AICc Corrected Akaike information criterion AMOVA Analysis of molecular variance ANOVA Analysis of variance ARC Appalachian Regional Commission CAP Canonical analysis of principal coordinates CBHR Center of Bottomland Hardwood Research COI Cytochrome oxidase subunit I CPUE Catch per unit effort D16 particle sizes the 16% of particles were smaller than D50 Mean particle size D84 particle size that 84% of particles were smaller than DNA Deoxyribonucleic acid DO Dissolved oxygen ERDAS Earth Resources Data Analysis System FCT Proportion of genetic variance explained by difference among groups FST Haplotype frequency-based genetic differentiation v GIS Geographic information system h number of haplotypes hd Haplotypic diversity IBD Isolation by distance K Number of genetic groups LDA Linear discriminant analyses LME Linear mixed-effect repeated-measures LOO Leave-one-out LWD Large woody debris m Migration rate M Mutation-scaled immigration rate MEGA Molecular evolutionary genetic analysis mtDNA Mitochondrial deoxyribonucleic acid Ne Effective population size NID National Inventory of Dams NMDS Non-metric multidimensional scaling NOAA National Oceanic and Atmospheric Administration NRCS Natural Resource Conservation Service PCR Polymerase chain reaction PERMANOVA Permutational multivariate analysis of variance POCL Postorbital carapace length vi PRIMER Plymouth Routines in Multivariate Ecological Research Rkm River kilometer RVI Relative variable importance Sest Average number of species estimated in a sample SAMOVA Spatial analysis of molecular variance SD Standard deviation SWD Small woody debris TVA Tennessee Valley Authority UM University of Mississippi USA United States of America USDA United States Department of Agriculture USFS United States Forest Service USGS United States Geological Survey vii ACKNOWLEDGEMENTS The USDA Forest Service, Birmingham Audubon Society, Alabama Fisheries Association, and University of Mississippi provided financial and logistical support for this project. Without these funding sources my research would not have been possible. I would like to thank my advisor Dr. Clifford Ochs for his invaluable support and advice. His guidance throughout this process pushed me to expand my research into new fields, while also helping me balance working full time while pursuing my PhD. I would also like to thank the members of my dissertation committee, Dr. Susan Adams, Dr. Ryan Garrick, Dr. Jason Hoeksema, and Dr. Greg Easson for their guidance on this project. They have not only helped develop this project, but they have also helped me develop numerous research skills. I would like to give special thanks to Dr. Garrick for graciously allowing me access to his lab and helping develop my genetic laboratory and statistical skills and Dr. Hoeksema for his statistical advice throughout the project. Without the inspiration, patience, ideas, and encouragement from my committee I would not be the person I am today. This project would not have been possible without the support of my colleagues at the USDA Forest Service, Center of Bottomland Hardwood Research (CBHR), Aquatic Ecology lab. Dr. Adams (committee member and CBHR supervisor) has been one of my biggest advocates since I began working for the lab. She’s also been a mentor and friend. I am forever grateful to her for introducing me to the world of crayfishes and pushing me to continue to explore and grow as an astacologist. It has been an honor to work, travel the country, and learn from her. I will continue to strive to be as productive, down to earth, and efficient as she is. My CBHR team viii played a great role in field collections and data entry, with special thanks to Mickey Bland, Gordon McWhirter, and Carl Smith. None of this would have been possible without their hard work and dedication. I would like to thank a colleague turned-friend, Stuart McGregor (Geological Survey of Alabama), for assisting me with finding landowners with stream access, crayfish collections, permit struggles and sharing his vast knowledge of stream ecology. I would also like to thank the numerous volunteers for assisting with field collections, and land owners for allowing access to streams through their properties. The Tennessee Valley Authority and Birmingham Water Works also provided land access and invaluable data on impoundment management. I also thank all my lab mates from Dr. Ochs’ (Dr. Audrey Harris, Jarrod Sackreiter, and Jason Payne) and Garrick’s (Stephanie Burgess, Dr. Rebecca Symula, Chaz Hyseni, and John Banusiewicz) labs. This dissertation would not have been possible without the numerous discussions, sharing of ideas, field and lab assistance, and advice from each of you. Lastly, but definitely not least, I’d like to thank my family and friends for all their love and support, and always reminding me that I have everything it takes to accomplish anything I put my mind to. I thank my mom (Rose Choice) and siblings (Zenobia Washington
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