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A Habitat Risk Assessment and Breeding Site Projection for Slackwater Darter (Etheostoma Boschungi) in Limestone Creek

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A Habitat Risk Assessment and Breeding Site Projection for Slackwater Darter (Etheostoma Boschungi) in Limestone Creek A habitat risk assessment and breeding site projection for Slackwater Darter (Etheostoma boschungi) in Limestone Creek by Meagan Bailey Roy A thesis submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Master of Science Auburn, Alabama May 6, 2017 Keywords: environmental DNA, geographic information systems, environmental modelling, land use, conservation Copyright 2017 by Meagan Bailey Roy Approved by Carol Johnston, Chair, Professor of Fisheries, Aquacultures, and Aquatic Sciences Eve Brantley, Extension Specialist and Associate Professor, College of Agriculture Brian Helms, Assistant Research Professor and Invertebrate Collections Manager, Department of Biological Sciences Abstract Catalysts for species decline are difficult to identify and are rarely single. The use of predictive models that incorporate multiple factors have proven useful in recognizing major drivers of species declines in multiple systems. In this study, a geographic information systems model was used to evaluate factors contributing to the decline of the Slackwater Darter throughout its distributional range. The species has suffered a precipitous decline, and it is essential to understand conservation threats and to prioritize habitat for restoration and protection. Variables incorporated into the habitat model included land use/land cover, soil and geographic descriptions, hydrologic variables, and others. Habitat where the species has become extirpated or undetectable by conventional sampling was compared to extant populations to identify factors contributing to population loss. Land cover and farm pond density were identified as potential drivers of extirpation. Finally, a model of suitable habitat was used to predict spawning areas in Limestone Creek, where the species was recently discovered. This model identified eight new spawning sites for Slackwater Darter in the system where breeding sites were unknown, and was 44% accurate in its predictive capabilities; however, positive detections were noticeably clustered and indicate the likely influence of some untested variable. With the information provided by this analysis, a framework for habitat protection can be created to assist with restoration of this species. ii Acknowledgments I would like to thank my advisor, Dr. Carol Johnston, for sharing her considerable knowledge of and passion for fish ecology and conservation. I would also like to thank my committee members, Dr. Eve Brantley and Dr. Brian Helms, for their invaluable suggestions and assistance with this project. Jenna Crovo, Davis Todd, Warren Stiles, Drew Jarrett, and Jeff Zeyl, my friends and lab mates from the fish biodiversity lab, were invaluable in data collection and processing, as well as in providing moral support. The Alabama Department of Conservation and Natural Resources funded this project, and Steve Rider was an instrumental source of advice and input. This project would not have been possible without the assistance and coaching of Dr. Alexis Janosik and her lab at UWF, who provided instruction on the eDNA extraction procedure and performed all of the relevant PCRs and gels for this research. iii Table of Contents Abstract ......................................................................................................................................ii Acknowledgments.....................................................................................................................iii List of Tables ............................................................................................................................. v List of Illustrations .................................................................................................................... vi List of Abbreviations ...............................................................................................................vii Introduction .............................................................................................................................. 1 Methods and Materials ............................................................................................................. 4 Results ...................................................................................................................................... 7 Discussion .............................................................................................................................. 10 References .............................................................................................................................. 16 Appendix 1 ............................................................................................................................. 54 Appendix 2 ............................................................................................................................. 57 iv List of Tables Table 1. Descriptive statistics of land use/land cover categories across known Slackwater Darter populations .................................................................................................................... 24 Table 2. Distribution of Slackwater Darter in relation to hydric soil classifications ............... 25 Table 3. Distribution of Slackwater Darter in relation to water table depth ........................... 26 Table 4. Distribution of Slackwater Darter in relation to soil drainage class ......................... 27 Table 5. Descriptive statistics of suitable Slackwater Darter habitat throughout known distribution .............................................................................................................................. 28 Table 6. Results of a stepwise generalized linear model comparing the effects of environmental variables on Slackwater Darter Presence ......................................................... 29 Table 7. Logistic regression analyzing the effects of the three most influential habitat variables on Slackwater Darter persistence ............................................................................. 30 Table 8. Comparison of the effect of land use categories on Slackwater Darter persistence 31 Table 9. Distribution of at-risk land for Slackwater Darter across known distribution .......... 32 Table 10. Extant Slackwater Darter populations within the top 25% of determined risk ....... 33 Table 11. Environmental DNA results for Limestone Creek ................................................. 34 v List of Figures Figure 1. Habitat suitability map for Slackwater Darter in the Buffalo River watershed ...... 35 Figure 2. Habitat suitability map for Slackwater Darter in the Cypress Creek watershed ...... 36 Figure 3. Habitat suitability map for Slackwater Darter in the Flint River watershed ............ 37 Figure 4. Habitat suitability map for Slackwater Darter in the Shoal Creek watershed ........ 238 Figure 5. Habitat suitability map for Slackwater Darter in the Swan Creek watershed .......... 39 Figure 6. Habitat suitability map for Slackwater Darter in the Limestone Creek watershed .. 40 Figure 7. Non-metric multidimensional scaling model of all Slackwater Darter populations overlaid with corresponding habitat vectors ........................................................................... 41 Figure 8. Habitat risk assessment for the Buffalo River system .............................................. 42 Figure 9. Habitat risk assessment for the Cypress Creek system ............................................ 43 Figure 10. Habitat risk assessment for the Flint River system ................................................ 44 Figure 11. Habitat risk assessment for the Shoal Creek system .............................................. 45 Figure 12. Habitat risk assessment for the Swan Creek system .............................................. 46 Figure 13. Habitat risk assessment for the Limestone system ................................................. 47 Figure 14. Slackwater Darter populations displayed according to relative calculated risk ..... 48 Figure 15. Map of eDNA sample sites in Limestone Creek .................................................... 49 Figure 16. Map of eDNA sample sites in Limestone Creek compared to viable habitat ........ 50 Figure 17. Map of eDNA sample sites in Limestone Creek compared to pasture land within the drainage .............................................................................................................................. 51 Figure 18. Map of eDNA sample sites in Limestone Creek compared to cropland within the drainage .................................................................................................................................... 52 Figure 15. Map of eDNA sample sites in Limestone Creek compared to farm pond locations within the drainage ................................................................................................................... 53 vi List of Abbreviations eDNA environmental DNA GLM Generalized Linear Model NLCD National Land Cover Dataset SSURGO Soil Survey Geographic Database USFWS U.S. Fish and Wildlife Service UTM Universal Transverse Mercator UWF University of West Florida vii Introduction It is important to understand the variables driving the decline of species with declining populations. Many threatened species occupy specific habitats within narrow distributions, making sudden environmental shifts within these regions potentially devastating to populations (Taylor et al. 1994, Cummings et al. 1998). Freshwater
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