Quantitative methods for integrating instream biological monitoring data into aquatic natural resource management decision making by Kathryn Dawn Mickett Kennedy A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 9, 2015 Keywords: freshwater resource management, multiple-use systems, flow regulation, species occupancy, decision making, Alabama Copyright 2015 by Kathryn Dawn Mickett Kennedy Approved by Elise R. Irwin, Chair, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Mary C. Freeman, Affiliate Assistant Professor of Fisheries, Aquaculture, and Aquatic Sciences Conor P. McGowan, Assistant Professor of Forestry and Wildlife Sciences Todd Steury, Assistant Professor of Forestry and Wildlife Sciences James Stoeckel, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Abstract Freshwater aquatic resource management is fraught with challenges, as managers of multiple-use, highly diverse systems must frequently make management decisions with limitations including unclear management objectives and inadequate knowledge of system state and response. In this dissertation, I present three different freshwater aquatic resource management problems and examine the application of quantitative methods to address specific limitations in each. The first management context was a small wildlife refuge faced with making land use decisions that consider impacts to aquatic resource objectives. I examined hypotheses relating fish species occupancy to land use using multiple model comparison. Four species – striped shiner Luxilus chrysocephalus, redbreast sunfish Lepomis auritus, orangespotted sunfish L. humilis, and longear sunfish L. megalotis – had strong support for land use as a predictor of occupancy. However, only orangespotted sunfish had an estimated occupancy probability that was predicted to decrease with increasing urban and agricultural land use. Results suggest both the dominance of a mainstem reservoir in defining patterns of fish species distribution and the tolerance to urban and agricultural land use of most encountered species. The second management context was a hydropower-regulated river in which an adaptive management program has been initiated. Also using multiple model comparison, I examined patterns of fish species occupancy to evaluate the potential response to an implemented management action and to inform the next adaptive management iteration. Nine of 13 fish ii species had distributions that reflected downstream impacts of the hydropower dam. Model results for three species – two minnows and one darter – indicated a potential positive response to management action, whereas up to five species – largescale stoneroller Campostoma oligolepis, Alabama hogsucker Hypentelium etowanum, speckled madtom Noturus leptacanthus, redbreast sunfish Lepomis auritus, and muscadine darter Percina smithvanizi – demonstrated potential negative responses. I hypothesize that an altered thermal regime may be inhibiting occupancy of several fish species, and recommend that the next iteration of adaptive management focus on thermal restoration. The final management context considered statewide management of aquatic resources. In many states, established biomonitoring programs are expected to inform decision making. However, use of these data is often restricted to site classification decisions. To facilitate broader use, I provide a general framework to incorporate the index of biotic integrity (IBI), a widely used multi-metric index, into aquatic resource management decision making. I demonstrate use of the framework for a specific decision context wherein the IBI provides a basis for informing the selection of instream flow management alternatives that meet defined objectives of a state resource agency. Data collected as part of a freshwater monitoring program may be used to inform and support management decision making by adding to our knowledge of system state and of system response to management actions. However, the most successful freshwater aquatic resource management program will include explicit definition of management objectives and hypotheses of system response, a monitoring plan linked directly these objectives and hypotheses, and a flexible management framework, such as adaptive management, that allows for the integration of monitoring data to update hypotheses and improve future management decision making. iii Acknowledgments The work presented herein was funded in part by the Alabama Department of Conservation and Natural Resources, the U.S. Fish and Wildlife Service, Alabama Power Company, and Auburn University. I thank my advisor Elise Irwin for providing the means and resources necessary for me to complete this work, and for introducing me to the concepts and ideas of river ecology, management, and research that have come to define my thinking and my career. I thank my committee members – Mary Freeman, Jim Stoeckel, Todd Steury, and Conor McGowan – for offering support, encouragement, and expert advice when it was needed. I consider you the best, and wish that I had had more opportunity to absorb your knowledge, expertise, and life experience. I thank Peter Sakaris, Taconya Goar, Ben Martin, Molly Martin, Jeff Holder, Gareth Turner, Chase Katechis, Gus Katechis, Allen Nichols, and the many graduate and undergraduate students who helped with field and lab work. I also thank Taconya Goar, as well as Stan Cook, Andrew Henderson, and Heath Haley for their assistance in the development of Chapter 4 and the context for Alabama’s instream flow challenges. I thank Mike Bozek and Seth Wenger for providing critical and helpful review of drafts of the manuscript that is Chapter 2. I also thank Amy Silvano and the late Kevin Kleiner for their assistance with land cover data and map making. Thanks to Bill “Gator” Gates and Wheeler NWR personnel for their input on project objectives and study design. Thanks also to Willard Bowers, Bill Dykes, and their colleagues at Alabama Power for their engagement in the Tallapoosa work. My experience with Alabama iv Power has been incredibly influential in my current path and my optimistic outlook on management of regulated rivers. I am tremendously thankful to all my friends and colleagues who have been helpful and supportive along the way. I thank my new colleagues at The Nature Conservancy and American Rivers for their day-to-day support and encouragement, and for giving my husband a break from my madness. I am also thankful for the support of my new colleague Rachel Katz, and especially for her insights during coffee shop musings and moanings that were helpful in development of the IBI work – I am hopeful there will be more of these conversations to come! I thank my family – Mom, Dad, Stan, John, and Amity – for their support, for offering advice, help, and prayers when our house started falling apart in the midst of dissertation writing, and for being so understanding when I needed to be left to my writing. Abounding thanks to my kind, patient, loving, forgiving husband, Ryan – and to that person who once informed him that it was normal for someone who was working on their dissertation to be a “raving lunatic.” This dissertation has been part-and-parcel to the biggest trial of our lives – I’m looking forward to doing all those things that we said we would do “when I’m finished.” Finally, this dissertation was not an isolated trial. It has been accompanied by difficulties few people know or understand. Those who do know have expressed wonderment at how anyone could possibly endure and persist in the midst of such difficulty. What is true is this: I can do all things through Christ who strengthens me; when I am weak, He is strong; He has lifted me from the mire and set me on solid ground; He has guided me through the darkness with a light that never fades. Simply put, faith in my God and Savior and the strength and power that He imparts is what has allowed my family to endure and survive the past several years: Thanks be to Him for His indescribable gift. v Table of Contents Abstract ........................................................................................................................................ ii Acknowledgments ....................................................................................................................... iv List of Tables ............................................................................................................................ viii List of Figures ............................................................................................................................ xii List of Abbreviations ................................................................................................................ xiv Chapter 1. Introduction ............................................................................................................... 1 Chapter 2. Using models of species occupancy to assess impacts to aquatic resources in managed multiple-use systems .................................................................................................... 7 Introduction ...................................................................................................................... 8 Methods ............................................................................................................................ 9 Results ...........................................................................................................................