Effects of uncertainty on conservation decisions and ecological inference by Kylee Denise Dunham 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 August 3, 2019 Copyright 2019 by Kylee Denise Dunham Doctoral Committee Members James B. Grand, Chair, Cooperative Research Unit Supervisor, U.S. Geological Survey Christopher A. Lepczyk, Professor of Wildlife Sciences Conor P. McGowan, Associate Research Professor of Wildlife Sciences David N. Koons, Associate Professor, Colorado State University Abstract Uncertainty is pervasive in ecology and conservation. Ecological systems are dynamic, and therefore inference from observations and subsequent decision-making can be hampered due to observation and process error. Assessing and characterizing the relative impacts of observation and process errors is important for sound ecological inference and conservation or management decisions. My research evaluates the effects of uncertainty on a threatened species listing decision and explores the reduction of uncertainty on predictive measures of species viability, understanding demographic and ecological mechanisms influencing population variation, and the impacts of accounting for these uncertainties on making conservation decisions. I apply this research to spectacled eiders (Somateria fischeri), a federally threatened species listed under the Endangered Species Act. My research aims to further our understanding of the effects of uncertainty by addressing the following questions; (1) How does uncertainty affect conservation decisions? and (2) What is the relative value of accounting for, and ultimately reducing those uncertainties for ecological inference and decision-making? I specifically address the impacts of imperfect detection, sampling variation, ecological uncertainty, and structural uncertainty on gaining ecological knowledge and making ii conservation decisions. Understanding the role of uncertainty in studying species ecology and informing conservation decisions is imperative for effective biodiversity conservation strategies. iii Acknowledgements I would like to express my deepest thanks to all those who made this dissertation possible. To my major advisor, Barry Grand, for taking a chance on me back in 2013 for my M.S. and again for my Ph.D. I have learned, grown, and experienced so much over the past six years and two graduate degrees. I am so grateful for the many hours long coding sessions and insightful conversations. The multiple trips to Alaska for work on the project certainly didn’t hurt either! To my committee, Conor McGowan, Chris Lepczyk, and Dave Koons, I could not have done this without you. Over the years you have provided a great deal of wisdom, opportunity, and helped me become the scientist I am today. Conor, you graciously adopted me into your lab and I could not be more grateful for the weekly meetings with you and the members of lab McGowan. Further, you offered multiple teaching and networking opportunities that have been and will continue to be beneficial for my career. Chris, you fostered philosophical discussions with graduate and undergraduate students in your reading classes that pushed me to think critically and to develop skills to communicate science effectively. Dave, I am forever grateful for your help with my project and for providing me with such a great opportunity to continue pursuing my passions in a postdoctoral position. I am deeply indebted to two key mentors from high school and college for their immense help that made all of this possible. Mr. Donald Quindley, without you, I do not believe I would have pursued college at all. I certainly would not have developed a love iv for writing that has become the cornerstone of my career. I cannot thank you enough for your guidance through those tumultuous years at Holliston High. To my undergraduate mentor, Dr. Steven Dinkelacker, you provided me with the opportunities that made all of this possible. You took a chance on a girl that thought pinto beans in lab were “gross” and tossed me into the field to wade through muck to capture turtles and alligators. I can never thank you enough for giving me the opportunities to work with you in the field and to manage your lab. I did not know then just how important that experience would be for sparking my love of research and for getting me into graduate school. I cannot express my gratitude for your advice and support over the years. I wish to thank my friends and family whose support and encouragement has been invaluable. I am specifically grateful that my husband, Nick, has been willing to take this journey with me. Last but not least, I need to thank my dogs, Oscar, Ellie, and Mia, whose unwavering enthusiasm for life has been an inspiration. There has been no greater feeling than coming home after a long day of work to find three dogs waiting by the door to greet you. I will be forever grateful to you for reminding me to smile and laugh each and every day. v Table of Contents Abstract ............................................................................................................................... ii Acknowledgments ............................................................................................................. iv List of Tables ..................................................................................................................... ix List of Figures ......................................................................................................................x Chapter 1: General Introduction ........................................................................................1 Literature Cited .....................................................................................................10 Chapter 2: Evaluating the probability of meeting population management thresholds .....14 Abstract ................................................................................................................14 Introduction ...........................................................................................................15 Methods ................................................................................................................18 Results ...................................................................................................................21 Discussion ............................................................................................................22 Literature Cited .....................................................................................................26 Tables ....................................................................................................................29 Figures ...................................................................................................................30 vi Chapter 3: Assessing recovery of spectacled eiders using a Bayesian decision analysis ..31 Abstract ................................................................................................................31 Introduction ...........................................................................................................32 Methods ................................................................................................................35 Results ...................................................................................................................41 Discussion ............................................................................................................42 Literature Cited .....................................................................................................46 Tables ....................................................................................................................51 Figures ...................................................................................................................53 Supporting Information .........................................................................................55 Chapter 4: Demographic responses to climate change and predation pressure in a threatened Arctic species ..................................................................................................57 Abstract ................................................................................................................57 Introduction ...........................................................................................................58 Methods ................................................................................................................61 Results ...................................................................................................................70 Discussion ............................................................................................................72 Literature Cited .....................................................................................................77 Tables ....................................................................................................................84 Figures ...................................................................................................................86 Supporting Information .........................................................................................95 Chapter 5: Advantages of integrated population modeling for species classification decisions ..........................................................................................................................102