RESTORATION POTENTIAL FOR REPRODUCTION BY STRIPED BASS (Morone saxatilis) IN THE SAINT JOHN RIVER, NEW BRUNSWICK by Samuel Nelson Andrews Previous Degrees (BSc, Dalhousie, 2012) (MSc, Acadia University, 2014) A Dissertation Submitted in Partial Fulfilment of the Requirements for the Degree of Doctor of Philosophy in the Graduate Academic Unit of Biology Supervisors: R. Allen Curry, Ph.D., Biology, FOREM, and CRI Tommi Linnansaari, Ph.D., Biology, FOREM, and CRI Examining Board: Mike Duffy, Ph.D., Biology, UNB Scott Pavey, Ph.D., Biology, UNBSJ Tillmann Benfey, Ph.D., Biology, UNB External Examiner: Roger A. Rulifson, Ph.D., Biology/Fisheries and Fish Ecology, Thomas Harriot College of Arts and Sciences, East Carolina University This dissertation is accepted by the Dean of Graduate Studies THE UNIVERSITY OF NEW BRUNSWICK December 2019 © Samuel Nelson Andrews, 2020 Abstract In 2012 the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) listed the Striped Bass (Morone saxatilis) of the Saint John River, New Brunswick, as endangered as part of the Bay of Fundy designatable unit. This listing was due to an apparent rapid collapse and subsequent absence of presumed native origin Striped Bass, juvenile recruitment, and spawning by the species following the completion of the large Mactaquac Dam in 1968. Expert reports hypothesized that alteration in the river flow and temperature regime imposed upon the Saint John River downstream from the Mactaquac Dam were responsible for the disappearance, however, no recovery efforts or exploratory studies were conducted, and the native Striped Bass population was deemed extinct. This dissertation explored the collapse of the Saint John River Striped Bass starting with a complete historic perspective of the species in the Saint John River and concluded with a possible means to recover the population that was once believed to be lost. Within the chapters of this thesis I first summarize the history of Striped Bass in the Saint John River and explore why the current understanding of the species status needs to be updated. I locate and sample juvenile Striped Bass within the Saint John River for the first time since 1979, prove their native ancestry, and monitor their year class success. Native adult Striped Bass matching juvenile ancestry are tagged and tracked to determine the timing and location of their upstream spawning migration and the migrations of non-native adult Striped Bass within the Saint John River are also explored. I summarize information on Striped Bass winter ecology in Canada, then locate and describe four key winter habitats used by Striped Bass in the Saint John ii River. Finally, I draw a possible connection between the regulated discharges at the Mactaquac Generating Station to the success of Striped Bass juvenile recruitment observed in the Saint John River over six consecutive years of sampling. My general conclusion is that spawning by native Striped Bass in the Saint John River downstream of the Mactaquac Dam has been severely impacted, though not eliminated, by the regulated discharges resulting for power production. These discharge regimes have resulted in infrequently successful year classes, poor recruitment and possible spawning failures; however, spawning by surviving native origin Striped Bass may be recovered through the management of spring discharges. Managing for extended periods of moderate, sustained flow of sufficient volume and duration to keep Striped Bass eggs in suspension during the incubation period may restore successful Striped Bass spawning and juvenile recruitment in the Saint John River, New Brunswick. iii Acknowledgements Dr. Allen Curry and Dr. Tommi Linnansaari supervised my doctoral studies and together provided the perfect challenging yet supportive environment in which to complete this project. I want to sincerely thank Allen for providing thoughtful discussion and answers to my many questions, having enough faith in my work to allow me to develop my own research direction, methods, and explorations, and for carefully reading, commenting, and correcting all my chapters and articles. Allen has given me the confidence to take on large projects from start to finish and worked tirelessly to help me improve upon my writing. I also want to thank Tommi for always being interested in my progress and ideas and for always being available for discussions despite his chaotic schedule. Talking to Tommi has always meant learning something new, sharing a laugh, and has left me feeling the passion and motivation to keep on working. None of this project could have been accomplished without the kind and solid support of these two incredible supervisors. I also want to thank my committee, Rick Cunjak and Steve Peake, for their direction and helpful discussions concerning this ever-evolving project. This doctoral work was conducted as part of the Mactaquac Aquatic Ecosystem Study (MAES) directed by Dr. Allen Curry to study the status of the Saint John River in anticipation of large changes being proposed for the Mactaquac Dam. This project was funded in part by New Brunswick Power and NSERC and I am very grateful to have had the unique opportunity to conduct such a large and important project within the Saint John River across the last 5 years. Throughout this project I also received support from the Canadian Rivers Institute (Create WATER) grant, the Wildlife Trust Fund (WTF), iv and the Atlantic Salmon Conservation Foundation (ASCF) without which this project would not have been nearly as successful. As this project required a large field component, this work could not have been completed without the passionate and tireless work of all the CRI summer students and technicians. I would like to thank Mark Gautreau, Caitlin Tarr, and Ben Wallace for their help with vehicles and technical equipment and I would particularly like to thank our many students especially Chris Palmer, Lisa Rickard, Matt Miller, Eric Meng and Sarah Hirtle, and Post-doc Meaghan Bruce for spending long days in the field checking drift nets and retrieving receivers. Finally, I could not have completed this project without the help of the many hardworking graduate students on the MAES project including Daniel Arluison, Kaleb, Zelman, Antòin O’Sullivan, Bernhard Wegscheider and Amanda Babin who were always available to help with field work and research question no matter how large or complex. I also owe Dr. Wendy Monk and Bronwyn Fleet-Pardy a very sincere thank you for their patience in helping me with statistical and GIS questions, I learned so much and you both helped me streamline this project tremendously. I want to extend a special thank you to Steve Delaney who took keen interest in my work from the first day on the river and provided a lifetime of Striped Bass angling knowledge and observations. Steve has proven time and again to be a living fisheries archive to which I returned for insight and information on countless occasions. Many adventures on the Saint John River were shared on his boat, often with fishing rod in hand. I also want to thank Danny Sears for first sparking my interest in Striped Bass so many years ago on the Stewiacke River and perhaps sincerely, or maybe in jest, v suggesting that I study the species for my PhD. Regardless, I fell for the joke and he has kept in touch to provide support every step of the way. I am also very grateful to have had the support of Dr. Mike Dadswell who wrote so many of the first and most influential papers documenting and describing Striped Bass on the Saint John River. His kindness and incredible knowledge were always freely given, and his history of work formed the foundation upon which this project was built. Without his original explorations, hard work, and thoughtful guidance this project would hardly have achieved any of what is presented within these covers. I must also sincerely thank Scott Young and his late father Keith Young who graciously allowed me to accompany them at their family commercial fishing operation. Both were always kind and welcoming to me and any accompanying students, and openly shared their incredible depth of knowledge and love for the Saint John River. Keith fished with me until his very final season and his perspective, knowledge and love for the river will be irreplaceable. Finally, I would like to sincerely thank my family for their continuous support throughout the last 5 years, I could not have completed this project without them. vi Table of Contents Abstract .......................................................................................................................................... ii Acknowledgements ....................................................................................................................... iv List of Figures ............................................................................................................................... xi List of Tables .............................................................................................................................. xvi General Introduction and Background ........................................................................................... 1 1.1 Introduction .................................................................................................................... 1 1.2 Objectives of and purpose for Dissertation .................................................................... 3 1.3 Overview of Chapters ...................................................................................................