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The Atlantic Salmon (Salmo Salar) Is an Economically and Socially Important Species Throughout Its Range Worldwide

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The Atlantic Salmon (Salmo Salar) Is an Economically and Socially Important Species Throughout Its Range Worldwide In-stream habitat enhancement for juvenile Atlantic salmon in the Little Main Restigouche River, New Brunswick by Peter Emerson Bachelor of Science (Natural Science), Lyndon State College, 2001 Bachelor of Science (Aeronautical Science), Embry-Riddle Aeronautical University, 1995 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science In the Graduate Academic Unit of Biology Supervisor: R.A. Cunjak, Ph.D., Dept. of Biology Examining Board: Tommi Linnansaari, Ph.D., Dept. of Biology, Chair Katy Haralampides, Ph.D., Dept. of Civil Engineering This thesis is accepted by the Dean of Graduate Studies THE UNIVERSITY OF NEW BRUNSWICK September, 2014 ©Peter W. Emerson, 2014 ABSTRACT Boulder clusters were placed at three sites with small, homogeneous substrate in the Little Main Restigouche River in northern New Brunswick, Canada, in late summer 2005 to improve the rearing habitat for pre-smolt Atlantic salmon (Salmo salar). Population estimates were conducted at enhancement, control and reference sites between 2005-2007 prior to enhancement and for two years following enhancement to compare response of salmon parr. Age-2 parr density increased at enhancement sites following enhancement. During December 2005, a 25-year flood event and subsequent ice up and freshet in spring disturbed the study sites. A method was designed to interpret and rank boulder cluster stability degradation, and the data were compared with electrofishing estimates of abundance of salmon ages 0+, 1+ and 2+. Age 2+ parr abundance and biomass and age 1+ parr abundance were significantly higher at clusters ranked stable than at clusters ranked degraded. ii ACKNOWLEDGEMENTS I thank my supervisor, Dr. Rick Cunjak, for his patience during this project. I am particularly grateful for his understanding as I continued the long writing process while employed full time and while raising a family. His guidance was priceless throughout. Dr. Cunjak’s enthusiasm for science and the natural world was infectious from my first introduction and continued as he encouraged my through the lengthy editing process. I also wish to thank my other graduate committee members: Dr. Miriam Barbeau and Peter Cronin, they too provided guidance throughout the project. I am particularly grateful for the time and knowledge that Dr. Barbeau shared. I thank J.D. Irving, Limited for giving me the opportunity to conduct this project out of their Boston Brook Lodge. Their commitment to fisheries research has made this project possible. I was proud and thankful for the opportunity to live, albeit seasonally, with J.D. Irving staff Bill and Jane Lee. Their kindness, guidance and great cooking and company made this project possible and more enjoyable. I am thankful for the financial assistance for the project provided by J.D. Irving, Limited and a NSERC Collaborative Research and Development grant provided to Dr. Rick Cunjak. My time at UNB is most memorable because of the numerous friends I made, and the countless acts of kindness I experienced. Canada was a new place to me, and New iii Brunswick lived up to its deserved reputation as a province of hospitality. I will forever remember it as a place filled with amicable and gregarious men and women. I am especially grateful to the many colleagues at UNB that offered their assistance. Particularly, Dr. T. Linnansaari for the lessons in fish tracking and for the many days our families spent together, Dr. T. Jardine for his repeated generosity, J. Poole and C. Poole for being so welcoming to a new student, Dr. C. Breau, A. Fraser, Dr. J. Kurek and to M. Gallant for the shared experiences during the planning and installation of the clusters, K. Connell, M. Sabean, B. Savage, J. Peart and S. Fraser for their persistence during the worst weather and their shared love of the Restigouche and its fish. Thanks also to Dr. D. Drolet for his repeated statistics lessons that he selflessly offered between climbing excursions. Finally, thanks to C. Connell for the time he took to bring me up to speed on the project and for the introduction to the Restigouche and Miramichi Rivers. I want to thank my family, particularly my mother who steadfastly encouraged me as my life bounced around, to stick with it. Dad…this work is dedicated to you. I wish you were still here to share a toast…cheers big ears. Ramona, thank you for travelling this crazy road with me, and for encouraging me as I considered giving up. My boys! Clay and Sam…someday we’ll make it back and give you a lesson with a pole. iv Table of Contents ABSTRACT........................................................................................................................ ii ACKNOWLEDGEMENTS ............................................................................................... iii Table of Contents ................................................................................................................ v List of Tables .................................................................................................................... vii List of Figures .................................................................................................................... xi 1 In-stream enhancement on the Little Main Restigouche River, New Brunswick....... 1 1.1 The status of Atlantic salmon ....................................................................................... 1 1.2 Atlantic salmon biology - Lifecycle ............................................................................. 3 1.3 Atlantic salmon biology - juvenile requirements.......................................................... 5 1.4 Habitat enhancement history......................................................................................... 7 1.5 Salmon and habitat characteristics in the Little Main Restigouche River .................... 9 1.6 The NSERC - CRD project ......................................................................................... 11 1.7 Thesis overview .......................................................................................................... 13 1.8 Bibliography........................................................................................................... 14 2 The response of Atlantic salmon parr to boulder enhancement in the Little Main Restigouche River, New Brunswick ................................................................................. 26 2.1 Abstract ....................................................................................................................... 26 2.2 Introduction ................................................................................................................. 26 2.3 Research Objectives ............................................................................................ .…..32 2.4 Study Area .................................................................................................................. 33 2.5 Methods....................................................................................................................... 37 2.5.1 Substrate surveys .................................................................................................... 37 2.5.2 Electrofishing and tagging...................................................................................... 40 2.5.3 PIT tagging ............................................................................................................. 44 2.5.4 Statistical analysis .................................................................................................. 45 2.6 Results....................................................................................................................... ..46 2.6.1 Substrate surveys .................................................................................................... 47 2.6.2 Electrofishing and tagging...................................................................................... 47 2.6.3 Pre-treatment dates versus post-treatment dates .................................................... 48 2.6.4 Enhancement versus control - fish density ............................................................. 49 2.6.5 Enhancement versus reference - fish density ......................................................... 49 2.6.6 Enhancement versus control - fish weight ............................................................. 50 2.6.7 Enhancement versus reference - fish weight ......................................................... 50 2.6.8 Other species .......................................................................................................... 51 2.6.9 VIE and PIT recapture............................................................................................ 51 2.6.10 PIT tracking .......................................................................................................... 52 2.7 Discussion ................................................................................................................... 53 2.7.1 Habitat .................................................................................................................... 53 2.7.2 Biological response ................................................................................................ 54 2.7.3 Tagging and emigration.......................................................................................... 57 v 2.8 Bibliography ..........................................................................................................
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