Canadian Science Advisory Secretariat (CSAS) Research Document 2018/043 Maritimes Region Review of the Inner Bay of Fundy Atlantic Salmon (Salmo salar) Monitoring Activities Associated with the Live Gene Bank Ross A. Jones1, Stephanie M. Ratelle1, Sarah M. Tuziak1, Carolyn Harvie2, Beth Lenentine3, and Patrick T. O’Reilly2 1Fisheries and Oceans Canada Gulf Fisheries Centre 343 University Avenue Moncton, NB, E3C 9B6 2Fisheries and Oceans Canada Bedford Institute of Oceanography PO Box 1006, 1 Challenger Drive Dartmouth, NS, B2Y 4A2 3Fisheries and Oceans Canada Coldbrook Biodiversity Facility 1420 Fish Hatchery Lane Coldbrook, NS B4R 1B5 February 2020 Foreword This series documents the scientific basis for the evaluation of aquatic resources and ecosystems in Canada. As such, it addresses the issues of the day in the time frames required and the documents it contains are not intended as definitive statements on the subjects addressed but rather as progress reports on ongoing investigations. Published by: Fisheries and Oceans Canada Canadian Science Advisory Secretariat 200 Kent Street Ottawa ON K1A 0E6 http://www.dfo-mpo.gc.ca/csas-sccs/ [email protected] © Her Majesty the Queen in Right of Canada, 2020 ISSN 1919-5044 Correct citation for this publication: Jones, R.A., Ratelle, S.M., Tuziak, S.M., Harvie, C., Lenentine, B., and O’Reilly, P.T. 2020. Review of the Inner Bay of Fundy Atlantic Salmon (Salmo salar) Monitoring Activities Associated with the Live Gene Bank. DFO Can. Sci. Advis. Sec. Res. Doc. 2018/043. vii + 128 p. Aussi disponible en français : Jones, R.A., Ratelle, S.M., Tuziak, S.M., Harvie, C., Lenentine, B. et O’Reilly, P.T. 2020. Examen des activités de surveillance du saumon atlantique (Salmo salar) de l’intérieur de la baie de Fundy associées à la banque de gènes vivants. Secr. can. de consult. sci. du MPO, Doc. de rech. 2018/043. vii + 141 p. iii TABLE OF CONTENTS LIST OF ABBREVIATIONS ........................................................................................................ V ABSTRACT ............................................................................................................................... IV 1.0 INTRODUCTION................................................................................................................... 1 1.1 INNER BAY OF FUNDY ATLANTIC SALMON ECOLOGY .............................................. 1 1.2 INNER BAY OF FUNDY ATLANTIC SALMON STATUS .................................................. 1 1.3 REVIEW OBJECTIVES .................................................................................................... 2 2.0 MATERIALS AND METHODS ............................................................................................... 3 2.1 LIVE GENE BANK............................................................................................................ 3 2.1.1 Collections and Distributions ..................................................................................... 3 2.1.2 Genetic Analysis ........................................................................................................ 4 2.2 SMOLT ASSESSMENT ................................................................................................... 4 2.2.1 Big Salmon River ....................................................................................................... 5 2.2.2 Stewiacke River ......................................................................................................... 6 2.2.3 Gaspereau River ....................................................................................................... 6 2.3 ADULT ASSESSMENT .................................................................................................... 7 2.3.1 Big Salmon River ....................................................................................................... 7 2.3.2 Gaspereau River ....................................................................................................... 8 2.4 LIVE GENE BANK SURVIVAL ......................................................................................... 8 2.4.1 Freshwater Survival Estimates .................................................................................. 9 2.4.2 Marine Survival Estimates ......................................................................................... 9 2.5 PROJECTS ...................................................................................................................... 9 2.5.1 2010-2016 Crossbreeding Experiment in the Petitcodiac River ................................. 9 2.5.2 Electrofishing Surveys ..............................................................................................10 2.5.3 Statistical Analysis ....................................................................................................12 3.0 RESULTS ........................................................................................................................... 13 3.1 LIVE GENE BANK...........................................................................................................13 3.1.1 Collections ................................................................................................................13 3.2 SMOLT ASSESSMENT ..................................................................................................13 3.2.1 Big Salmon River ......................................................................................................13 3.2.2 Stewiacke River ........................................................................................................16 3.2.3 Gaspereau River ......................................................................................................17 3.3 ADULT ASSESSMENT ...................................................................................................18 3.3.1 Big Salmon River ......................................................................................................18 3.3.2 Gaspereau River ......................................................................................................20 3.4 LIVE GENE BANK SURVIVAL ........................................................................................22 3.4.1 Freshwater Survival Estimates .................................................................................22 3.4.2 Marine Survival Estimates ........................................................................................22 3.5 PROJECTS .....................................................................................................................23 iii 3.5.1 Petitcodiac River Crossbreeding Experiment ............................................................23 3.5.2 Stewiacke River Electrofishing Surveys ....................................................................24 3.5.3 Broadscale Electrofishing Survey Results ................................................................26 4.0 CONCLUSIONS .................................................................................................................. 28 4.1 CONCLUSION FROM LGB PROGRAM RELEASES ......................................................28 4.2 CONCLUSIONS ON THE OVERALL STOCK STATUS ..................................................30 4.3 OTHER POINTS FOR CONSIDERATION ......................................................................31 5.0 ACKNOWLEDGEMENTS ................................................................................................... 31 6.0 REFERENCES ................................................................................................................... 32 7.0 TABLES .............................................................................................................................. 36 8.0 FIGURES ............................................................................................................................ 68 9.0 APPENDICES ................................................................................................................... 103 iv LIST OF ABBREVIATIONS 1SW: one sea winter DNA: deoxyribonucleic LGBPG: Live Gene Bank acid pre-grilse 2SW: two sea winter DU: Designatable Unit Lgth: length 3SW: three sea winter Eff.: efficiency Loc.: location A: angling EQU: equalized LoP: Long Pool ABL: Aquatic Biotechnology Laboratory EU: European LP: Lodge Pool Ad.: adipose F: female M: mark Ad: adult FC: fin clip M: male AE: aquaculture escapee FFFN: Fort Folly First m: metres Nations AgeR: river age MB: Mast Brow FFHR: Fort Folly Habitat Age : sea age MBF: Mactaquac S Restoration Biodiversity Facility ANOVA: Analysis of FL: fork length Variance Meth.: method FMP: fish management AP: Amateur Pool MLC: mid-lower caudal practice BB: Bonnell Brook MM: month GAK: Gaspereau River BD: blue dye Morts.: mortalities GB: Gravelly Bar BF: Biodiversity Facility MP: Miller Pool GPS: Global Positioning BP: bypass System MSW: multi-sea winter BSR: Big Salmon River H/AC: hatchery adipose- MUC: mid-upper caudal Capt.: capture clip stray N/A: data not available Cat.: category HSD: Honest Significant NB: New Brunswick Difference CBF: Coldbrook NBDERD: New Brunswick Biodiversity Facility IBoF: Inner Bay of Fundy Department of Energy and Resource Development CER: conservation egg JD: Julian day requirement Juv: juvenile NC: not collected cm: centimetres KP: King Pool NMB: New Minas Basin Colc.: Colchester L: large NS: Nova Scotia COSEWIC: Committee on LC: lower caudal NSH: Nashwaak River the Status of Endangered