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Recovery Potential Assessment for Eastern Cape Breton Atlantic Salmon (Salmo Salar): Habitat Requirements and Availability; and Threats to Populations

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Recovery Potential Assessment for Eastern Cape Breton Atlantic Salmon (Salmo Salar): Habitat Requirements and Availability; and Threats to Populations Canadian Science Advisory Secretariat (CSAS) Research Document 2014/071 Maritimes Region Recovery Potential Assessment for Eastern Cape Breton Atlantic Salmon (Salmo salar): Habitat Requirements and Availability; and Threats to Populations A.J.F. Gibson, T.L. Horsman, J.S. Ford, and E.A. Halfyard Fisheries and Oceans Canada Science Branch, Maritimes Region P.O. Box 1006, Dartmouth, Nova Scotia Canada, B2Y 4A2 December 2014 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. Research documents are produced in the official language in which they are provided to the Secretariat. 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, 2014 ISSN 1919-5044 Correct citation for this publication: Gibson, A.J.F., Horsman, T., Ford, J. and Halfyard, E.A. 2014. Recovery Potential Assessment for Eastern Cape Breton Atlantic Salmon (Salmo salar): Habitat requirements and availability; and threats to populations. DFO Can. Sci. Advis. Sec. Res. Doc. 2014/071. vii + 141 p. TABLE OF CONTENTS ABSTRACT ................................................................................................................................. v RÉSUMÉ ................................................................................................................................... vi 1.0 INTRODUCTION...................................................................................................................1 1.1 SALMON RIVERS IN EASTERN CAPE BRETON ........................................................... 2 2.0 FUNCTIONAL DESCRIPTION OF HABITAT PROPERTIES (TOR 7) ...................................3 2.1 FRESHWATER ENVIRONMENT ..................................................................................... 3 2.2 ESTUARINE ENVIRONMENT .......................................................................................... 7 2.3 MARINE ENVIRONMENT ...............................................................................................10 3.0 SPATIAL EXTENT OF HABITAT FOR EASTERN CAPE BRETON SALMON POPULATIONS (TOR 8) .....................................................................................................12 3.1 FRESHWATER ENVIRONMENT ....................................................................................12 3.2 ESTUARINE ENVIRONMENT .........................................................................................13 3.3 MARINE ENVIRONMENT ...............................................................................................13 4.0 RESIDENCE REQUIREMENTS OF ATLANTIC SALMON (TOR 6) .................................... 15 4.1 REDDS ...........................................................................................................................16 4.2 HOME STONES ..............................................................................................................17 4.3 STAGING POOLS ...........................................................................................................18 5.0 SUPPLY OF SUITABLE HABITAT ......................................................................................18 5.1 INFLUENCE OF BARRIERS ON HABITAT ACCESSIBILITY (TOR 11) ..........................19 5.2 ABILITY OF HABITAT TO MEET DEMANDS AT PRESENT (TOR 12) ...........................19 5.3 ABILITY TO MEET HABITAT DEMANDS IN THE FUTURE (TOR 13) ............................20 5.4 TRADE-OFFS ASSOCIATED WITH HABITAT ALLOCATION OPTIONS (TOR 15) ........20 6.0 MAGNITUDE, EXTENT AND SOURCE OF THREATS TO EASTERN CAPE BRETON ATLANTIC SALMON IN FRESHWATER ENVIRONMENTS (TOR 9, 16, 20) ...................... 21 6.1 WATER QUALITY AND QUANTITY ................................................................................22 6.2 CHANGES TO BIOLOGICAL COMMUNITIES ................................................................28 6.3 PHYSICAL OBSTRUCTIONS .........................................................................................36 6.4 HABITAT ALTERATION ..................................................................................................39 6.5 DIRECTED SALMON FISHING .......................................................................................45 6.6 BY-CATCH IN OTHER FISHERIES ................................................................................46 7.0 MAGNITUDE, EXTENT AND SOURCE OF THREATS TO EASTERN CAPE BRETON ATLANTIC SALMON IN MARINE ENVIRONMENTS (TOR 9, 16, 20) ................................. 46 7.1 CHANGES TO BIOLOGICAL COMMUNITIES ................................................................47 7.2 CHANGES IN OCEANOGRAPHIC CONDITIONS ..........................................................52 7.3 PHYSICAL OR ABIOTIC CHANGE .................................................................................54 7.4 DIRECTED SALMON FISHERIES ..................................................................................55 7.5 BY-CATCH IN OTHER COMMERCIAL FISHERIES .......................................................56 7.6 COMMERCIAL FISHERIES ON PREY SPECIES OF SALMON .....................................57 8.0 EXTENT TO WHICH THREATS HAVE REDUCED HABITAT QUALITY AND QUANTITY (TOR 20) .............................................................................................................................57 iii 9.0 FEASIBILITY OF RESTORING HABITATS TO HIGHER VALUES (TOR 14) ..................... 58 10.0 SUMMARY ........................................................................................................................58 11.0 REFERENCES..................................................................................................................59 12.0 TABLES ............................................................................................................................82 13.0 FIGURES ........................................................................................................................113 APPENDIX 1 ...........................................................................................................................133 A.1 GEOGRAPHIC INFORMATION SYSTEMS ANALYSES ..............................................133 A.2 DELINEATION OF WATERSHED BOUNDARIES AND FLOW NETWORK .................. 133 A.3 GEOPHYSICAL CHARACTERISATION OF WATERSHEDS .......................................134 A.4 SPATIAL ANALYSES IN THE MARINE ENVIRONMENT .............................................135 A.5 LAND USE AND THREATS INFORMATION FOR EASTERN CAPE BRETON WATERSHEDS ............................................................................................................136 iv ABSTRACT The purpose of this Research Document is to provide background information on the habitat characteristics required by Atlantic Salmon in eastern Cape Breton to complete their life-cycle, as well as the stressors and threats impacting those processes. The document includes information related to: 1. functional descriptions of habitat properties, 2. the spatial extent of areas in eastern Cape Breton having these properties, 3. identified threats to habitat, as well as threats to populations that are not habitat-related, 4. the extent to which threats have reduced habitat quality or quantity in eastern Cape Breton, and 5. the potential for mitigation of identified threats. Each of these components was requested by the Terms of Reference for the Recovery Potential Assessment for eastern Cape Breton salmon. Information is presented for the fresh water and marine (and estuarine where appropriate) environments separately. Habitat requirements of Atlantic Salmon in freshwater include properties, such as water quality, substrate composition, discharge characteristics, and accessibility. Several life stages (eggs, age-0, age-1 and age-2+ juveniles) have residences that individuals defend and that are required to support essential life-cycle processes. At the current low population sizes of eastern Cape Breton Atlantic Salmon, freshwater habitats are unlikely to be limiting recovery in rivers as there remains a large proportion of accessible area. Habitat requirements in marine and estuarine environments have not been delineated spatially, but are thought to be primarily related to food availability and oceanographic conditions, as individuals require resources and water conditions that support rapid growth. As such, the areas occupied by Atlantic Salmon populations from eastern Cape Breton likely vary over time with oceanographic environments (currents, temperature, food availability). Tagging data are limited, however, eastern Cape Breton salmon are likely to use much of the northwest Atlantic, in particular the waters of coastal Cape Breton, the southern coast of Newfoundland, western Newfoundland, the Labrador sea and the West Greenland sea. There is no evidence for a residence in the marine environment. Research on population dynamics of Atlantic Salmon demonstrate that survival in the marine environment is not resource-limited, so the availability of habitat in marine environments is not limiting population size. Threats have been identified that are likely to have an effect on Atlantic
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