NOAA Technical Memorandum NMFS-NWFSC-78 Independent Populations of Chinook Salmon in Puget Sound July 2006 U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service NOAA Technical Memorandum NMFS Series The Northwest Fisheries Science Center of the National Marine Fisheries Service, NOAA, uses the NOAA Techni- cal Memorandum NMFS series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible due to time constraints. Documents published in this series may be referenced in the scientific and technical literature. The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Center continues the NMFS- F/NWC series established in 1970 by the Northwest & Alaska Fisheries Science Center, which has since been split into the Northwest Fisheries Science Center and the Alaska Fisheries Science Center. The NMFS-AFSC Techni- cal Memorandum series is now being used by the Alaska Fisheries Science Center. Reference throughout this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. This document should be cited as follows: Ruckelshaus, M.H., K.P. Currens, W.H. Graeber, R.R. Fuerstenberg, K. Rawson, N.J. Sands, and J.B. Scott. 2006. Independent populations of Chinook salmon in Puget Sound. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-78, 125 p. NOAA Technical Memorandum NMFS-NWFSC-78 Independent Populations of Chinook Salmon in Puget Sound Mary H. Ruckelshaus, Kenneth P. Currens1, William H. Graeber2,3, Robert R. Fuerstenberg4, Kit Rawson5, Norma J. Sands, and James B. Scott6 Northwest Fisheries Science Center Conservation Biology Division 2725 Montlake Boulevard East Seattle, Washington 98112 1 Northwest Indian Fisheries Commission 6730 Martin Way East Olympia, Washington 98516 2 Washington Department of Natural Resources PO Box 47001 Olympia, Washington 98504 3 National Marine Fisheries Service Regional Office 510 Desmond Drive Southeast, Suite 103 Lacey, Washington 98503 4 King County Department of Natural Resources and Parks 201 South Jackson Street, Suite 700 Seattle, Washington 98104 5 Tulalip Tribes 6700 Totem Beach Road Tulalip, Washington 98271 6 Washington Department of Fish and Wildlife 600 Capitol Way North Olympia, Washington 98501 July 2006 U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service Most NOAA Technical Memorandums NMFS-NWFSC are available online at the Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov) Copies are also available from: National Technical Information Service 5285 Port Royal Road Springfield, VA 22161 phone orders (1-800-553-6847) e-mail orders ([email protected]) ii Table of Contents List of Figures...............................................................................................................................................v List of Tables ..............................................................................................................................................vii Executive Summary.....................................................................................................................................ix Acknowledgments......................................................................................................................................xiii Abbreviations and Acronyms .....................................................................................................................xv Introduction...................................................................................................................................................1 Definition of a Population Used in this Approach ....................................................................................1 Structure below and above Population Level............................................................................................3 Conceptual Approach to Identifying Populations.........................................................................................4 Indicators of Population Structure.............................................................................................................4 Geography .............................................................................................................................................4 Migration Rates .....................................................................................................................................4 Genetic Attributes..................................................................................................................................5 Patterns of Life History and Phenotypic Characteristics.......................................................................5 Population Dynamics.............................................................................................................................5 Environmental and Habitat Characteristics ...........................................................................................5 Data Quality ..............................................................................................................................................6 Evaluating Similarity Between Groups.....................................................................................................6 Methods and Results.....................................................................................................................................8 Geographic Distribution of Puget Sound Chinook Salmon ......................................................................8 Direct Observations of Migration..............................................................................................................8 Genetic Attributes ...................................................................................................................................12 Methods ...............................................................................................................................................12 Results .................................................................................................................................................14 Patterns in Life History Characteristics...................................................................................................17 Methods ...............................................................................................................................................17 Results .................................................................................................................................................19 Spatial Synchrony in Spawner Abundance .............................................................................................22 Habitat Characteristics ............................................................................................................................22 Population Structure Decisions ...............................................................................................................22 Genetic Indicators................................................................................................................................25 Life History Indicators.........................................................................................................................26 Migration Indicators ............................................................................................................................26 iii Population Dynamics Indicators..........................................................................................................26 Habitat Indicators ................................................................................................................................27 Conclusions.................................................................................................................................................28 Habitats and Fish Outside Primary Spawning Areas: Implications for Recovery Planning.......................32 Naturally Spawning Chinook Salmon not Assigned to an Independent Population ...............................32 Importance of Habitats Outside Watersheds Containing Primary Spawning Areas ...............................32 Independent Populations in Puget Sound................................................................................................33 Nooksack River Basin .........................................................................................................................33 Skagit River Basin ...............................................................................................................................36 Stillaguamish River Basin ...................................................................................................................39 Snohomish River Basin .......................................................................................................................41 Central and South Puget Sound ...........................................................................................................44 Lake Washington.................................................................................................................................46 Duwamish/Green River .......................................................................................................................48