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Eagle Creek Radio Telemetry Report

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Eagle Creek Radio Telemetry Report Ecological and Genetic Interactions between Hatchery and Wild Steelhead in Eagle Creek, Oregon Final Report Jeff Hogle and Ken Lujan collecting genetic and fish health samples in Eagle Creek, Oregon. Photo Credit: Maureen Kavanagh Ecological and Genetic Interactions between Hatchery and Wild Steelhead in Eagle Creek, Oregon Final Report Prepared by: Maureen Kavanagh, William R. Brignon and Doug Olson U.S. Fish and Wildlife Service Columbia River Fisheries Program Office Hatchery Assessment Team Vancouver, WA 98683 -and- Susan Gutenberger U.S. Fish and Wildlife Service Lower Columbia River Fish Health Center Willard, WA 98605 -and- Andrew Matala and William Ardren U.S. Fish and Wildlife Service Abernathy Fish Technology Center Applied Research Program in Conservation Genetics Longview, WA 98632 July 23, 2009 Table of Contents 1.0 Executive Summary ................................................................................................................................ 9 2.0 Introduction ........................................................................................................................................... 10 3.0 Geographic Area ................................................................................................................................... 12 4.0 Background Information on Winter Steelhead in the Clackamas River & Eagle Creek ....................... 13 5.0 Methods ................................................................................................................................................ 14 5.1 Adult Return Timing, Distribution, and Abundance .......................................................................... 14 5.1.1 Lower Ladder Trap Operations 2005-2007 ............................................................................... 14 5.1.2 Radio-Telemetry 2005-2007 ...................................................................................................... 15 5.1.3 Spawning Ground Surveys ........................................................................................................ 16 5.1.4 Mark-Recapture Population Estimates 2007-2008 ................................................................... 16 5.1.5 Length, Sex, and Age Class Structure ...................................................................................... 17 5.2 Smolt Migration Monitoring and Abundance ..................................................................................... 17 5.2.1 Radio-Tagging and Tracking of Steelhead Smolts 2005-2008 ................................................. 17 5.2.2 Smolt Trap Operation and Abundance Estimates 2006 and 2008 ............................................ 18 5.3 Distribution, Summer Rearing Density, and Habitat Selection of Juvenile Fish ............................... 19 5.3.1 Habitat Surveys 2007 ................................................................................................................ 19 5.3.2 Snorkel Surveys and Population Estimates 2007 ..................................................................... 20 5.4 Disease Profile 2005-2007 ............................................................................................................... 21 5.5 Genetic Analysis ............................................................................................................................... 22 5.5.1 Genetic Sample Collections 2005-2007 .................................................................................... 22 5.5.2 Microsatellite Amplification and Analysis .................................................................................. 23 5.5.3 Species ID: hybrid screening ..................................................................................................... 25 6.0 Results .................................................................................................................................................. 25 6.1 Adult Steelhead Return Timing, Distribution and Abundance .......................................................... 25 6.1.1 Lower Ladder Trap Operations 2005-2007 ............................................................................... 25 6.1.2 Radio-Telemetry 2005-2007 ...................................................................................................... 26 6.1.3 Spawning Ground Surveys ........................................................................................................ 27 6.1.4 Mark-Recapture Population Estimates 2007-2008 ................................................................... 28 6.1.5 Length, Sex and Age Class Structure ....................................................................................... 28 6.2 Smolt Migration Monitoring and Abundance ..................................................................................... 28 6.2.1 Radio Tagging and Tracking of Steelhead Smolts 2005-2008 ................................................. 28 6.2.2 Smolt Trap Operations and Abundance Estimates 2006 and 2008 .......................................... 31 6.3 Distribution, Summer Rearing Density,and Habitat Selection of Juvenile Fish ................................ 32 6.3.1 Habitat Surveys 2007 ................................................................................................................ 32 6.3.2 Snorkel Surveys and Population Estimates 2007 ..................................................................... 32 6.3.3 Fish Distribution and Density 2007 ........................................................................................... 32 6.3.4 Wild Fish Displacement by Residual Hatchery Winter Steelhead ............................................. 33 6.4 Disease Profile 2005-2007 ............................................................................................................... 33 6.5 Genetic Analysis ............................................................................................................................... 34 6.5.1 Descriptive Statistics 2005-2007 ............................................................................................... 34 6.5.2 Population Genetic Structure Analysis ...................................................................................... 35 6.5.3 Baseline Assignment Tests ....................................................................................................... 36 7.0 Discussion ............................................................................................................................................. 36 7.1 Adult Return Timing, Distribution, and Abundance .......................................................................... 36 7.2 Smolt Migration Monitoring and Abundance ..................................................................................... 39 7.3 Distribution, Summer Rearing Density, and Mesohabitat Selection of Juvenile Fish....................... 41 7.4 Disease Profile .................................................................................................................................. 43 7.5 Genetic Analysis ............................................................................................................................... 46 8.0 Recommendations ................................................................................................................................ 47 9.0 Tables.................................................................................................................................................... 51 10.0 Figures ................................................................................................................................................ 69 Literature Cited .......................................................................................................................................... 106 i Appendix 1: List of loci amplified for the Eagle Creek analysis (2005-2007). The symbol (*) designates a locus that is standardized in the Stephen Phelps Allele Nomenclature (SPAN) standardization effort. The annealing temperatures and MgCl2 concentrations are optimized PCR conditions for the conservation genetics program at Abernathy Fish Technology Center ......................................................................... 116 Appendix 2: Results from wild fish health survey conducted on juvenile salmon and steelhead in Eagle Creek from 2004-2007. Unless otherwise noted, all fish were tested for the following fish pathogens: infectious hematopoietic necrosis virus (IHNV), infectious pancreatic necrosis virus (IPNV), viral hemorrhagic septicemia virus (VHSV), Oncorhynchus masou virus (OMV), infectious salmon anemia virus (ISAV), Aeromonas salmonicida (AS, furunculosis), Yersinia ruckeri (YR, enteric redmouth disease), Flavobacterium columnare (CD, columnaris), Flavobacterium psychrophilum (CWD, coldwater disease), Renibacterium salmoninarum, (RS, bacterial kidney disease), and Myxobolus cerebralis (MC. whirling disease). Larger fish were screened for RS using the enzyme-linked immunosorbent assay (ELISA); a positive finding of RS denotes that ELISA results were confirmed by a second test, the polymerase chain reaction assay (PCR). All methods for detecting and identifying fish pathogens were based on standardized procedures from the AFS Fish Health Blue Book (USFWS and AFS-FHS 2007) and the National Wild Fish Health Survey – Laboratory Procedures Manual (Puzach 2006). .............................. 117 Appendix 3: Results
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