WILD ADULT STEELHEAD AND CHINOOK SALMON ABUNDANCE AND COMPOSITION AT LOWER GRANITE DAM, SPAWN YEAR 2012 2012 ANNUAL REPORT Photo: IDFG Prepared by: William C. Schrader, Principal Fishery Research Biologist Michael W. Ackerman, Fishery Research Biologist Timothy Copeland, Senior Fishery Research Biologist Carl Stiefel, Regional Fisheries Biologist Matthew R. Campbell, Fisheries Genetics Program Coordinator Matthew P. Corsi, Regional Fisheries Biologist Kristin K. Wright, Fishery Research Biologist Patrick Kennedy, Senior Fishery Research Biologist IDFG Report Number 14-16 October 2014 WILD ADULT STEELHEAD AND CHINOOK SALMON ABUNDANCE AND COMPOSITION AT LOWER GRANITE DAM, SPAWN YEAR 2012 2012 Annual Report By William C. Schrader Michael W. Ackerman Timothy Copeland Carl Stiefel Matthew R. Campbell Matthew P. Corsi Kristin K. Wright Patrick Kennedy Idaho Department of Fish and Game 600 South Walnut Street P.O. Box 25 Boise, ID 83707 To U.S. Department of Energy Bonneville Power Administration Division of Fish and Wildlife P.O. Box 3621 Portland, OR 97283-3621 Project Numbers #1990-055-00, 1991-073-00, 2010-026-00 Contract Numbers 50973, 55728, 55703, 57343 IDFG Report Number 14-16 October 2014 ACKNOWLEDGEMENTS Report Authors: William C. Schrader (IDFG) Michael W. Ackerman (IDFG / PSMFC) Timothy Copeland (IDFG) Carl Stiefel (IDFG) Matthew R. Campbell (IDFG) Matthew P. Corsi (IDFG) Kristin K. Wright (IDFG / PSMFC) Patrick Kennedy (IDFG) Report Contributors: Data, reviews, and other assistance (alphabetical) IDFG • Laura Redfield NMFS Northwest • Ron Roberts Fisheries Science Center • Amber Barenberg • Craig Steele • Randy Bartels • Thea Vanderwey • Vicky Brenner • Grant Bruner • Ninh Vu • Janine Fetke • Alan Byrne • Tiffani Marsh • Pete Hassemer • Ken McIntyre • Lance Hebdon Columbia River Inter- • Darren Ogden • Brian Leth Tribal Fish Commission • Neil Paasch • Charleen Neal • Ken Thomas • Charlie Petrosky • Jon Hess • Leslie Reinhardt • Amanda Matala • Lynn Schrader • Andrew Matala Quantitative • Chris Sullivan • Shawn Narum Consultants, Inc. • Chuck Warren • Jeff Stephenson • Allen Bartels • Jody White IDFG / PSMFC University of Idaho • Paul Bunn • Kirk Steinhorst • Tyler Gross • Kala Hernandez • Cliff Hohman • Tyler Johnson • Dylan Kovis • Jesse McCane i ACKNOWLEDGEMENTS (CONTINUED) Project Administration: Funding and other assistance (alphabetical) • Bonneville Power Administration (BPA); projects: 1990-055-00 Idaho Steelhead Monitoring and Evaluation Studies 1991-073-00 Idaho Natural Production Monitoring and Evaluation Program 2010-026-00 Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam • Idaho Office of Species Conservation (IOSC) • Idaho Power Company (IPC) • Northwest Power and Conservation Council (NPCC) • Pacific States Marine Fisheries Commission (PSMFC) • Quantitative Consultants, Inc. (QCI) • U. S. Fish and Wildlife Service, Lower Snake River Compensation Program (LSRCP) Suggested citation: Schrader, W. C., M. W. Ackerman, T. Copeland, C. Stiefel, M. R. Campbell, M. P. Corsi, K. K. Wright, and P. Kennedy. 2014. Wild adult steelhead and Chinook salmon abundance and composition at Lower Granite Dam, spawn year 2012. Idaho Department of Fish and Game Report 14-16. Annual report 2012, BPA Projects 1990-055-00, 1991-073-00, 2010-026-00. ii ABBREVIATIONS AND ACRONYMS BPA Bonneville Power Administration BY Brood Year CI Confidence Interval COE U. S. Army Corps of Engineers CWT Coded Wire Tag DPS Distinct Population Segment ESA Endangered Species Act ESU Evolutionarily Significant Unit F Female FL Fork Length GSI Genetic Stock Identification IA Individual Assignment ICBTRT Interior Columbia Basin Technical Recovery Team IDFG Idaho Department of Fish and Game IOSC Idaho Office of Species Conservation IPC Idaho Power Company ISEMP Integrated Status and Effectiveness Monitoring Project LGR Lower Granite Dam LSRCP Lower Snake River Compensation Plan M Male MCMC Markov Chain Monte Carlo MM Mixture Modeling MPG Major Population Group MY Smolt Migration Year NMFS National Marine Fisheries Service PBT Parentage Based Tag PIT Passive Integrated Transponder PSMFC Pacific States Marine Fisheries Commission QCI Quantitative Consultants, Inc. SNP Single Nucleotide Polymorphism SY Spawn Year TAC Technical Advisory Committee, U.S. v. Oregon VSP Viable Salmonid Population WDFW Washington Department of Fish and Wildlife iii TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ............................................................................................................ i ACKNOWLEDGEMENTS (continued) ......................................................................................... ii ABBREVIATIONS AND ACRONYMS ........................................................................................ iii ABSTRACT ................................................................................................................................. 1 INTRODUCTION ........................................................................................................................ 2 METHODS .................................................................................................................................. 3 Adult Trap Operations at Lower Granite Dam .......................................................................... 3 Trap Data Management ........................................................................................................... 4 Valid Sample Selection ............................................................................................................ 4 Scale Processing and Analysis ................................................................................................ 5 Genetics Tissue Processing and Analysis ................................................................................ 6 Escapement by Origin, Size, Age, Sex, and Stock ................................................................... 8 Wild Stock Escapement by Sex, Age, and Size...................................................................... 10 RESULTS ................................................................................................................................. 10 Steelhead Escapement .......................................................................................................... 10 Wild Steelhead Age, Sex, and Stock Composition ................................................................. 11 Chinook Salmon Escapement ................................................................................................ 13 Wild Chinook Salmon Age, Sex, and Stock Composition ....................................................... 13 Age Validation ........................................................................................................................ 15 DISCUSSION............................................................................................................................ 15 LITERATURE CITED ................................................................................................................ 20 TABLES .................................................................................................................................... 26 FIGURES .................................................................................................................................. 32 APPENDICES ........................................................................................................................... 49 iv LIST OF TABLES Page Table 1. Major population groups and independent populations within the Snake River steelhead distinct population segment (DPS) and spring-summer Chinook salmon evolutionary significant unit (ESU; ICBTRT 2003, 2005; Ford et al. 2010; NMFS 2011). ........................................................................... 27 Table 2. Status of the fish ladder, the fish counting window and video, and the adult trap sample rate at Lower Granite Dam, 7/1/2011 to 8/17/2012 (COE 2011, 2012; Ogden 2012, 2013). .............................................................. 29 Table 3. External mark and internal tag key used to determine hatchery origin steelhead and Chinook salmon at Lower Granite Dam (LGR), spawn year 2012. .................................................................................................................. 30 Table 4. Estimated annual total escapement, by fish size and origin, of steelhead at Lower Granite Dam (LGR), spawn years 1976-2012. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Estimates for 1987 and later were generated by IDFG and are the COE window counts decomposed using NMFS adult trap data (Alan Byrne, IDFG, personal communication; Schrader et al. 2011, 2012, 2013; present study). Estimates for 1986 and earlier are the COE window counts decomposed using an unknown method. ................................................................................ 31 v LIST OF FIGURES Page Figure 1. Genetic stocks and baseline collections used for steelhead mixed stock analysis at Lower Granite Dam, spawn year 2012 (Ackerman et al. 2014). The Hells Canyon Tributaries MPG (shaded gray) does not support independent populations and is considered extirpated (NMFS 2011). ................ 33 Figure 2. Genetic stocks and baseline collections used for Chinook salmon mixed stock analysis at Lower Granite Dam, spawn year 2012 (Ackerman et al. 2014). Reintroduced fish exist in functionally extirpated TRT populations as mapped. ........................................................................................................ 34 Figure 3. Daily number of steelhead counted at the Lower Granite Dam window or by video, spawn year 2012. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 98.9% of the total run (n = 180,320). ........................................................................................................... 35 Figure 4. Estimated escapement, by fish size and origin, of steelhead at Lower Granite Dam, spawn year 2012. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%. .................................. 36 Figure 5. Estimated hatchery and wild steelhead escapement at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. ................................. 37 Figure 6. Estimated escapement by age class, grouped by smolt migration year (MY), of wild adult steelhead at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Confidence intervals are at 95%. ............. 38 Figure 7. Estimated escapement by brood year of wild adult steelhead at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Confidence intervals are at 95%. ....................................................................... 39 Figure 8. Estimated escapement by gender of wild adult steelhead at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Confidence intervals are at 95%. ....................................................................... 40 Figure 9. Estimated escapement by genetic stock of wild adult steelhead at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Confidence intervals are at 95%. See Appendix Table B-1 for stock abbreviations. .................................................................................................... 41 Figure 10. Daily number of Chinook salmon counted at the Lower Granite Dam window or by video, spawn year 2012. Horizontal bar indicates when the adult trap was open or closed; overall, it was open during 99.0% of the total run (n = 84,771). ......................................................................................... 42 Figure 11. Estimated escapement by origin of Chinook salmon at Lower Granite Dam, spawn year 2012. Clipped and unclipped refer to the adipose fin. Confidence intervals are at 95%. ....................................................................... 43 Figure 12. Estimated hatchery and wild Chinook salmon escapement at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. ..................... 44 Figure 13. Estimated escapement by age class, grouped by smolt migration year (MY), of wild adult Chinook salmon at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. .............................................................. 45 Figure 14. Estimated escapement by brood year of wild adult Chinook salmon at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. .......... 46 vi List of Figures, continued. Page Figure 15. Estimated escapement by gender of wild adult Chinook salmon at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. ..................... 47 Figure 16. Estimated escapement by genetic stock of wild adult Chinook salmon at Lower Granite Dam, spawn year 2012. Confidence intervals are at 95%. See Appendix Table B-2 for stock abbreviations. ............................................... 48 vii LIST OF APPENDICES Page Appendix A. Lower Granite Dam trap sampling protocols, SY2012. ....................................... 50 Appendix B: Snake River genetic baselines v2.0 (Ackerman et al. 2014) used for stock identification at Lower Granite Dam, spawn year 2012....................................... 64 Appendix Table B-1. Genetic stocks and baseline collections used for steelhead mixed stock analysis at Lower Granite Dam, spawn year 2012 (Ackerman et al. 2014). MPG = major population group. ...................................................... 65 Appendix Table B-2. Genetic stocks and baseline collections used for Chinook salmon mixed stock analysis at Lower Granite Dam, spawn year 2012 (Ackerman et al. 2014). MPG = major population group. .................................... 67 Appendix C: Wild adult steelhead at Lower Granite Dam, spawn year 2012. ......................... 68 Appendix Table C-1. Weekly window or video counts and adult valid trap samples of steelhead at Lower Granite Dam (LGR), spawn year 2012. ............................... 69 Appendix Table C-2. Number of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGR), spawn year 2012. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. .......................................... 70 Appendix Table C-3. Percentage of steelhead captured in the adult trap, by fish size and origin, at Lower Granite Dam (LGR), spawn year 2012. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. Percentages may not sum to 100.0% due to rounding error. ................................................................ 71 Appendix Table C-4. Estimated weekly escapement, by fish size and origin, of steelhead at Lower Granite Dam (LGR), spawn year 2012. Large fish are greater than or equal to 78 cm (FL) and small fish are less than 78 cm (FL). Clipped and unclipped refer to the adipose fin. .......................................... 72 Appendix Table C-5. Number of wild adult steelhead scale and genetics samples collected at Lower Granite Dam and subsequently aged or genotyped, spawn year 2012. Large and small fish were combined. .................................... 73 Appendix Table C-6. Weekly age frequencies by smolt migration year, brood year, and age class of wild adult steelhead sampled at Lower Granite Dam, spawn year 2012. Large and small fish were combined. .................................... 74 Appendix Table C-7. Weekly age percentages by smolt migration year, brood year, and age class of wild adult steelhead sampled at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error. .......................................................... 75 Appendix Table C-8. Weekly gender frequencies of wild adult steelhead sampled at Lower Granite Dam, spawn year 2012. Large and small fish were combined. .......................................................................................................... 76 Appendix Table C-9. Weekly gender percentages of wild adult steelhead sampled at Lower Granite Dam, spawn year 2012. Large and small fish were combined. Percentages may not sum to 100.0% due to rounding error. ............ 77 viii