19-05 Upstream Migration Timing of Columbia Basin Chinook and Sockeye Salmon and Steelhead in 2017 Jeffrey K. Fryer, John Whiteaker, Denise Kelsey, and Jon Hess May 24, 2019 Upstream Migration Timing of Columbia Basin Chinook and Sockeye Salmon and Steelhead in 2017 Columbia River Inter-Tribal Fish Commission Technical Report for BPA Project 2008-518-00, Contract 76151 Report date range: 1/17–12/17 Jeffrey K. Fryer John Whiteaker Denise Kelsey Jon Hess May 24, 2019 ABSTRACT Between April 19 and October 18, 2017, we sampled Chinook (Oncorhynchus tshawytscha) and Sockeye (Oncorhynchus nerka) salmon as well as steelhead (Oncorhynchus mykiss) at the Bonneville Dam Adult Fish Facility (AFF). Fish were measured for fork length, scales were collected for analysis of age, tissue samples collected for genetic analysis, and the fish were tagged with Passive Integrated Transponder (PIT) tags. These fish were tracked upstream as they passed through sites with PIT tag antennas, including fish ladders at dams, juvenile bypasses, hatcheries, weirs, as well as in-stream antennas. Total numbers of fish tracked upstream were 829 spring Chinook, 1,005 summer Chinook, 971 fall Chinook, 836 steelhead, and 1,079 Sockeye Salmon. Chinook Salmon median migration rates between mainstem dams ranged between 18.7 km/day for fall Chinook migrating between McNary and Priest Rapids dams and 42.0 km/day for spring Chinook migrating between The Dalles and McNary dams. An estimated 31.8% of spring Chinook passed into the Snake Basin upstream of Ice Harbor Dam, while an estimated 58.0% of summer Chinook passed upstream of Priest Rapids dam into the Upper Columbia Basin. Among fall Chinook, the primary terminal area was between McNary Dam (passed by 45.0% of fall Chinook) and Ice Harbor Dam (passed by 8.6% of Fall Chinook) and Priest Rapids Dam (passed by 5.9% of all Fall Chinook). Escapement estimates for the entire Chinook run derived from PIT tag detections result in estimates differing from those estimated by visual counts by -15.8%% to -2.2% at mainstem dams. Steelhead median migration rates reported between mainstem dams ranged from 11.2 km to 33.2 km/day. Among Steelhead classified as B-run (greater or equal to 78 cm fork length) that were last detected in terminal areas (tributaries between Bonneville and McNary Dam and above McNary Dam), 83.3% were detected in the Snake Basin. Based on the data reported, the percentage of steelhead classified as B-run at Bonneville Dam reached its highest level at 30.0% of the run in Statistical Week 37. The number of B-run steelhead peaked in Week 37 at 3,601 steelhead while the number of A-run (<78 cm) peaked in Week 34 at 22,728 fish. It should be noted that in Week 37, the total sample size was 10 steelhead, 3 of which were B-run. Also, sampling restrictions meant that no picket leads could be deployed in Week, 27, meaning the fish we sampled that week i entered the trap volitionally and may not have been representative of the run. A total of 64 steelhead PIT tagged and tracked in 2017 (were detected moving downstream (mostly in juvenile bypasses) after spawning, recovered or detected in kelt programs, or detected moving upstream in summer/fall 2017 or in 2018, and were designated as kelt. A total of 1095 Sockeye Salmon were sampled in 2017 and 1079 tracked upstream. The principle age components of the run were Age 1.2 (47.6%), Age 1.3 (36.3%), and Age 1.1 (11.7%). Sockeye median migration rates between mainstem dams ranged between 28.4 and 51.7 km/day. Escapement estimates for the entire Sockeye run derived from PIT tag detections at mainstem Columbia River dams result in estimates differing from those estimated by visual counts by - 18.0% to +23.4% at Columbia River dams. ii ACKNOWLEDGMENTS The following individuals assisted in this project: Christine Petersen and Peter Lofy of the Bonneville Power Administration, David Graves, Doug Hatch, Melissa Holland, Chrissy Bynum, Britney Oseth, Joe Nowinski, Jeremiah Newell, Jayson FiveCrows, Agnes Strong, Crystal Chulik, Amber Cate, Aaron Ikemoto, and Zach Penney of CRITFC; Ben Hausmann, Brian Bissell, and Andrew Derugin of the US Army Corps of Engineers, and Nicole Tancreto of the Pacific States Marine Fisheries Commission. This report summarizes research funded by the Bonneville Power Administration under the Columbia Basin Fish Accords (2008-518-00) and the Pacific Salmon Commission. iii TABLE OF CONTENTS ABSTRACT ........................................................................................................ i ACKNOWLEDGMENTS ................................................................................... iii TABLE OF CONTENTS ................................................................................... iv LIST OF TABLES ............................................................................................. vi LIST OF FIGURES ............................................................................................ x INTRODUCTION ............................................................................................. 13 METHODS ....................................................................................................... 14 Sampling .................................................................................................. 14 Upstream Detection ................................................................................. 15 Site Detection Efficiencies ....................................................................... 16 Age Analysis ............................................................................................ 17 Escapement ............................................................................................. 17 Migration Rates and Passage Times ....................................................... 18 Upstream Age and Length-at-Age Composition Estimates ...................... 18 Fallback ................................................................................................... 18 Night Passage ......................................................................................... 19 Steelhead B-Run Analyses ...................................................................... 20 Steelhead Kelt Analyses .......................................................................... 20 Straying .................................................................................................... 20 RESULTS-CHINOOK ...................................................................................... 22 Sample Size ............................................................................................. 22 Distribution of Sample .............................................................................. 24 Detection Numbers .................................................................................. 26 Age Analysis ............................................................................................ 26 Mainstem Dam Recoveries, Mortality, and Escapement Estimates ......... 26 Migration Rates and Passage Time ......................................................... 34 Upstream Age and Length-at-Age Composition ...................................... 35 Fallback ................................................................................................... 43 Night Passage ......................................................................................... 44 Straying .................................................................................................... 45 RESULTS-STEELHEAD ................................................................................. 47 Sample Size ............................................................................................. 47 Distribution of Sample .............................................................................. 48 Detection Numbers .................................................................................. 48 Age Analysis ............................................................................................ 48 Mainstem Dam Recoveries, Mortality, and Escapement Estimates ......... 49 Migration Rates and Passage Time ......................................................... 53 iv Upstream Age and Length-at-Age Composition ...................................... 54 Fallback ................................................................................................... 57 Night Passage ......................................................................................... 58 B-Run Analyses ....................................................................................... 59 Kelt Analyses ........................................................................................... 61 Straying .................................................................................................... 68 RESULTS-SOCKEYE ..................................................................................... 72 Sample Size ............................................................................................. 72 Age Composition ..................................................................................... 72 Detection Numbers .................................................................................. 73 Mainstem Dam Recoveries, Mortality, and Escapement Estimates ......... 74 Migration Rates and Passage Time ......................................................... 78 Night Passage ........................................................................................