20-01 Studies into Factors Limiting the Abundance of Okanagan and Wenatchee Sockeye Salmon in 2018 Jeffrey Fryer, Denise Kelsey, Howie Wright, Skyeler Folks, Richard Bussanich, Kim Hyatt, Dan Selbie, and Margot Stockwell April 10, 2020 Studies into Factors Limiting the Abundance of Okanagan and Wenatchee Sockeye Salmon in 2018 Columbia River Inter-Tribal Fish Commission Technical Report for BPA Project 2008-503-00, Contract 010774 Report date range: 1/18–12/18 Jeffrey K. Fryer and Denise Kelsey Columbia River Inter-Tribal Fish Commission Howie Wright, Skyeler Folks, and Richard Bussanich Okanagan Nation Alliance Kim D. Hyatt, Dan Selbie, and Margot M. Stockwell Department of Fisheries and Oceans, Canada April 10, 2020 1 EXECUTIVE SUMMARY A total of 1,871 Sockeye Salmon, Oncorhynchus nerka, were sampled and 1,859 PIT tagged at the Bonneville Dam Adult Fish Facility in 2018. Sockeye PIT tagged by this project, along with previously PIT tagged Sockeye Salmon, were tracked upstream using data from detection arrays at mainstem Columbia River dam fish ladders as well as in- river arrays in the Wenatchee and Okanagan basins. Upstream detections of adult PIT tagged Sockeye Salmon tracked by this project resulted in an estimated survival of 93.3% to The Dalles Dam, 88.9% to McNary Dam and 80.7% to Rock Island Dam in 2018. Genetic stock identification (GSI) was used to classify the stock of 1,858 Sockeye Salmon sampled at Bonneville Dam. Concurrence between Sockeye Salmon classified both by genetics and final PIT tag detection site was 100% for the Okanagan and Wenatchee River stocks. Stock composition at Bonneville Dam in 2018 was estimated as 90.2% Okanagan, 9.0% Wenatchee, 0.6% Yakima, 0.2% Snake, and 0.0% Deschutes. The estimated minimum fallback rates at Columbia River mainstem dams ranged from 0.1% at Bonneville Dam to 4.5% at John Day Dam. In the Okanagan Basin, PIT tag antennas installed and maintained by this project at Zosel Dam (ZSL) and the Okanagan Channel (OKC) were operational for the entire year (Appendix A). Between January 1, and December 31, 2018, at Zosel Dam a total of 695 Sockeye, four Chinook, 19 steelhead, two Coho, and one White Sturgeon were detected. High flows in 2018 resulted in spill gates open sufficiently to allow salmon to swim upstream through the spillway without being detected by fishway PIT tag antennas. As a result, only 41.9% of passing PIT tagged Sockeye detected upstream of Zosel were detected at Zosel Dam. At Wells Dam, 805 Sockeye Salmon were sampled, eight of which were previously PIT tagged by this project at Bonneville Dam. The remaining 797 Sockeye were PIT tagged at Wells Dam. The stock composition for Sockeye tagged at Wells Dam based on GSI and PIT tags was 97.4% Okanagan and 2.6% Wenatchee compared to 99.9% Okanagan and 0.1% Wenatchee stock for Sockeye tagged at Bonneville Dam detected at Wells Dam. Okanagan juvenile PIT tagging resulted in 10,943 smolts being tagged between April 16 and May 9, 2018 at three sites, SKAHAL (Skaha Lake), OSOYOBR (downstream i of the Highway 3 Bridge at the Osoyoos Narrows) and OSOYOL (Osoyoos Lake North Basin) (Appendix C). Reliable estimates of survival from release to Rocky Reach Dam could be calculated for all three release groups with survival estimates ranging from 0.576 (SE=0.036) for the SKAHAL group to 0.691 (SE=0.039) for the OSOYHA group. From Rocky Reach Dam to McNary Dam, survival estimates ranged from 0.599 (se=0.144) for the OSOYOL group to 0.913 (se=0.132) for the SKAHAL group. After McNary, error associated with survival estimates for both release groups, individually and combined, was large. Travel time from release to Rocky Reach Dam ranged from 14.0 days for the SKAHAL group to 25.7 days for the OSOYOL group. This project is proposed to continue and evolve over the next several years. One area of continuing concern is adult survival between Wells Dam and Osoyoos Lake. We had a good understanding of mortality sites upstream of Wells Dam, thanks to PIT tag detection in Zosel fish ladders as well as acoustic tag results. However, in 2016, acoustic tagging was dropped due to the large expense for the relatively small number of tags deployed, and instead focus was placed on PIT tags. PIT tag detection of returning adult Sockeye Salmon at Zosel Dam has varied from year to year depending on flow. At high flows, such as in 2018, a high percentage of Sockeye pass undetected through the spillway. Of the Sockeye Salmon passing Wells Dam in 2018, only 58.5% of the Bonneville-tagged Sockeye and 51.8% of the Wells-tagged Sockeye were detected upstream. It is unknown what portion of this mortality may have been associated with migration conditions downstream of Zosel Dam or in Osoyoos Lake. PIT tag detection improvements at, or near, Zosel Dam could improve understanding of adult survival to this point during high flows when Sockeye Salmon do not use the fish ladders. Lake Wenatchee acoustic trawl surveys (ATS) are expected to continue along with limnological sampling to better estimate the annual production and future productive potential of Lake Wenatchee Sockeye Salmon (Appendices F and G). The ATS data from Skaha, Osoyoos, and Wenatchee lakes are also used in Columbia Basin run forecasting for Sockeye. There are several unanswered questions regarding Lake Wenatchee Sockeye that may be addressed by this project. A primary question is why Lake Wenatchee Sockeye, in recent years, have not increased in relative abundance as much as Okanagan Sockeye, or even Snake River Sockeye. Limnology and ATS work should help to answer this question, but it is also uncertain what the optimal spawning escapement goal is for this stock. An optimal escapement analysis is being completed, ii using other funding, for Osoyoos and Skaha Sockeye (Okanagan stock). A similar analysis is being considered for the Wenatchee stock. iii ACKNOWLEDGMENTS The following individuals assisted in this project: Steve Anglea and Brett Turley of Biomark, Victoria Bohlen, Maureen Kavanagh, and Christine Peterson of Bonneville Power Administration, Joe Nowinski, Ryan Branstetter, Amber Cate, Crystal Chulik, Brittney Oseth, David Graves, Doug Hatch, Jayson FiveCrows, Jon Hess, Aaron Ikemoto, and Agnes Strong of the Columbia River Inter-Tribal Fish Commission; Sonya Schaller of the Confederated Tribes of the Colville Reservation; Ben Hausmann, Tammy Mackey, Jon Rerecich, and Casey Welch of the US Army Corps of Engineers; Dan Selbie of Canada Department of Fisheries and Oceans; Tom Kahler of Douglas County PUD; Don McQueen; Ryan Benson, Jessica Hilton-McPherson, Sheena Hooley, Chelsea Mathieu, Amanda Stevens, Jamison Squakin, Cash Tonasket, Lynnea Wiens, and Nicholas Yaniw of the Okanagan Nation Alliance; Jay O’Brien and Derek Mendoza of the Okanagan- Tonasket Irrigation District; Nicole Tancreto of the Pacific States Marine Fisheries Commission; Al Josephy of Washington Department of Ecology, Travis Maitland, Ben Truscott, and Andrew Murdoch of Washington Department of Fish and Wildlife; and Keely Murdoch, Corey Kampaus, Kraig Mott, Casey Heemsah, Clifford Smith, and Terri Benson of the Yakama Nation. This report summarizes research funded by the Bonneville Power Administration under the Columbia Basin Fish Accords and the Pacific Salmon Commission. iv TABLE OF CONTENTS EXECUTIVE SUMMARY ............................................................................................................................... i ACKNOWLEDGMENTS .............................................................................................................................. iv LIST OF TABLES ....................................................................................................................................... vii LIST OF FIGURES ..................................................................................................................................... xii INTRODUCTION ......................................................................................................................................... 15 METHODS .................................................................................................................................................. 19 Adult PIT Tag Detection Infrastructure ................................................................................................... 19 Zosel and OKC PIT tag arrays ........................................................................................................... 19 Adult Sampling at Bonneville, Wells, and Priest Rapids dams ............................................................... 19 Bonneville Dam Sampling .................................................................................................................. 19 Wells Dam Sampling .......................................................................................................................... 20 Stock Identification and Classification .................................................................................................... 21 Genetic Stock Identification (GSI) and Parental Based Tagging (PBT) ................................................. 21 PIT Tag Stock Identification ............................................................................................................... 22 Final Stock Classification Rules ......................................................................................................... 23 Age Analysis ..........................................................................................................................................