2013 Yankee Fork Salmon River Chinook Salmon Run Report Lytle P. Denny, William S. Youmans, and David J. Evans Shoshone‐Bannock Tribes 2013 Yankee Fork Salmon River Chinook Salmon Run Report Annual Report Prepared by: Lytle P. Denny, William S. Youmans, and David J. Evans Shoshone-Bannock Tribes Fish and Wildlife Department 3rd and B Avenue Fort Hall, Idaho (208) 239-4560 Prepared for: United States Fish and Wildlife Service Lower Snake River Compensation Plan – Office 1387 S. Vinnell Way, Suite 343 Boise, Idaho 83709 Cooperative Agreement F13AC00031 October 1, 2012 – September 30, 2013 March 1, 2014 ii TABLE OF CONTENTS LIST OF FIGURES .................................................................................................................................... IV LIST OF TABLES ........................................................................................................................................ V ABSTRACT ................................................................................................................................................ VI PROGRAM PERSONNEL .......................................................................................................................VII AUTHORS .................................................................................................................................................VII ACKNOWLEDGEMENTS ......................................................................................................................VII INTRODUCTION ........................................................................................................................................ 1 PROJECT BACKGROUND ............................................................................................................................. 2 PROGRAM PHASES, GOALS, AND OBJECTIVES ............................................................................................ 4 STUDY AREA .............................................................................................................................................. 5 SMOLT RELEASE AND ACCLIMATION STUDY ............................................................................... 6 JUVENILE TRAPPING .............................................................................................................................. 7 ADULT TRAPPING .................................................................................................................................. 16 POLE FLAT WEIR ...................................................................................................................................... 16 ADULT TRAPPING ..................................................................................................................................... 19 RUN-TIMING ............................................................................................................................................. 21 AGE STRUCTURE ...................................................................................................................................... 22 FIVE MILE WEIR ....................................................................................................................................... 26 HATCHERY ADULT OUTPLANTS ....................................................................................................... 27 POLE FLAT WEIR HATCHERY OUTPLANTS ............................................................................................... 27 SAWTOOTH HATCHERY OUTPLANTS ........................................................................................................ 27 HARVEST MONITORING ...................................................................................................................... 30 SPAWNING GROUND SURVEYS .......................................................................................................... 30 REDD COUNTS .......................................................................................................................................... 30 CARCASS SURVEYS .................................................................................................................................. 33 MARK-RECAPTURE EVALUATION ................................................................................................... 33 FISH PER REDD ESTIMATION ............................................................................................................. 34 POLE FLAT TO FIVE MILE WEIR ............................................................................................................... 34 ABOVE FIVE MILE WEIR .......................................................................................................................... 35 TOTAL ESCAPEMENT ........................................................................................................................... 36 DISCUSSION AND RECOMMENDATIONS ........................................................................................ 36 CITATIONS ................................................................................................................................................ 38 APPENDIX A: REGIONAL PARTICIPATION .................................................................................... 41 iii LIST OF FIGURES Figure 1. Map of Yankee Fork Salmon River, Idaho, displaying weir locations. ............. 6 Figure 3. Yankee Fork rotary screw trap, May 17, 2012. .................................................. 7 Figure 4. Yankee Fork screw trap tagging trailer. ............................................................. 9 Figure 5. Frequency of life-stage specific juvenile Chinook salmon observed at the screw trap. ........................................................................................................................... 11 Figure 6. Daily trapping frequency and proportion of juvenile Chinook salmon observed at the screw trap. ....................................................................................................... 12 Figure 7. Length-weight relationship of juvenile Chinook salmon observed at the screw trap. ........................................................................................................................... 13 Figure 8. Length frequency of juvenile Chinook salmon. ............................................... 14 Figure 9. Fork length (mm) (a), weight (g) (b), and condition (C) of juvenile Chinook salmon. Box plots show the 10th, 25th, 50th, 75th, and 90th percentiles, and individual data points outside the 10th and 90th percentiles. ...................................................... 15 Figure 10. Pole Flat weir, catwalk, fish trap, live-wells, and work station. ..................... 18 Figure 11. Trapping frequency of natural and hatchery-origin Chinook salmon at Pole Flat weir. ................................................................................................................... 20 Figure 12. Length-weight relationship of adult Chinook salmon. ................................... 21 Figure 13. Run-timing of natural and hatchery-origin Chinook salmon at Pole Flat weir. ................................................................................................................................... 22 Figure 14. Length frequency of hatchery and natural-origin Chinook salmon trapped at Pole Flat weir. ........................................................................................................... 23 Figure 15. Age structure of hatchery and natural-origin Chinook salmon trapped at Pole Flat weir. ................................................................................................................... 24 Figure 16. Age structure and gender of hatchery (A) and natural-origin (B) Chinook salmon trapped at Pole Flat weir. .............................................................................. 25 Figure 17. Photo of Five Mile weir, fish trap, live-wells, and workstation. .................... 26 Figure 18. Length frequency of hatchery-origin Chinook salmon obtained from Sawtooth Fish Hatchery. ........................................................................................................... 29 Figure 19. Age distribution of hatchery-origin Chinook salmon obtained from Sawtooth Fish Hatchery. ........................................................................................................... 29 Figure 20. Chinook salmon redds in Yankee Fork, 1956 - 2012. .................................... 33 iv LIST OF TABLES Table 1. Number and percentage of natural and hatchery-origin Chinook salmon trapped at Pole Flat weir from 2008 – 2012. ........................................................................... 3 Table 2. Sex ratio of natural and natural Chinook salmon trapped at Pole Flat weir from 2008 – 2012................................................................................................................. 3 Table 3. Sex ratio of all fish, hatchery-origin fish, and natural-origin fish observed at Pole Flat weir. ........................................................................................................... 19 Table 4. Age class totals for all Chinook salmon trapped at Pole Flat weir. ................... 22 Table 5. Number, location, and percentages of hatchery-origin male and female Chinook salmon trapped at Pole Flat weir and outplanted in upper Yankee Fork. ................. 27 Table 6. Number, location,