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Lower American River, California Juvenile Salmonid Emigration Monitoring in the Lower American River, California January – June 2020 By Cory Starr Logan Day Prepared for: U.S. Fish and Wildlife Service, Comprehensive Assessment and Monitoring Program and California Department of Fish and Wildlife by the Pacific States Marine Fisheries Commission The suggested citation for this report is: Starr, C. and L. Day. 2020. Juvenile Salmonid Emigration Monitoring in the Lower American River, California January – June 2020. Unpublished report prepared for the U.S. Fish and Wildlife Service and California Department of Fish and Wildlife, Sacramento, California. 54 pp. ii Table of Contents Table of Contents ............................................................................................................................ iii List of Figures ................................................................................................................................... v List of Tables .................................................................................................................................. vii Acronyms and Abbreviations ........................................................................................................ viii Abstract ........................................................................................................................................... ix Introduction .................................................................................................................................... 1 Study Area ....................................................................................................................................... 3 Methods .......................................................................................................................................... 4 Trap Operations ........................................................................................................................... 4 Safety Measures ........................................................................................................................... 5 Environmental Parameters .......................................................................................................... 6 Catch and Fish Data Collection .................................................................................................... 6 Trap Efficiency .............................................................................................................................. 9 Passage Estimates ...................................................................................................................... 11 Retention in Analysis.................................................................................................................. 15 Confidence Interval Estimates ................................................................................................... 15 Fulton’s Condition Factor ........................................................................................................... 15 Results ........................................................................................................................................... 16 Trap Operations ......................................................................................................................... 16 Environmental Summary ........................................................................................................... 17 Catch .......................................................................................................................................... 19 Fall-run Chinook Salmon ...................................................................................................... 19 Fulton’s Condition Factor ..................................................................................................... 23 Trap Efficiency ...................................................................................................................... 23 Passage Estimate for Fall-Run Chinook Salmon ................................................................... 24 Genetic Analysis ................................................................................................................... 25 Spring-run and Winter-run Chinook Salmon ....................................................................... 27 Steelhead ............................................................................................................................. 28 Non-salmonid Species .......................................................................................................... 29 Discussion...................................................................................................................................... 31 Project Scope ............................................................................................................................. 31 Passage Estimate and Catch ...................................................................................................... 31 Biological Observations .............................................................................................................. 33 Limitations and Recommendations ........................................................................................... 36 Management Implications ............................................................................................................ 37 Acknowledgements ....................................................................................................................... 38 References .................................................................................................................................... 39 Appendix 1: Points of interest on the Lower American River. ..................................................... 42 Appendix 2: Weekly environmental conditions on the Lower American River during the 2020 survey season. ................................................................................................................ 43 iii Appendix 3: List of natural origin fish species caught during the 2020 season using rotary screw traps on the Lower American River. ............................................................................. 44 Appendix 4: Genetic results for fin-clip samples from Chinook Salmon caught in the Lower American River during the 2020 survey season. ......................................................... 45 Appendix 5: Fulton’s condition factor (K), overall, and by life stage, of fall-run Chinook Salmon during the 2020 Lower American River rotary screw trap survey season. ............... 50 Appendix 6: Median seasonal discharge (cfs), total catch of fall-run Chinook Salmon, winter-run Chinook Salmon, spring-run Chinook Salmon, and steelhead, and the associated passage estimate with 95% confidence intervals (CI) for fall-run Chinook Salmon from the 2013 – 2020 Lower American River rotary screw trap sampling seasons. ................................................................................................................................... 51 Appendix 7: Annual comparison of daily average water temperatures at Watt Avenue between 2006 and 2020. Daily average water temperature (°C), highest temperature year, lowest temperature year, 15 year average, and the current year (2020)..................... 52 Appendix 8: Annual comparison of daily average discharge at Fair Oaks on the American River between 2006 and 2020. Daily average discharge (cfs), highest water year, lowest water year, 15 year average, and the current year (2020). ........................................ 53 Appendix 9: A view of the American River at Watt Ave under different flow conditions. .......... 54 iv List of Figures Figure 1: Rotary screw trap locations in the north and south channels of the Lower American River. Inset image illustrates the side-by-side trapping configuration in the north channel. ........ 4 Figure 2: The two north channel 8 foot traps (8.1 and 8.2) on the lower American River just downstream of the Watt Avenue overcrossing. ............................................................................. 4 Figure 3: Dates sampling occurred during the 2020 Lower American River rotary screw trap survey season. ............................................................................................................................... 16 Figure 4: Weighted average hours per Julian week that both traps sampled successfully, sampled unsuccessfully, or did not sample during the 2020 lower American River rotary screw trap survey season. ....................................................................................................................... 16 Figure 5: Dates sampling occurred, daily average discharge (cfs) measured at Fair Oaks, and the daily minimum, maximum, and average water temperature (°C) measured at Watt Avenue during the 2020 Lower American River rotary screw trap survey season. .................................. 17 Figure 6: Daily average velocity (m/s), turbidity (NTU), and dissolved oxygen (DO) (mg/L), recorded during the 2020 American River rotary screw trap survey season. .............................. 18 Figure 7: Weekly minimum, maximum, and average fork length (mm) and total catch of natural origin fall-run Chinook Salmon during the 2020 Lower American River rotary screw trap sampling season. ..........................................................................................................................
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