U.S. Fish & Wildlife Service Arcata Fisheries Technical Report TR 2018-33 Estimating Freshwater Productivity, Overwinter Survival, and Migration Patterns of Klamath River Coho Salmon Christopher V. Manhard, Nicholas A. Som, Russell W. Perry, Jimmy R. Faukner and Toz Soto U.S. Fish and Wildlife Service Arcata Fish and Wildlife Office 1655 Heindon Road Arcata, CA 95521 (707) 822-7201 February 2018 Funding for this study was provided by a variety of sources, including the Klamath River Fish Habitat Assessment Program administered by the Arcata Fish and Wildlife Office and the Bureau of Reclamation Klamath Falls Area Office. Disclaimer: The mention of trade names or commercial products in this report does not constitute endorsement or recommendation for use by the Federal Government. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service. The Arcata Fish and Wildlife Office Fisheries Program reports its study findings through two publication series. The Arcata Fisheries Data Series was established to provide timely dissemination of data to local managers and for inclusion in agency databases. Arcata Fisheries Technical Reports publish scientific findings from single and multi- year studies that have undergone more extensive peer review and statistical testing. Additionally, some study results are published in a variety of professional fisheries aquatic habitat conservation journals. To ensure consistency with Service policy relating to its online peer-reviewed journals, Arcata Fisheries Data Series and Technical Reports are distributed electronically and made available in the public domain. Paper copies are no longer circulated. key words: Population Dynamics, Productivity, Survival, Movement, Coho Salmon The correct citation for this report is: Manhard, C. V., N. A. Som, R. W. Perry, J. R. Faukner, and T. Soto. 2018. Estimating freshwater productivity, overwinter survival, and migration patterns of Klamath River Coho Salmon. U.S. Fish and Wildlife Service. Arcata Fish and Wildlife Office, Arcata Fisheries Technical Report Number TR 2018-33, Arcata, California. ii Table of Contents page List of Tables ....................................................................................................................... iv List of Figures ................................................................................................................... viii Introduction .......................................................................................................................... 2 Methods ................................................................................................................................ 4 Data sources: weirs and rotary screw traps ......................................................................... 4 Video counting weirs ⋅ ...................................................................................................... 4 Rotary screw traps ⋅ .......................................................................................................... 4 Data sources: PIT tag monitoring ....................................................................................... 8 Overwinter survival and winter emigration ⋅ ..................................................................... 8 Summer refuge entry timing ⋅ .......................................................................................... 12 Winter emigration timing ⋅ .............................................................................................. 13 Winter refuge entry timing ⋅ ............................................................................................ 15 Smolt emigration timing ⋅ ................................................................................................ 15 Data sources: environmental data ..................................................................................... 16 Statistical methods: freshwater productivity ..................................................................... 16 Ricker model of productivity ⋅ ......................................................................................... 16 Bayesian estimates of model parameters ⋅ ....................................................................... 17 Covariates of parr abundance ⋅ ....................................................................................... 18 Covariates of smolt abundance ⋅ ..................................................................................... 18 Statistical methods: overwinter survival and winter emigration ........................................ 21 Detection efficiencies and emigration rates ⋅ .................................................................. 21 Statistical methods: migration timing ............................................................................... 23 Logistic mixed effects model ⋅ ......................................................................................... 23 Covariates of adult migration timing ⋅ ............................................................................ 23 Covariates of parr emigration timing in the Scott and Shasta Rivers ⋅ ............................ 24 Covariates of smolt emigration timing in the Scott and Shasta Rivers ⋅ .......................... 24 Covariates of summer refuge entry timing ⋅ .................................................................... 25 Covariates of winter emigration timing ⋅ ......................................................................... 25 Covariates of winter refuge entry timing ⋅ ....................................................................... 25 Covariates of smolt emigration timing ⋅ .......................................................................... 27 Model predictive performance ⋅ ...................................................................................... 27 Statistical methods: mainstem migration rates .................................................................. 28 iii page Results ................................................................................................................................ 32 Freshwater productivity .................................................................................................... 32 Ricker models of Scott River abundance ⋅ ....................................................................... 32 Ricker models of Shasta River abundance ⋅ ..................................................................... 35 Overwinter survival and winter emigration ......................... 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Migration timing .............................................................................................................. 40 Adult migration timing in the Scott River, Shasta River, and Bogus Creek ⋅ ................... 40 Emigration timing in the Scott and Shasta Rivers ⋅ ......................................................... 47 Summer refuge entry timing in small tributaries ⋅ ........................................................... 52 Winter emigration timing in small tributaries ⋅ ............................................................... 58 Winter refuge entry timing in small tributaries ⋅ ............................................................. 58 Smolt emigration timing in small tributaries ⋅ ................................................................. 61 Mainstem migration rates ⋅ ............................................................................................. 68 Discussion .......................................................................................................................... 70 Literature Cited .................................................................................................................. 73 List of Tables Table 1. Annual abundance estimates of Scott River spawners ( ), outmigrating parr ( + 1), and outmigrating smolts ( + 2) used to estimate freshwater productivity models. The dates on which the weir was removed and the methods used to estimate juvenile abundance are each listed. ...................................................... 6 Table 2. Annual abundance estimates of Shasta River spawners ( ), outmigrating parr ( + 1), and outmigrating smolts ( + 2) used to estimate freshwater productivity models. The dates on which the weir was removed and the methods used to estimate juvenile abundance are each listed. ...................................................... 6 Table 3. Counts of adult Coho Salmon (N) observed at the Scott River, Shasta River, and Bogus Creek video counting weirs during years that were used to estimate models of adult migration timing. Weeks of weir operation are listed for each year and site. ......................................................................................................................... 7 Table 4. Counts (n) of age-0+ and age-1+ Coho Salmon at the Scott River rotary screw trap and abundance estimates ( ) in years that were used to estimate models of parr and smolt emigration timing. Weeks of trap operation and estimation methods are listed for each year and life stage. ............................................ 7 Table 5. Counts (n) of age-0+ and age-1+ Coho Salmon at the Shasta River rotary screw trap and abundance estimates ( ) in years that were used to estimate models of parr and smolt emigration timing. Weeks of trap operation and estimation methods are listed for each year and life stage. ...........................................