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Prepared in cooperation with the Bureau of Reclamation

Survival and Migration Behavior of Juvenile Coho Salmon in the Klamath River Relative to Discharge at Iron Gate Dam, Northern California, 2007

By John W. Beeman and Steve Juhnke, U.S. Geological Survey, Greg Stutzer and Nicholas Hetrick, U.S. Fish and Wildlife Service

Abstract

This report describes a study of survival and migration behavior of radio-tagged juvenile coho salmon (Oncorhynchus kisutch) in the Klamath River, northern California, in 2007. This was the third year of a multi-year study with the goal of determining the effects of discharge at Iron Gate Dam (IGD) on survival of juvenile coho salmon downstream. Survival and factors affecting survival were estimated in 2006 and 2007 after work in 2005 showed radio telemetry could be used effectively. The study has included collaborative efforts among U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service (USFWS), the Karuk and Yurok Tribal Fisheries Departments, and the U.S. Bureau of Reclamation. The objectives of the study included: (1) estimating the survival of wild and hatchery juvenile coho salmon in the Klamath River downstream of Iron Gate Dam, determining the effects of discharge and other covariates on juvenile coho salmon survival (2) and migration (3), and (4) determining if fish from Iron Gate Hatchery (IGH) could be used as surrogates for the limited source of wild fish.

We have been able to meet the first objective by estimating the survivals of hatchery and wild fish (when available) downstream of IGD. We have not yet met the second or third objectives, because we have been unable to separate effects of discharge from other environmental variables as they pertain to the survival or migration of juvenile coho salmon. This was foreseen when the study began, as it was known there would likely be no experimental discharges. A multi-year analysis will be conducted after the data for the third planned year are available. The fourth objective was initiated in 2006, but wild fish were not available in 2007. The next year wild fish may be available is in 2009, based on their 3-year cycle of abundance.

River discharges during the 2007 study period (April 10 through July 28, 2007) were below average compared to the period of record beginning in 1962. Average daily discharge at IGD was 1,518 cubic feet per second (ft³/s) and ranged from 1,020 to 2,460 ft³/s. Average daily discharge near the estuary at river kilometer (rkm) 13 was 9,820 ft³/s and ranged from 3,270 to 20,500 ft³/s.

This study was based on hatchery fish taken directly from a holding tank at IGH. Wild fish were not available in numbers sufficient for use in 2007. Fish tagging began on April 9 and concluded on May 17, 2007. A total of 246 hatchery coho salmon were tagged and released, split evenly between releases in the Klamath River near IGH (rkm 309) and near the Tree of Heaven campground at rkm 280.

The two release sites were used to enable estimation of a relative survival between IGH and the campground using the paired-release design, because potential effects of tagging and handling can be cancelled out with this method. However, the assumption that the survival probabilities of fish from each release site are equal in the reaches they have in common was violated, preventing its use in 2007. All estimates of survival were therefore calculated using the single-release design.

The reach-specific estimates of survival were lower in 2007 than in 2006, but a similar survival pattern was evident among reaches in each year. The survival from IGH to rkm 33 was 0.653 [standard error (SE) 0.039] in 2006 and 0.497 (SE 0.044) in 2007. In each year, the reaches with the lowest survivals were upstream of the Scott River, which also is the area with the greatest differences in survivals between years. The reach with the highest survivals were in the Salmon River-to-Trinity River reach (at or near 1.0 in each year). The cause of the difference in survivals in each year were not identified, but could be related to differences in discharge or turbidity, as these are the primary differences between the years. These differences and other effects will be analyzed when the data from all study years (initially planned for 2006 through 2008) are available. Models of survival with and without a year effect were nearly equally supported by the data, indicating uncertainty in the importance of the difference between years. Estimates of survival were lower in fish released near Tree of Heaven campground than those released near IGH in the reaches they had in common. For example, estimated survival for fish released near the campground to rkm 33 were 0.301 (SE 0.041) and 0.700 (SE 0.058) for fish released near IGH. The largest difference in survival between the groups of fish released was in the reach from the campground to the Scott River, in which the survivals were 0.589 (SE 0.045) and 0.814 (SE 0.044); the point estimates of survival of fish released near IGH were higher than fish released near the campground in every reach. The cause of this difference is unknown, but possible explanations include differences in expression of tagging effects, slower migration of fish released near the campground, or the potential for a greater exposure to disease in these fish based on the prevalence of Manayunkia speciosa, a host in the life cycle of Ceratomyxa shasta and Parvicapsula minibicornis, near the campground.

The effects of discharge on migration in 2007 were affected by fish migration behavior. As in 2006, few hatchery fish released near IGH were detected passing the Shasta River site until May, despite releases that began in early April. The change in fish behavior from non-migrant to migrant affects the relation of discharge and migration, because of fish released near IGH those fish upstream of the Shasta River primarily are non-migrants and those downstream are migrants. The effects of discharge on passage rate were small at the Scott River site in 2007, and large in 2006—the slowest passage rates occurred during the highest discharges. The results are consistent with the data: fish migration rate increased with date of release, water temperature increased with date, and discharge generally decreased with date. The effects of discharge, water temperature, and date are often confounded.

Analyses prompted by the current results have led to increased knowledge of the factors affecting migration and survival. Data collected in 2006 and 2007 clearly indicate that hatchery fish released near IGH early in the study period reside upstream of the Shasta River for much longer than fish released later, because few fish migrate until about mid-May. Greater time in the river is often assumed to infer a greater risk of mortality, but the data do not support this inference. Models with a relation between release week and survival in 2006 and 2007 were not supported by the data, but the data do support a positive relation between fish weight and survival upstream of the Scott River. The comparison of release week and survival between years was based on a subset of the data available to eliminate the potential for seasonal differences between years, and some results contradict earlier analyses. We hypothesize that larger fish either out-compete smaller ones for the best cover habitat, spend less time feeding during periods of high mortality risk than smaller fish (for example, during the day), or both. These migration behaviors are well-supported in the literature.

We will alter the study design in 2008 based on data from 2006 and 2007. We will not implement the paired-release design, because (1) an important assumption was violated in 2007, (2) the design reduces sample sizes in the IGH-to-Shasta River reach by 50 percent, and (3) the tagging and handling mortality was negligible when the design was used in 2006. We will tag and release fish from a tank at IGH as well as hatchery fish captured in traps near the I-5 Bridge. The purpose of this added activity will be to see if the use of migrant hatchery fish will result in migration behavior more similar to the behavior of wild fish in 2006. An additional group of wild fish would improve this design, but wild fish probably will not be available in sufficient numbers for our use in 2008.

Contents

Abstract
Introduction
Methods
Results
Summary
Acknowledgments
References Cited
Appendix 1. Tag life test.
Appendix 2. Results of Analyses of Tissues for Bacterial Kidney Disease.
Appendix 3. Capture Histories of Hatchery Fish from Control and Treatment Groups Released from April 10 through May 18, 2007.
Appendix 4. Capture Histories of Hatchery Fish from the Treatment Group Released from April 10 through May 18, 2007.
Appendix 5. Capture Histories of Hatchery Fish from the Treatment Groups Released During Week (Wk) 15 through 19 in 2006 and 2007.

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Send questions or comments about this report to the author, J.W. Beeman, (509) 538-2299, ext. 257