The Klamath River basin is one of the country’s most biological diverse regions. Photo by Rebecca M. Quiñones, 2008

By Rebecca M. Quiñones

The Klamath River basin presents one of the best opportunities for the reform of hatchery practices and the recovery of wild salmon and trout populations in California.

Much of the habitat for the Klamath’s Chinook, coho and steelhead fisheries is in relatively good shape compared with conditions in the Sacramento and San Joaquin river systems. Also, political and legal support for Klamath River restoration is growing.

Congress has already designated the stretch below Iron Gate Dam a Wild and Scenic River because of the value of its salmonids – anadromous salmon and trout. Also, the Klamath River system – the second largest in California, next to the Sacramento River – is the cultural and spiritual center to the Hupa, Karuk, Klamath, Modoc, Shasta, Yahooskin and Yurok peoples.

More recently, water and energy utilities, farmers, American Indian tribes and other interests have reached legal settlements calling for restoration of fisheries while sustaining basin communities. Central to the agreements is the removal of four dams on the Klamath, which would open up hundreds of miles of rearing and spawning habitat.

The Iron Gate Dam on the Klamath River. Photo by Rebecca M. Quiñones, 2008

Hatcheries were built to mitigate for the loss of spawning grounds upstream of dams. Removing four dams gives hatcheries at the Iron Gate Dam and on the Trinity River that much less reason to continue supplementing the Klamath fisheries – at least not at the current rate of 12 million juveniles a year.

These hatcheries were built with the good intentions of supplementing wild populations of salmon and steelhead. But the hatchery fish may actually be replacing naturally spawning wild salmon and steelhead in many streams, resulting in runs dominated by genetically and behaviorally uniform fish. Such fish are much more vulnerable to vagaries in natural conditions, such as rearing conditions in the ocean, make them prone to long-term declines.

My recent research on Klamath fisheries indicates that interactions with hatchery fish are facilitating the decline of certain runs of wild Klamath River fish, particularly steelhead trout. I analyzed trends in the number of wild and hatchery Chinook, coho and steelhead spawning in the Klamath River system and returning to the hatcheries. I also modeled the effects of hatchery releases and returns and several other stressors on four runs of wild salmon and steelhead in the basin.

The studies are the first to empirically analyze interactions between hatchery and wild salmonids basin-wide and to concurrently analyze these effects with other stressors, such as ocean conditions, habitat degradation and fisheries harvest. My studies were possible because we now have more than 30 years of data, thanks to collaborative efforts between government agencies, volunteer groups and the Klamath tribes.

My results suggest that hatcheries’ harm to wild salmonids spans the entire Klamath River basin. The trends are even more dire for wild steelhead, previously thought to be the most stable population in the basin. For fall Chinook salmon, the decline is concurrent with increases in hatchery returns – a trend that could lead to a homogenous population of hatchery-reared Chinook.

Hatchery fish are already replacing wild salmon in the Sacramento River, historically the largest salmon producer in the state. Decades of hatchery supplementation of fall-run Chinook and related straying of adults into spawning streams have decreased genetic diversity of Central Valley Chinook to the point that hatchery and wild populations are indistinguishable. The dominance of hatchery fish has made the declining wild populations fall-run Chinook more vulnerable to environmental change, likely contributing to years of dismally low adult spawner abundance (e.g., 2007 and 2008) and threatening the persistence of this run.

Though hatcheries have been supplementing the Klamath River fisheries for nearly 125 years, it’s not too late to prevent the homogenization of wild and artificially propagated salmonids in that basin.

The Iron Gate Dam on the Klamath River. Photo by Rebecca M. Quiñones, 2008

My studies show that hatchery operations and harvest rates are some of the most important stressors driving adult salmonids abundances in the Klamath basin. For some populations, including steelhead, hatchery practices may be as important as ocean conditions in producing downward trends in adult abundances. This is an important finding because resource managers can change hatchery operations, while factors such as ocean conditions cannot be changed.

A thorough analysis of alternatives to present hatchery operations – including closure – would help establish conditions that best benefit the viability of wild salmonids. For example, closure of Iron Gate Hatchery for 10 years, with monitoring for relative abundances of wild and hatchery fish, could be done as an experiment while the Trinity River hatchery continues to support the fishery. Likewise, marking all hatchery fish to ensure targets of naturally-spawning adult numbers are met before setting harvest quotas could help build dwindling runs.

Determining the carrying capacities for wild and hatchery salmonids in the Klamath basin and Pacific Ocean under different conditions would be especially useful. Such data would help managers make more scientifically based decisions on levels of hatchery production – including closure.

Rebecca M. Quiñones is a post-doctoral researcher with the UC Davis Center for Watershed Sciences.

Further reading

CHSRG (California Hatchery Scientific Review Group). 2012. California hatchery review report. Prepared for the U.S. Fish and Wildlife Service and Pacific States Marine Fisheries Commission. June 2012. 100 pgs.

Hamilton, J. B., G. L. Curtis, S. M. Snedaker, and D. K. White. 2005. Distribution of anadromous fishes in the Upper Klamath River watershed prior to hydropower dams – a synthesis of the historical evidence. Fisheries 30:10-20.

Hamilton, J., D. Rondorf, M. Hampton, R. M. Quiñones, J. Simondet, and T. Smith. 2011. Synthesis of the effects to fish species of two management scenarios for the Secretarial Determination on removal of the lower four dams on the Klamath River. U.S. Fish and Wildlife Service Yreka.

Huntington, C. W. 2006. Estimates of anadromous fish runs above the site of Iron Gate Dam. Canby, OR, Clearwater BioStudies, Inc.: 7 p..

Katz, J. V., P. B. Moyle, R. M. Quiñones, J. Israel, S.E. Purdy. 2012. Impending extinction of salmon, steelhead and trout (Salmonidae) in California. Environmental Biology of Fishes DOI 10.1007/s10641-012-9974-8.

Kier, W. M. and Associates. 1991. Long range plan for the Klamath River Basin Conservation Area Fishery Restoration Program. Klamath River Basin Fisheries Task Force, Yreka.

Lindley, S. T., et al. 2009. What caused the Sacramento River fall Chinook stock collapse? National Marine Fisheries Service, Santa Cruz.

Moyle, P. B., J. A. Israel, and S. E. Purdy. 2008. Salmon, steelhead, and trout in California – status of an emblematic fauna. Center for Watershed Sciences, U.C. Davis, San Francisco.

Moyle, P. B., J. D. Kiernan, P. K. Crain, and R. M. Quiñones. 2013. Climate change vulnerabiltiy of native and alien freshwater fishes of California: a systematic assessment approach. Plos One 8(5): e63883. doi:10.1371/journal.pone.0063883

Myers, J. M., et al. 1998. Status review of Chinook salmon from Washington, Idaho, Oregon, and California. NOAA Technical Memorandum NMFS-NWFSC-35, Northwest Fisheries Science Center, Seattle, Long Beach, Newport, Tiburon.

NRC (National Research Council). 2004. Endangered and threatened fishes in the Klamath River basin: causes of decline and strategies for recovery. The National Academies Press, Washington D.C.

Quiñones, R.M. 2011. Recovery of Pacific salmonids (Oncorhynchus spp.) in the face of climate change: a case study of the Klamath River basin, California. PhD dissertation, University of California at Davis, Department of Wildlife, Fish and Conservation Biology.

Quiñones, R.M., M.L. Johnson, and P.B. Moyle. 2013. Hatchery practices may result in replacement of wild salmonids: adult trends in the Klamath basin, California. Environmental Biology of Fishes DOI 10.1007/s10641-013-0146-2.
Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, and

R. S. Waples. 1995. Status review of coho salmon from Washington, Oregon, and California. National Marine Fisheries Service, Seattle.

Williams, J. G. 2006. Central Valley salmon: a perspective on Chinook and steelhead in the Central Valley of California. eScholarship Repository