Population Genetics of   Klamath River Steelhead


Work Products

In 2004, a final report was provided to US Fish and Wildlife Service.

In 2007, a peer-reviewed publication was published in Journal of Applied Ichthyology.


Work in this study was undertaken with the Yurok Tribal Fisheries Program and North Coast Association of River Guides.  Phase 1 of this project is funded by U.S. Fish and Wildlife Service. Phase two and part of Phase 3 were completed by the Molecular Ecology group at NMFS's Southwest Science Center in Santa Cruz.  Work still is necessary on the relationship between anadromous steelhead and O. mykiss subspecies in the upper and lower Klamath River basins.

Background and Significance of Study

        The Klamath-Trinity River system supports the greatest number of coastal steelhead (Oncorhynchus mykiss irideus (Behnke  1992)) in California (McEwan et al, 1996).   O. m. irideus in the Klamath River basin display one of the most diverse set of life history patterns found in the Onchornychus genus.  This subspecies encompasses two distinct phenotypes.  NMFS recognizes two distinct reproductive ecotypes of coastal steelhead in the Klamath based upon sexual maturation (NMFS 2001).  Summer steelhead enter the mainstem sexually immature between May and October (Busby et al. 1994) or May through June (McEwan 1996).  Known populations of summer steelhead within the Klamath basin include Bluff Creek, Red Cap Creek, Dillon Creek, Clear Creek, Indian Creek, Elk Creek, Wooley Creek, and the Salmon River.   Although these populations each comprise a stock group identified in the Long Range Plan (KRBFTF 1991), it goes on to say that “It is possible that considerable diversity, worthy of preserving, may be found on a smaller geographic scale between stream within these areas.”(Chapter 4).   As for the reproductive isolation that may explain these variations, Smith (1968) suggested that summer steelhead “may select mates and be prepared to defend spawning territories against winter steelhead which might arrive several months later than summer fish in the same stream.”  Another possible explanation could be these populations receive a genetic contribution from a common source like resident rainbow trout.

        Busby et al. (1996) consolidated a third run-timing with the summer ecotype.  This run enters the Klamath River as sexually mature individuals between  July and October (Hopelain, unpublished).  This run contains a non-sexually mature steelhead called the half-pounder (Hopelain unpublished, Kesner and Barnhardt 1972, Everest 1973).  Half-pounders typically spends only 2-4 months in the estuary or nearshore before returning to the river to overwinter. They outmigrate back to the ocean the following spring.  Half-pounders are unique to the Rogue, Mad and Eel Rivers and a few smaller basins of Northern California and Southern Oregon (Kesner and Barnhardt 1972, Snyder 1931).  The relationship of “half pounders” to the summer, fall and winter steelhead is unknown.  It has been suggested that these fish spawn only in the Rogue and Klamath river basins (Cramer et al. 1995) after their second freshwater migration. 

        Winter steelhead, which comprise the second reproductive ecotype (Busby et al. 1996), mature sexually in the ocean.  Typically they enter the river between December and February, and find suitable spawning habitat relatively quickly.  However, the identification of steelhead stocks by time of return to the river is questionable (Roelofs 1983).  Everest (1973) found that early fall steelhead spawned with earlier returning summer steelhead in the Rogue River.  Because of weather, late fall fish may wait until after sufficient rain to permit migration into tributaries and spawning could overlap with winter steelhead.  

        The possibility that sympatric runs of steelhead comprise a polymorphic population was supported by Allendorf (1975) who found that summer and winter steelhead within a particular coastal basin resembled each other genetically more than populations of similar run-timings in adjacent basins.  This conclusion was supported with later allozyme studies(Chilcote et al. 1980, Schreck et al. 1986), including one on the Rogue River in the KMP ESU (Reisenbichler 1992).  Similar results were supported with analysis of microsatellite DNA variation in summer and winter steelhead in the Middle Fork Eel River (Nielsen and Fountain 1999).  Although, these different run-timings were found to be more akin to each other than they were to winter run steelhead from adjacent watersheds, Nielsen and Fountain (1999) described significant variations in microsatellite allelic frequencies, which should be considered in management for this species.  These results from others basins have not investigated in the Klamath River, yet is crucial to informed management decisionmaking.  Population genetic data is becoming an essential element of salmonid population management programs focusing on restoration and conservation (Waples 1994).  Steelhead management should be focused on protecting stocks for their life-history variability and other natural characteristics and not just based on groups defined by “race” or run-timing (McEwan et al. 1996).  These results may provide analysis that will more adequately protect imperiled summer stocks of steelhead migrating or holding in the mainstem Klamath River.   Since  distinct populations steelhead likely exist in the Klamath mainstem and their degree of isolation have not been previously identified or studied, the populations most affected by over-fishing are unknown.  


Phase 1 Objectives

1) Describe the genetic variation between coastal steelhead populations associated  with different run-timings.
2) Assess the frequencies of genotypes within each common population (temporal variation).
3) Recommend new sampling design for genetic studies and monitoring, and provide collection materials for future projects.  

Phase 2 Objectives

1)  Refine sampling design and methodology with input for collaborators
2)   Provide collection materials and have samples collected.
3)  Acquire and catalog samples from different subbasin populations and hatcheries from CDFG, Yurok Tribe, Karuk Tribe, USFS, USFWS,      and public.
4)  Extract, amplify, and score microsatellite DNA variation.
Identify genotype frequencies over run-timings in different basins (spatial variation) and data analysis. 

Phase 3 Objectives

1)  Compare genetic diversity in Klamath-Trinity steelhead to NMFS-listed  populations being assess by NMFS Technical Recovery teams. 
2)  Identify relationship of Klamath-Trinity steelhead to coastal steelhead population in transition zones and further north and south.
Identify phylogenetic relationship of Klamath-Trinity steelhead to resident rainbow trout and redband populations.


Materials and Methods for Phase 1

   Sample Collections.  Fin clips samples of Klamath River steelhead have been collected by the Yurok Tribal Fisheries Program.  Additional samples will be obtained from Northcoast Association of River Guides' guides, California Department of Fish and Game, U.S. Fish and Wildife Service, and volunteers at sites throughout the Klamath-Trinity basin.   Following this study, all samples will be archived with NMFS-Santa Cruz. 

   Genetic Analysis. Whole genomic DNA will be isolated from fin clip samples using standard protocols. Microsatellite loci previously shown in this laboratory to be polymorphic in various lineages of the rainbow trout (O. mykiss spp.) complex will then be amplified from the isolated DNA samples via the polymerase chain reaction (PCR).  The screening will concentrate on easily validated and highly polymorphic microsatellite loci.  For this study, we hope to utilize at least 10 loci.  We will utilize forward primers labeled with a florescent phosphoamidite.  This will permit for electrophoretically separated PCR products to be visualized on the MJ/GeneSys BaseStation Genotyper/Sequencer.  Gels will be manually scored by two researchers and results compared for verification. Differences in the presence/ absence and frequencies of alleles will be used to assess population structure in different run-timings of Klamath steelhead.

    Data Analysis .  Genetic analysis will include standard measures of genetic variation.   Fst values will be used for population structure analysis.  This analysis of molecular variance (AMOVA) will compare the measured genetic variation among and between the groups of each distinct run-timing. Partitioning of relatedness will be utilized to look at the diversity of genotypes between runs.       


Are you a fisherperson on the Klamath?  You can participate in this important study!

For Phase 1, adult steelhead samples will be needed from below the Trinity River confluence throughout the year.

Click here to read and print a sampling protocol to assist you in getting tissue samples to UC-Davis for inclusion in this study.