Science Spotlight

The Klamath River is back in the news as juvenile salmon are turning up dead, and there are questions about parasites. Here’s what’s happening.

CDFW is working closely with our scientific colleagues at the U.S. Fish and Wildlife Service, Cal Poly Humboldt and Oregon State University to monitor Klamath River salmon and the impacts of the naturally occurring, microscopic C. Shasta parasite (short for Ceratonova shasta). This parasite is common in the Klamath and other Pacific Northwest rivers and its impact ebbs and flows with environmental conditions. Hot weather, warm water and low flows – conditions the Klamath is currently experiencing – can increase its prevalence.

On the evening of May 14, CDFW’s Fall Creek Fish Hatchery released 675,000 certified pathogen-free Chinook salmon smolts into the Fall Creek tributary of the Klamath River about 7 miles upstream of the former Iron Gate Dam location.

The release was also timed when C. Shasta levels in the river had decreased and ahead of forecasted storms, which would improve water quality and accelerate the smolts’ outmigration to the Pacific Ocean. Since then, C. Shasta levels have increased and some of these hatchery fish have been found dead in monitoring traps upstream of the Interstate 5 bridge near the former Iron Gate Dam location. Lab results have confirmed the presence of C. Shasta and another parasite, Parvicapsula minbicornis, in these dead fish. CDFW continues to track the movement of hatchery fish and remains confident that a proportion of Fall Creek Fish Hatchery-origin salmon escaped the impacts of C. Shasta and other parasites.

Additionally, CDFW tributary monitoring of wild juvenile salmon populations indicates the majority of wild fish had already outmigrated ahead of elevated levels of C. Shasta. The C. Shasta parasite does not impact ocean salmon or ocean salmon fishing.

It’s important to understand that some mortality due to pathogens is expected and is a natural part of the salmon life cycle. A pair of Chinook salmon will typically produce around 4,000 offspring but even under ideal conditions, more than 99 percent of those offspring will succumb to pathogens or predation prior to reaching adulthood. While the C. Shasta levels in the Klamath are elevated and somewhat concerning, early spring C.Shasta levels were lower than levels seen in previous drought years prior to Klamath dam removal, and C.Shasta related mortalities in the spring of 2024 and 2025 following dam removal were significantly lower, which are encouraging signs for the future.

CDFW will continue to monitor and track basin-wide conditions through the Klamath Fish Health Assessment Team as adult salmon return to the Klamath River over the summer.

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Media Contact:
Peter Tira, CDFW Communications, (916) 215-3858

At Iron Gate Hatchery in Hornbrook, the fall 2018 spawning operation has just concluded. Iron Gate spawns both Fall-Run Chinook Salmon and Coho Salmon from the Klamath River. For Chinook, the hatchery staff manually collect the eggs and mix it with the milt immediately after the fish come into the facility. CDFW environmental scientists also collect heads from adipose fin clipped salmon, in order to retrieve implanted tags in the snout. The retrieved tags tell the biologists which hatchery the fish is from, and when it was released. They also collect scales, which enable them to determine the age of the fish.

For Coho Salmon, the process is a little more involved. The Coho are measured and samples taken, but the samples are sent off to a National Oceanic and Atmospheric Administration (NOAA) laboratory in Santa Cruz for analysis. While the samples are processing, the fish are kept in individually-numbered holding tubes at the hatchery. They will be spawned after the tissue analysis determines which fish are the best genetic match.

CDFW Photos

For more information about Iron Gate Hatchery, please visit: www.wildlife.ca.gov/Fishing/Hatcheries/Iron-Gate.

Media Contact:
Kirsten Macintyre, CDFW Communications, (916) 322-8988

The latest issue of California Fish and Game, CDFW’s scientific journal, is now available online. This century-old quarterly journal contains peer-reviewed scientific literature that explores and advances the conservation and understanding of California’s flora and fauna.

The endangered salt marsh harvest mouse (Reithrodontomys raviventris) graces the cover of California Fish and Game, Volume 103, Issue I. Researchers ventured into the pickleweed to study the tiny mouse, which is endemic to the marshes surrounding the San Francisco Estuary Bay and its tributaries. The mice were fitted with tiny radiotelemetry collars and tracked for three years. Researchers documented some curious behavior in the resulting paper, “Potential evidence of communal nesting, mate guarding, or biparental care.” The accompanying photos provide a fascinating glimpse into an active nest.

Another paper, “Documentation of mountain lion occurrence and reproduction in the Sacramento Valley of California,” explores the potential for mountain lions to exist in fragmented habitats if there is adequate connectivity with larger blocks of suitable habitat and sufficient prey. The study used camera traps to document populations of mountain lions in the Sacramento Valley’s Butte Sink, which is made up of relic riparian habitats interspersed with managed wetlands. The photos show healthy mountain lions moving through habitat that has long been considered unsuitable due to extensive agricultural and urban development.

The article, “Mussels of the Upper Klamath River, Oregon and California,” reports on sampling efforts that expand existing baseline population data on freshwater mussels in the Upper Klamath River. The sampling efforts may ultimately assist with protection, mitigation and enhancement efforts for large bi-valve species.

The final paper provides insights into the benefits deer and elk derive from licking mineral rocks. Researchers took samples of “lick sites” that were used by California black-tail deer (Odocoileus hemionus columbianus) and Roosevelt elk (Cervus canadensis roosevelti) in the Klamath Mountains, Siskiyou County. After performing a detailed analysis of the elemental content of each lick site, the researchers concluded that each lick site offers a different smorgasbord of minerals, and in varying concentrations. The study’s objective is to begin identifying, classifying, and analyzing important mineral lick sites to benefit future ungulate management efforts.

As it has for the past 103 years, California Fish and Game continues to publish high-quality, peer-reviewed science that contributes to the understanding and conservation of California’s wildlife. We look forward to witnessing the contributions of the next installment.

Download the entire Winter Issue 103 (PDF) in high resolution, or browse individual articles in low resolution.