Science Spotlight

The National Oceanic and Atmospheric Administration (NOAA) has recognized a CDFW senior environmental scientist for his role in the historic effort to return endangered winter-run Chinook salmon to the McCloud River for the first time since construction of the Shasta Dam in the 1940s.

Matt Johnson, CDFW’s fisheries supervisor for the winter-run Chinook salmon reintroduction pilot project, was given NOAA’s Partner in the Spotlight Award on Jan. 25, 2024. Johnson oversaw many of the project’s critical components including remote site incubation, trapping of juvenile winter-run and coordinating with project partners including the Winnemem Wintu Tribe.

“It was a surprise and an honor. I threw myself 100 percent into the project so I’m appreciative of the recognition. The project turned into a fascinating and unique opportunity to do something new and historic. It was all unexpected,” Johnson said.

The project launched in summer 2022 in response to drought conditions affecting Shasta reservoir and the lower Sacramento River downstream of Shasta reservoir. Multiple years of severe drought drastically reduced cold-water storage that endangered Chinook needed to live and spawn. CDFW, NOAA, Winnemem Wintu Tribe and the U.S. Fish and Wildlife Service (USFWS) partnered to move winter-run eggs upstream to the McCloud. The river offered favorable habitat including summer cold water conditions required for spawning but was inaccessible to fish because of the dam.

Partners initially relocated about 20,000 fertilized winter-run Chinook salmon eggs from USFWS’ Livingston Stone National Fish Hatchery near Redding. The eggs were transported 80 plus miles to the banks of the McCloud where the species historically spawned prior to construction of the Shasta Dam. The eggs were then placed in specialized incubators. In early August, another 20,000 eggs were transferred to the incubators.

The eggs were released into the river as fry, which were then collected in rotary screw traps and fyke nets, which are devices used that safely capture small salmon. Once collected, the fry were transported downstream of Shasta Dam and successfully released into the Sacramento River so the fry could migrate to the Pacific Ocean.

“Matt and his CDFW colleagues truly went above and beyond to return winter-run Chinook salmon to their historical home in the McCloud River for the first time in over 80 years. It’s clear that this was not just a job for him – he cares deeply about these species, this river, and this ecosystem and he put his heart into bringing them back,” said Brian Ellrott, NOAA’s Central Valley Salmonid Recovery Coordinator.

“Matt is dedicated to ensuring that this historic winter-run salmon pilot project succeeds. He recognized the insight and history the Winnemem Wintu Tribe provided and embraced their contribution to the reintroduction of the McCloud winter-run salmon,” said CDFW Director Charlton H. Bonham. “Matt is humble and passionate about his profession and we’re proud that he is part of our CDFW family.”

Johnson added: “I couldn’t have done any of this without my team. We were a small but dedicated crew and we were fortunate to have support from management, NOAA, the Winnemem Wintu Tribe, UC Davis and the Mount Shasta Fish Hatchery. Seeing an iconic California species returned to its historic habitat after a nearly 80-year absence was pretty incredible.”

###

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

CDFW Environmental Scientist Emily Fisher checks DNA tagged fall-run Chinook salmon fry prior to their release into the American River in February 2023.

Under cover of darkness and with a series of cold, late-winter storms building, California Department of Fish and Wildlife (CDFW) staff gingerly released approximately 1.1 million fall-run Chinook salmon fry (Oncorhynchus tshawytscha) into the American River at the Nimbus Fish Hatchery in Sacramento County.

It was an evening of firsts for CDFW on Feb. 23, 2023. It was the first release of fall-run Chinook salmon into the American River in more than three years. Since the spring of 2020, drought conditions have forced the trucking of Nimbus Fish Hatchery juvenile salmon to points within the San Francisco and San Pablo bays.

It was also the first time in decades CDFW has released fall-run Chinook salmon at such a small size. The salmon fry, just three months old and only 1.5- to 2-inches in length, had just absorbed their yolk sacks and had not yet been fed by the hatchery. Typically, fall-run Chinook salmon released from the hatchery are about 6 months old and 3.5- to 4-inches in length.

“By putting these fish out into the river now, they are going to experience the natural environment of the lower American River as natural-origin fish would,” said Jay Rowan, who oversees CDFW’s Fisheries Branch.

Most importantly, the 1.1 million fry released into the Nimbus Basin represent CDFW’s first experiment with DNA tagging fall-run Chinook salmon, what’s formally known in fisheries circles as “parentage-based tagging” or “PBT.” The emerging practice is also being tested at the Coleman National Fish Hatchery near Redding and has been widely used in the Pacific Northwest – but has never been attempted before by CDFW-operated hatcheries.

Not only are the experimental salmon fry half the age and half the size of typical, hatchery-released salmon smolts, they lack the adipose fin clips to visually identify them as hatchery-origin fish and are also without coded-wire tags that can later provide scientists with information about their life history. Instead, these salmon fry are genetically linked to the parents that produced them in a far-less invasive process requiring less human handling.

Three months earlier, on Nov. 29, 2022, CDFW collected and catalogued genetic material (a tissue clip from the caudal or tail fin) from the 500 adult salmon spawned that day at the Nimbus Fish Hatchery used to produce the 1.1 million salmon fry. By collecting future tissue samples from the released fish, CDFW’s fisheries geneticists can link every individual back to the Nimbus Fish Hatchery and the exact pair of parents that produced it.

That data could start arriving as early as this spring when CDFW and coordinating organizations will begin their downstream monitoring of juvenile salmon in the lower American River, taking tissue samples from young fish collected.

 “We will be able to see whether these fish are showing up in the monitoring surveys and following the same migratory cues and timing that we would expect from natural-origin fish,” said Jason Julienne, the senior environmental scientist who oversees CDFW’s Sacramento Valley anadromous fish hatcheries. “And then, over the next two to four years, we will collect genetic samples from unmarked Chinook salmon to estimate how many of these fish returned as adults to spawn.”

About a quarter of the fall-run Chinook salmon produced at Nimbus and CDFW’s other Central Valley anadromous fish hatcheries receive coded-wire tags and adipose fin clips. With parentage-based tagging, however, every individual fish is a potential data source.

CDFW’s research will help inform future fisheries management decisions, including the use of parentage-based tagging in coordination with current marking and tagging efforts, and could provide insight into how various release strategies contribute to survival, straying and adult returns.

“It’s going to take effort on the back end,” Julienne, said, “but we’re evaluating our long-term ability to implement PBT on a larger scale and its potential to be included as a release strategy representative of natural-born juvenile migration timing and whether it allows us to take advantage of more favorable river conditions earlier in the year.”

The 1.1 million experimental salmon fry are among 5.5 million fall-run Chinook salmon that will be raised and released by the Nimbus Fish Hatchery in 2023. That’s a recent production record, according to Nimbus Fish Hatchery Manager Gary Novak. Under normal years, the Nimbus Fish Hatchery produces 4 million fall-run Chinook salmon smolts for the U.S. Bureau of Reclamation as mitigation for the loss of spawning and rearing habitat associated with the construction of the Nimbus Dam. This year, production targets have been increased to help address issues related to drought and a thiamine deficiency impacting Sacramento Valley salmon populations. Even with near-ideal weather and river conditions accompanying the experimental salmon fry release, both Julienne and Novak acknowledged the long odds facing the fish on their journey to the Pacific Ocean.

Said Novak: “By conducting this release at night, we’re hoping to reduce predation from birds and, hopefully, give these fry a head start in finding good rearing habitat in the river.”

CDFW photos

###

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