Science Spotlight

Hallprint, spaghetti-style fish tags provide visual identification for Feather River Fish Hatchery staff that returning salmon are spring-run Chinooks that can be used for spawning and perpetuating the run of fish.


An early arrival to the Feather River Fish Hatchery receives a Hallprint, spaghetti style fish tag identifying it as a spring-run Chinook salmon before it is returned to the Feather River.


Feather River Fish Hatchery staff prepare spring-run Chinook salmon for tagging before these early arrivals are returned to the Feather River.


Spring-run Chinook salmon inside the Feather River Fish Hatchery.

The California Department of Fish and Wildlife’s Feather River Fish Hatchery in Butte County recently completed the tagging of 2,746 spring-run Chinook salmon in May and June.

The fish were early arrivals to the hatchery. After being outfitted with two external Hallprint, spaghetti-style fish tags on either side of their dorsal fin – two tags in case one comes out and is lost – the fish were returned to the Feather River. Unlike Passive Integrated Transponder (PIT) tags injected into many Chinook salmon smolts in order to monitor their movements, returns and hatcheries of origin, the external Hallprint tags are intended to provide visual identification to hatchery staff of returning spring-run Chinook salmon.

In September and October, the hatchery will spawn spring-run Chinook salmon, selecting among only those returning, externally tagged fish as broodstock in order to preserve the integrity of the spring-run fish and not mix genes with returning fall-run Chinook salmon. The ladder to the Feather River Fish Hatchery was closed July 1 to ensure only the early arriving spring-run Chinook salmon were tagged.

This process helps the hatchery achieve its goal of selecting and spawning salmon that represent the entire timeline of returning fish while keeping spring-run and fall-run salmon separated.

Feather River spring-run Chinook salmon are classified as threatened under both the state and federal endangered species acts. Tagging and spawning efforts help mitigate their decline. The goal is to ensure these native California fish can be enjoyed by generations to come.

CDFW Photos

Isaac Chellman, high mountain lakes environmental scientist for CDFW’s North Central Region, nets non-native trout from a lake to restore native frog habitat.


The Sierra Nevada yellow-legged frog is listed as a threatened species under both the California and federal endangered species acts.


Non-native trout introduced into high mountain lakes prey upon native Sierra Nevada yellow-legged frog tadpoles and young frogs. Removing these trout from select lakes is an important step in recovering native frog populations.

In the Tahoe National Forest, California Department of Fish and Wildlife scientists are working to balance native species restoration with recreational fishing.

This summer, for the first time in the Tahoe National Forest, CDFW will begin work to restore Sierra Nevada yellow-legged frog (Rana sierrae) habitat by removing introduced trout from four alpine lakes and four small ponds within the Five Lakes Basin area. The Sierra Nevada yellow-legged frog is listed as threatened under California’s Endangered Species Act and endangered under the federal Endangered Species Act. 

The Five Lakes Basin is located in Nevada County, south of French Lake and Faucherie Lake within the Grouse Ridge non-motorized area of the Tahoe National Forest. The area is a popular destination for backcountry recreation. The small lakes and ponds targeted for fish removal include Glacier Lake and are typically accessed from the Grouse Ridge Campground and Faucherie Lake.

“These types of projects highlight CDFW’s dual mission to both provide recreational opportunities and recover native species,” said Sarah Mussulman, Sierra fisheries supervisor for CDFW’s North Central Region. “In this case, we want to ensure anglers have a chance to catch a fish at a beautiful lake while simultaneously ensuring this iconic native frog remains on the landscape for generations to come. Because the fish are a major driver of frog declines, we’ve chosen one area near Grouse Ridge to recover frogs and a nearby area to plant fish.”

To remove the fish, which consist of non-native brook, rainbow and hybridized golden-rainbow trout, CDFW will use mechanical methods including monofilament gill nets and backpack electrofishing units. This project is funded by the U.S. Fish and Wildlife Service through its endangered species recovery grant program and will be conducted in collaboration with the Tahoe National Forest. Work is scheduled to begin by mid-summer and will continue through the fall 2022.

The Sierra Nevada yellow-legged frog was once one of the most abundant species in the Sierra and a critical part of the natural food chain. Non-native trout, which were introduced into historically fishless lakes and ponds throughout the range for many decades, consume young frogs and tadpoles. This predation has been a major contributor to the decline of these native amphibians. The restoration project will provide additional fishless habitat, which is needed for the long-term survival and eventual recovery of this species.

At the same time, CDFW is committed to promoting and maintaining the unique recreational fishing opportunities nearby. CDFW will continue to stock trout into many lakes in the Grouse Ridge area, including Carr, Culbertson, Feeley, Long, Milk, Upper and Lower Lindsey, Big and Little Island, and Lower and Upper Rock lakes. These locations provide fishing opportunities at beautiful, high elevation lakes within a few miles of the Five Lakes Basin.

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CDFW Photos

CDFW is a department with about 1,200 employees in scientific classifications, spread from Yreka in the north to Blythe in the southeast. Their expertise spans a broad spectrum of subjects – wildlife management, fisheries management, marine issues, habitat conservation and restoration, veterinary science, pathology, genetics, invasive species and so much more.

Coordinating the efforts of a department with such a wide range of specialties is no small task. But back in 2006, CDFW released its Strategic Initiative, which laid the groundwork to do just that. The document outlined the strategies and actions that the department should take in order to increase its effectiveness across the board. One specific goal was to expand the department’s scientific capacity – to establish best standards and practices, to improve access to scientific literature, and heighten visibility and awareness of scientific efforts.

CDFW Science Institute was launched in May 2012 as the means to accomplish those goals. Initially, it was led by a team of dedicated scientist that put the Science Institute on the map with a public website, a scientific lecture series, science symposium, policy and guidance documents on scientific practice, and ultimately hiring a Science Institute Lead in 2018. Since then, the Institute has grown to include a committed scientific staff of five employees who work to support CDFW’s scientists and scientific efforts.

CDFW’s Science Advisor and Science Institute Lead, Christina Sloop, points out that climate change and biodiversity conservation are two issues that affect all facets of the department -- yet specific resources on these topics are not readily available to many field staff. The Science Institute employs staff who are specifically trained to advise on these topics, and can provide a statewide, long-term perspective.

“We are ready to provide guidance and help connect the dots when climate change or biodiversity conservation principles could be incorporated into a study or a project,” Sloop explains. “We play a departmentwide facilitation role, so CDFW’s scientists and scientific programs can better respond to these challenges and be as efficient as possible as they work to support our important mission.”

CDFW recently published the Science Institute Progress Report 2018-2019 (PDF), which highlights the tools developed so far. The 2020-2025 Science Institute Strategic Action Plan will be released this summer. This document reflects input from the CDFW science community and lays out goals and strategies to guide the Science Institute’s priority actions in the next five years. Each year, the plan will be reassessed, reevaluated and updated as necessary, in order to keep one step ahead of current challenges. “Our goal is to be proactive and anticipatory rather than reactionary,” Sloop said. “We’ll always be on the lookout for new ways to build capacity, promote transparency and foster scientific excellence.”

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Media Contact:
Kirsten Macintyre, CDFW Communications, (916) 804-1714

Hermit warblers spend much of their time in forest canopy. They are rarely seen but very vocal and easily heard. Photo by Dr. Brett Furnas.


Scientists record songs of hermit warblers and use the data for surveys that support conservation efforts. Photo by Russ Landers.


Hermit warblers flee wildfires which ultimately creates opportunities for new birds to take over a habitat. This may explain why some areas have multiple mating dialects. Illustration by Sarah Noll..

New research shows that fire history seems to be shaping the diversity of bird songs throughout the state. The new paper, published in leading bird journal The Auk: Ornithological Advances, addresses the diversity of song dialects sung by hermit warblers – birds which get their name because they are rarely seen and spend much of their time in forest canopy. They are, however, very vocal and easily heard.

Interestingly, the paper’s lead author, CDFW Senior Environmental Scientist Dr. Brett Furnas, never set out to study the hermit warbler, which is a migratory songbird that breeds in California, Oregon and Washington.

Dr. Furnas’ journey studying the bird began a decade ago while he and his colleagues were doing surveys on songbirds in northern California. They noticed that songs from one species of songbird – the hermit warbler – were so complex that it was difficult to identify the species.

“We ultimately compiled a list of 35 different song dialects from the hermit warbler throughout California,” said Dr. Furnas

The team also noted, as had been confirmed in prior research, that all of the hermit warblers’ songs in a particular area sounded the same -- and they believed those songs to be the males’ mating calls.

“Females in that area were probably raised to recognize that one type of call. The males have to sing it perfectly,” said Dr. Furnas, noting that the birds do have a repertoire of other songs that males use to announce their territories to other males.

Then the team made a surprising find: In some areas they surveyed, there was more than one mating dialect. For example, two males singing different mating songs.

That finding led to Dr. Furnas’ hermit warbler research. He traveled throughout California and recorded and analyzed mating songs from more than 1,500 male hermit warblers during mating season, April through July, from 2009 to 2014.

What appeared to be causing the mixing of songs, he found, was wildfires.

“Hermit warblers are very sensitive to fire in the short term, and they typically abandon an area shortly after a fire. This creates a little bit of a vacuum, and other birds fill in that gap. The net result is that you get some areas with more than one dialect,” he said.

The new study also provides the first comprehensive description of hermit warbler mating song variants throughout California.

Results from the study have several uses:

• Now that scientists have a library of the hermit warblers’ complex songs, they can use that data to better survey the hermit warblers and other species.
• Although the hermit warbler is abundant in California, it does have some potential conservation concerns. In summer, the hermit warbler is only found in three states, and in Oregon and Washington the bird is hybridizing with a closely related but more aggressive species. One possible outcome is that California could ultimately be the only home to non-hybridized hermit warblers. The research could help with conservation efforts.
• The findings could improve scientists’ understanding of how song diversity functions, helping them disentangle the complex relationships involved with biodiversity.

Read Dr. Furnas’ paper “Wildfires and Mass Effects of Dispersal Disrupt the Local Uniformity of Type 1 Songs of Hermit Warblers in California.”

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CDFW Photos: Top Photo: Hermit_1: Hermit warblers are a migratory songbird that breeds in California, Oregon and Washington. Photo by Dr. Brett Furnas.

Media Contact:
Ken Paglia, CDFW Communications, (916) 825-7120

Adult Coho: Adult Coho Salmon released in Salmon Creek, Marin Co. (CDFW photo by Manfred Kittel).


Redwood Creek: CDFW biologists searching for juvenile Coho Salmon in Redwood Creek in summer 2014.

Coho salmon (Oncorhynchus kisutch), also known as silver salmon, have lived in California’s coastal watersheds for thousands of years. Today their populations have declined to just a fraction of historical levels, endangered by a wide range of factors. In Central California in particular, the situation is dire, with the species listed as endangered under both the state and federal Endangered Species Acts. Many populations are in danger of declining to the point of local extinction.

Recognizing the recovery of Coho salmon in central California’s streams and rivers as a high priority, the California Department of Fish and Wildlife (CDFW) is collaborating with NOAA’s National Marine Fisheries Service (NMFS), the U.S. Army Corps of Engineers (USACE), and other partner agencies and non-governmental organizations to develop and implement recovery actions. The tricky part is that there is no one-size-fits-all approach to saving the species.

Eric Larson, Fisheries Program Manager for CDFW’s Bay Delta Region, has monitored the decline of Coho on the Central Coast over the past three decades. As he sees it, an effective conservation strategy will do two things: prevent local extinction events, and implement specific recovery actions in streams that once functioned as Coho strongholds. “But,” says Larson, “each stream is a unique geographic and ecological system. In each watershed, any recovery actions -- including captive rearing and release efforts -- must be custom-tailored to that system to be successful.”

To date, some of those custom-tailored approaches include the following:

Captive breeding and monitoring (Sonoma County). Since 2001, CDFW has been working with NMFS, USACE and others to restore Coho populations in the Russian River basin in Sonoma County. A captive breeding program was developed at Warm Springs Hatchery, situated at Lake Sonoma Dam, to help re-establish populations in Russian River tributaries and other regional streams where Coho once flourished. The hatchery program relies on a genetically informed breeding matrix to minimize inbreeding and conserve genetic diversity. The program produces up to 200,000 Coho annually, which are released primarily as juveniles into tributaries of the Russian River and other streams, although some smolts and adults are also released in a few regional streams.

Concurrently, scientists from the University of California Sea Grant and Sonoma Water have been  actively monitoring juvenile Coho and adults returning to the Russian River system since the hatchery program began. The number of adult Coho returning to the river each year to spawn has gradually increased from just a handful in 2009, to more than 700 in 2017-2018.

Watershed restoration work and hatchery rearing of juveniles (Marin County). CDFW is collaborating with the National Park Service, USACE, State Parks and others to restore Coho salmon in Redwood Creek, which flows through the picturesque Muir Woods National Monument. The prolonged drought from 2013-2016, along with other factors, had brought Coho in Redwood Creek to the brink of local extinction, with fewer than 10 fish returning annually to the creek as adults to spawn.

From 2014 to 2016, approximately 200 juvenile Coho per year were collected in Redwood Creek and taken to Warm Springs Hatchery for rearing. The young salmon were grown to adulthood in the hatchery and, as three-year-old fish, released back into Redwood Creek in the winters of 2016 to 2018 to spawn. Tissue samples taken from juvenile Coho in summer 2017 and genotyped at the NOAA Southwest Fisheries Science Center in Santa Cruz confirmed that several of the fish released as adults in winter 2016 had spawned successfully and contributed to the persistence of this population in Redwood Creek.

Captive rearing (Mendocino County). Farther north, Coho populations are also declining in coastal watersheds such as the Garcia, Gualala and Navarro rivers. In recent years, the numbers of adult Coho returning to the Garcia and Navarro rivers have been below the threshold necessary to maintain viable populations, and no Coho have been detected in the Gualala River at all for several years. This low abundance raised concerns at CDFW and NMFS that without intervention, populations were likely headed towards local extinction.

For this reason, CDFW, NMFS and other partners developed a population recovery plan similar to those used for restoring Coho in the Russian River and Redwood Creek. As a first step, approximately 200 juvenile Coho were collected in October 2018 and again in 2019 in the Garcia and Navarro Rivers and taken to Warm Springs Hatchery. There the juveniles are being reared in captivity under the watchful eye of experienced hatchery staff. Meanwhile, CDFW and NMFS are developing plans for release of these fish, preferably as adults, back into their natal streams to spawn naturally. Although the fish could hypothetically be spawned at the hatchery and their offspring released back into the Garcia River, this option is unlikely due to hatchery space limitations. Releasing the Coho as adults also has the advantage of providing the released mature fish with free mate choice and exposing their offspring to natural selective pressures from the earliest life stage. Importantly, appropriate monitoring activities, including genetic parentage analysis, will be implemented to evaluate the success of the fish releases over the coming years.
The development and implementation of recovery programs, such as those outlined here, are urgently needed to conserve Central California coast coho salmon for future generations to enjoy and to make progress towards population recovery.

You can read more about efforts to conserve California’s Coho in the following documents:

• Recovery Strategy for California Coho Salmon (2004)
• Recovery Plan for Central California Coast Coho Salmon (2012)
• declaration of Central California Coast Coho salmon as one of eight species listed nationally as a ‘Species in the Spotlight’ (2015)

CDFW Photos. Top Photo by Manfred Kittel. Warm Springs Hatchery, adjacent to Dry Creek. Picture taken from the top of Lake Sonoma Dam.

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Media Contact:
Harry Morse, CDFW Communications, (208) 220-1169