Science Spotlight

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

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

The California Department of Fish and Wildlife’s (CDFW) Human-Wildlife Conflicts Program has been recognized for its innovative approach to promoting effective, integrated non-lethal human-wildlife conflict mitigation techniques in California.

The program was one of six recipients of this year’s Integrated Pest Management (IPM) Achievement Awards by the California Department of Pesticide Regulation (DPR) at the California Environmental Protection Agency.

Winners were selected for developing and adopting innovative IPM tools and practices and for helping increase awareness of IPM to inspire future generations of practitioners.

“We live in increasingly close contact with animals (and) continue to see increases in human-wildlife interactions,” said CDFW Statewide Conflict Programs Coordinator Vicky Monroe, who accepted the award on the program’s behalf at a virtual ceremony held on Feb. 23.

“With this program, we work to communicate that we don’t exist in isolation from other species,” Monroe said. “We are in fact a part of nature. We interact in that shared environment, and share space and resources, with those co-existing species. We offer up a clear vision for human-wildlife interactions and how to mitigate those from escalating into conflict, and how we can promote a safe co-existence with wildlife species. It's really meaningful work.”

“We’re humbled for this recognition, and we’re overwhelmed with gratitude to have been selected to receive this award – particularly for promoting integrated non-chemical and non-lethal human-wildlife management techniques,” she said.

The full 2022 IPM Achievement Awards ceremony (Video) and a shorter video highlighting the Human-Wildlife Conflicts Program’s work (Video) can be found on DPR’s YouTube page. Assemblyman Josh Hoover (R-Folsom), Los Angeles County Deputy Agricultural Commissioner Jim Hartman, and Cougar Conservancy Director Korinna Domingo all made videos congratulating the statewide team on winning the award.

CDFW is the lead state agency responsible for responding to human-wildlife conflict and depredation (wildlife damage to property) in California. The Human-Wildlife Conflicts Program, established in 2018 and expanded in 2022, works to increase CDFW’s ability to be responsive to local communities and to provide public education about wildlife conservation.

The Human-Wildlife Conflicts Program supports Wildlife Watch, created a Human-Wildlife Conflict “Toolkit,” and launched a Wildlife Damage Management speaker series. The program’s leadership helped recruit a statewide team of Regional Wildlife Conflict Specialists and have trained them with the skills and equipment needed to serve local communities, agency partners and the diverse constituent interests statewide. In April 2022, the program graduated the first ever training cohort from its Wildlife Conflict Training Academy.

CDFW would also like to congratulate co-winners of the 2022 IPM Achievement Awards: Cal Poly Strawberry Center, Oracle Park, Vineyard Team, the Appropriate Technology Transfer for Rural Areas Program, Western Regional Office of the National Center for Appropriate Technology, and Lifetime Achievement Award Winner Chris Geiger.

DPR Director Julie Henderson said, “Integrated Pest Management is an essential practice for protecting people and the environment and is a foundational element for the state’s approach to accelerating a systemwide transition to safer, more sustainable pest management.”

For more information see DPR’s news release on the Integrated Pest Management Achievement Awards.

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Media contact:
Ken Paglia, CDFW Communications

Thanks to funding approved in the state budget, the California Department of Fish and Wildlife (CDFW) is now in the process of building upon its existing beaver management policies and laying the groundwork for projects that harness beavers’ natural ability to improve California’s ecosystems.

The state budget approved $1.67 million in fiscal year 2022-23 and $1.44 million in fiscal year 2023-24 and ongoing for CDFW’s beaver restoration program.

CDFW is currently hiring five dedicated scientists to work on a comprehensive approach to beaver management. Once hired, staff will work on numerous projects and collaborations including developing a toolkit to help prevent property damage due to beaver activity and to foster co-existence with the keystone species. Staff will also collaborate with partners on ongoing and future restoration projects to relocate beavers into watersheds where their dams can help restore hydrologic connectivity and promote resiliency to climate change and wildfire.

“We’re incredibly excited about the direction the department is going with its beaver restoration program,” said CDFW Deputy Director Chad Dibble.

Anyone paying attention to wildlife in the media recently may be seeing that beavers are having a moment. A recent article in Mother Jones posed the question: “Is it possible that beavers got a publicist?” The article concludes that beavers are finally getting the “rebrand” they deserve. While beavers have always been known for building dams and altering waterways, perhaps less publicly known is the positive impact they have on larger ecosystems surrounding their dams.

“Beaver dams raise groundwater levels and slow down water flow which allows water to seep into the soil and helps create riparian wetlands that support plant, wildlife and habitat growth,” said CDFW Director Chuck Bonham in an Op-ed written for CDFW and published in Outdoor California magazine.

By aiding healthy riparian growth, beaver dams can mitigate drought impacts and support climate change resiliency. The process of increasing fuel moisture and helping larger areas of land retain water can potentially stop or slow the spread of wildfire moving through an area. Beaver dams also improve water quality and help rejuvenate habitat for salmon and aquatic insects.

At one point, there were between 100-200 million North American Beavers in North America. However, due to unregulated trapping and habitat loss, by the late 1800s they were eliminated from much of their natural range. The current beaver population in North America is estimated at about 10-15 million.

Over the past several years, CDFW has spent millions of dollars partnering with tribes, NGOs, landowners, and state and federal agencies implementing beaver restoration projects. With its new beaver restoration program, the department is embracing the paradigm shift surrounding beavers and continuing its work to bring together collective knowledge and implement a comprehensive approach to beaver management.

“We’re continuing collaboration with partners and stakeholders, continuing work on restoration sites where we’ve funded beaver dam analogues and continuing to lay the groundwork for re-introduction of beavers in areas where it may have ecosystem benefits. Scientists are confident that beaver restoration has the potential to be a nature-based strategy that can aid in reducing wildfire risk, mitigating drought and combating climate change. It’s another piece of the puzzle as CDFW works to implement solutions to some of our greatest environmental concerns,” said Bonham.

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

An Op-Ed by Charlton H. Bonham, Director of the Department of Fish and Wildlife

Beavers are having a well-deserved moment in the discussion around climate solutions.

Healthy beaver populations improve their environment in so many ways – from reducing wildfire risks, to making water conditions more hospitable for our native salmon and trout.

In fact, humans have so admired the skilled work of beavers they have spent millions of dollars trying to replicate the benefits they create. As managers of the state’s natural resources, the California Department of Fish and Wildlife (CDFW) is embracing the opportunity to elevate beaver restoration as part of a larger effort to help mitigate the impacts of wildfires, climate change and drought. Thanks to Governor Gavin Newsom’s leadership and the State Legislature, funding for beaver restoration is now part of our playbook, with funds approved in this year’s budget.

The program funds dedicated scientists who, once hired by CDFW, will begin working on projects that help the environment by bringing beavers back to California rivers where they once thrived.

Beaver dams raise groundwater levels and slow water flow. Slowing down the flow allows water to pool and seep, creating riparian wetlands that support plant, wildlife and habitat growth. Another benefit of beaver dams is the rejuvenation of river habitat for salmon and aquatic insects. The dams also improve water quality because they capture sediment, resulting in clearer water downstream.

Additionally, beaver dams help keep groundwater tables high which can help mitigate drought impacts by keeping vegetation green. This effect can also help fires burn less intensely in riparian areas, which, in the long run, can aid streams and habitats in recovering from fires more quickly. These positive ecosystem benefits are especially true in areas where there are intermittent streams or where streams can disconnect. Once beavers build dams in those areas, the habitat tends to hold water more effectively and allows it to percolate into soils.

Unfortunately, beavers were eliminated from much of their range by the late 1800s due to unregulated trapping and habitat loss. Environmental scientists have tried to duplicate the effectiveness of beaver dams utilizing human-engineered structures called beaver dam analogues. Through this, we have learned that human-created beaver dams can achieve similar carbon sequestration and habitat benefits to that of real beaver dams, but at a much higher cost. Nothing’s better than the real thing, and that means bringing beavers back to their historic habitat and teaching Californians how to coexist with the scientifically named Castor canadensis.

California’s next step is to expand partnerships with California native tribes, non-governmental organizations, private landowners, state and federal agencies, and restoration practitioners to lay the groundwork for implementing beaver restoration projects. The new funding will help develop a framework for these beaver relocation efforts. CDFW and its partners are looking at the feasibility of taking beavers from areas where they are causing conflict and relocating them to areas where they would have ecosystem benefits.

CDFW’s new beaver restoration program allows California to advance on all these fronts -- we’re continuing collaboration with partners and stakeholders, continuing to work on restoration sites where we’ve funded beaver dam analogues and continuing to lay the groundwork for re-introduction of beavers in areas where it may have ecosystem benefits. Scientists are confident that beaver restoration has the potential to be a nature-based strategy that can aid in reducing wildfire risk, mitigating drought and combating climate change. It’s another piece in the puzzle as CDFW works to implement solutions to some of our greatest environmental concerns.

CDFW Scientific Aid Stew Sloan measures pool depth at Pacific Creek.


A Lahontan cutthroat trout swims within Milk Ranch Creek.


Environmental Scientist Allison Scott records data on the banks of Pacific Creek.


A handheld multiparameter instrument displays several creek measurements at once.


CDFW's Allison Scott and Aaron Sturtevant measure pool depth within Milk Ranch Creek.

As holiday visitors vacated the Stanislaus National Forest at the conclusion of the long Fourth of July weekend, the California Department of Fish and Wildlife’s (CDFW) Heritage and Wild Trout Program moved in.

Four team members from the statewide program – Environmental Scientist Allison Scott, scientific aids Aaron Sturtevant and Stew Sloan, along with new program leader Farhat Bajjaliya – set up camp within the border region of Alpine and Stanislaus counties in the northern reaches of the Eastern Sierra.

The team spent the better part of three days rock-hopping, climbing and carefully picking their way upstream along three small creeks within the high elevations of the Carson-Iceberg Wilderness searching for and counting wild Lahontan cutthroat trout (Oncorhynchus clarkii henshawi). The goal was to see how the fish and their habitat were faring in a third summer of California drought. Along the way, the team paused regularly to record water temperatures, creek flows and dissolved oxygen levels and take pool depth measurements. They took photos, referenced waypoints on their Garmin unit and thoroughly explored any smaller tributaries feeding into the main creeks, some just a couple inches deep at points.

“One of the things we really key in on is pool habitat,” explained Bajjaliya. “When drought conditions get really bad, that’s where the fish will go and seek refuge so we want to keep an eye on that.”

The three small creeks surveyed – Marshall Canyon Creek, Pacific Creek and Milk Ranch Creek – share similar characteristics.

Their lower reaches are occupied by introduced non-native brook trout (Salvelinus fontinalis). Various impenetrable natural barriers such as steep, cascading waterfalls or sheer granite rock cliffs prevent the brookies from accessing the higher-elevation stretches home to the Lahontan cutthroats. The Lahontan cutthroat trout themselves are not necessarily native either as these particular creeks are situated outside of their historic watersheds. The fish were put there decades ago by biologists to serve as refuge populations just in case the fish, a federally listed threatened species, disappeared elsewhere within their native range.

CDFW’s trout team hiked almost 10 miles each day carrying a mix of high-tech and low-tech equipment. On one end of the technology spectrum was the YSI handheld digital “multiparameter instrument,” which simultaneously measures pH levels, dissolved oxygen, temperature and the ability of the water to absorb and break down waste products such as contaminants and dead plants and animals. On the other end of the spectrum was the collapsible stadia rod. Resembling a folding yardstick, it’s used to measure pool depth and creek width. No electrofishing gear was packed in. Lahontan cutthroat trout were counted and sized only through visual observations – and often fleeting observations at that.

The scientific work is formally known as drought stressor monitoring and it makes up a significant portion of the Heritage and Wild Trout Program’s field season, which stretches from May to November and occurs across the state wherever sensitive native trout populations exist. The program’s environmental scientists and part-time scientific aids typically spend eight consecutive days in the field followed by six consecutive days off work.

The value of this type of hands-on, eyes-on field work was driven home during California’s last drought. Drought monitoring surveys similar to the ones within the Carson-Iceberg Wilderness led to the dramatic rescues of McCloud River redband trout (Oncorhynchus mykiss stonei) and California golden trout (Oncorhynchus mykiss aguabonita) – the official state freshwater fish.

Drought monitoring in the summer of 2014 revealed deteriorating habitat conditions near Mount Shasta and prompted the rescue of McCloud River redband trout (Video) from four creeks among the headwater tributaries of the McCloud River. With no suitable options available to relocate the fish on the landscape, CDFW took the unusual step of bringing the wild trout – a designated state species of special concern – into its Mount Shasta Trout Hatchery until they could be returned to their native habitat when environmental conditions improved.by the fall of 2016.

While at the hatchery, CDFW was able to successfully spawn the redbands. The Mount Shasta Trout Hatchery has maintained a broodstock population ever since and stocks their offspring into local waters for recreational fishing to expose more trout anglers to this colorful and rare native species.

Drought stressor monitoring led to the September 2016 rescue of California golden trout from Volcanic Creek, situated high in the southern Sierra Nevada range at 9,000 feet within the Inyo National Forest. Fifty-two fish – a representative sample that could repopulate Volcanic Creek and save the genetically pure strain of goldens if conditions worsened – were collected and taken to the American River Trout Hatchery near Sacramento to wait out the drought before being returned to their native habitat in 2017 (Video) when environmental conditions improved.

The Lahontan cutthroat trout is in a far more precarious situation than either the McCloud River redband trout or the California golden trout. Lahontan cutthroat trout were listed as an endangered species by the federal government in 1970 – three years before the modern, federal Endangered Species Act was signed into law in 1973 by President Richard Nixon. The fish have languished as a federally listed species ever since. Their status was downgraded to “threatened” in 1975 but only to allow for more aggressive management and recovery efforts and to allow recreational fishing.

Once occupying a vast range east of the Sierra Nevada, Lahontan cutthroat trout have disappeared from nearly 95 percent of their native habitat in California, which includes Lake Tahoe, the Carson, Truckee, and Walker river basins, as a result of habitat degradation and competition from non-native trout.

The 50th anniversary of the species’ federal listing in 2020 was something of an ignominious milestone. Several state and federal agencies – including the U.S. Fish and Wildlife Service, the USDA Forest Service, CDFW and the Nevada Department of Wildlife – have joined forces recently to redouble efforts and accelerate Lahontan cutthroat trout recovery.

All of which helps explain why keeping close tabs on the few remaining wild, self-sustaining, genetically pure populations of Lahontan cutthroat trout left in California is a priority for CDFW and the Heritage and Wild Trout Program specifically.

Back at the Carson-Iceberg Wilderness within the Stanislaus National Forest in July, the day’s drought monitoring work ends when 200 Lahontan cutthroat trout have been tallied or the habitat simply disappears back into the ground at the headwaters source or becomes otherwise impenetrable by either fish or human.

At all three creeks, the trout habitat ran out before 200 fish were counted. The team observed 153 Lahontan cutthroat trout at Milk Ranch Creek, 33 in Marshall Canyon Creek and 23 at Pacific Creek. The team seemed satisfied with what it saw.

The habitat was holding up well for early summer conditions and enough Lahontan cutthroat trout – mostly 6 inches and shorter in length – were observed in the wildflower-laden, meadow sections of each creek’s upper reaches. The numbers of fish were reasonably consistent with drought monitoring conducted in 2020 and 2021. The numbers of fish observed in Marshall Canyon Creek and Milk Ranch Creek exceeded the numbers counted the previous two years.

No fish were spotted in the steeper, faster, rockier, lower portions of the creeks. No emergency rescue missions were discussed.

“There really is no reason for them to leave the meadows,” explained CDFW’s Scott. “That’s where the best habitat is and there are not so many fish that some are forced to move out.”

Media Contacts:
Farhat Bajjaliya, CDFW Heritage and Wild Trout Program, (916) 215-5330
Peter Tira, CDFW Communications, (916) 215-3858