Science Spotlight

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

Upper Independence Creek provides vital spawning habitat for the Lahontan cutthroat trout in Independence Lake.


State and federal agencies, joined by conservation groups such as Trout Unlimited, have worked for decades to safeguard the wild Lahontan cutthroat trout population at Independence Lake, the only self-sustaining lake population of the native species left in California. Trout Unlimited’s Brandon Reeder shows off a hefty Lahontan cutthroat captured at a temporary weir to count spawning fish.


Lahontan cutthroat trout spawn in upper Independence Creek, where biologists have worked for years to remove non-native brook trout.


Each spring, biologists and volunteers set up a weir at upper Independence Creek to trap spawning Lahontan cutthroat trout and assess the population.

The news out of UC Davis last spring knocked California native fish biologists for a loop.

Genetic testing of native Lahontan cutthroat trout from Independence Lake in the Tahoe National Forest near Truckee found evidence of hybridization with non-native rainbow trout.

To understand the magnitude of that news you have to understand that Independence Lake is the only lake in California – and just one of two lakes in the world – to support a self-sustaining lake population of Lahontan cutthroat trout, a trout native to the eastern Sierra range and the Lahontan basin of Nevada.

And you have to understand that for decades, California Department of Fish and Wildlife (CDFW) biologists – joined by colleagues at the U.S. Geological Survey, U.S. Forest Service, the U.S. Fish and Wildlife Service and conservation groups including The Nature Conservancy and Trout Unlimited – have worked to safeguard these fish, enhance their habitat, and reduce competition from non-native brook trout, brown trout and Kokanee salmon introduced over the years into Independence Lake.

Lahontan cutthroat trout are listed as a threatened species under the federal Endangered Species Act. Their original listing in 1970 predates the modern act itself, which was passed in 1973.

Each fall, as part of species recovery efforts, biologists from CDFW and partner organizations electrofish upper Independence Creek, which feeds into Independence Lake, to remove brook trout from the creek that the Lahontan cutthroat trout depend on to spawn. Also in the fall, biologists set up a weir on the creek to block any of the lake’s resident brown and brook trout from moving up the creek to spawn. Non-native trout staging for a fall spawning run at the mouth of Independence Creek are stunned to the surface through electrofishing and removed from the lake.

“For the past 20 years at Independence Lake, we’ve been trying to give the cutthroat a helping hand by removing the non-native trout. It’s not a done deal but we’ve been pretty successful at reducing brown and brook trout down to very low numbers,” explained Dave Lentz, CDFW’s native trout conservation coordinator. “Lahontan cutthroat trout did not evolve with brook trout or brown trout on the landscape and they have been out-competed and displaced by these and other non-native species throughout much of the cutthroat’s historic range.”

Each spring, when the Lahontan cutthroat trout move up to spawn in upper Independence Creek, biologists and volunteers return with their weir to capture and count the numbers of spawning fish to assess population trends.

This spring, however, the spawning surveys will take on a new sense of urgency. After last year’s disheartening news from genetics experts, CDFW staff and partners captured some 170 Lahontan cutthroat trout from Independence Lake, took genetic samples and outfitted each trout with an identifying Passive Integrated Transponder (PIT) tag before releasing the fish back to the lake.

The tissue samples were sent to two labs for genetic testing. The results indicate that some 20 percent of the cutthroats captured and tagged last year show evidence of hybridization with rainbow trout. Biologists are now discussing plans and options for the spring spawn. Cutthroat trout returning to upper Independence Creek will be trapped and scanned with a PIT reader. Unmarked fish will be given a PIT tag, genetic samples will be taken for later testing, and the fish will be returned to the lake.

“We want to prevent further spawning by hybridized trout. We’re using some emerging science and the latest genetics information to manage this fishery,” said Lentz. “The situation is dire for Independence Lake cutthroat trout but we hope to improve their status by taking these measures.”

There are no known populations of rainbow trout within Independence Lake that could account for the hybridization but they are present in lower portions of Independence Creek below the lake. The outlet of the lake, however, is controlled by a dam that does not allow for fish passage into the lake. CDFW and partners will continue to investigate how rainbow trout gained access to the lake. It is thought that the rainbow invasion and hybridization are recent events, likely in the last 10 years.

The effort to remove hybridized cutthroat trout from Independence Lake takes place as state and federal officials in California, Nevada and Oregon step up collaborative efforts to increase Lahontan cutthroat trout awareness and recovery across their native range. Among those efforts:

• A genetic assessment of Lahontan cutthroat trout across their historic range has been underway for the past several years. That process resulted in the UC Davis findings of hybridization within the Independence Lake cutthroat population.
• In May 2019, the U.S. Fish and Wildlife Service released a document that updates recovery goals and objectives from its 1995 Lahontan cutthroat trout recovery plan using current science and a new conservation framework for species recovery.
• In October 2019, the U.S. Fish and Wildlife Service released 5,000 Pilot Peak strain Lahontan cutthroat trout back into Lake Tahoe, returning the native, fast-growing strain to Lake Tahoe for the first time in nearly 90 years.
• This coming May, state and federal fisheries biologists are scheduled to begin planning Lahontan cutthroat trout recovery and outreach efforts within the Carson River drainage.
• CDFW’s Hot Creek Trout Hatchery in the eastern Sierra is preparing facilities to establish a new rearing program for the Walker River strain of Lahontan cutthroat trout native to the Walker River drainage and Nevada’s Walker Lake.

CDFW Photo. Top Photo: A windy day at Independence Lake in the Tahoe National Forest.

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