Science Spotlight

Rocky Mountain elk in Modoc County taken during a CDFW survey in 2019.


Scientists at UC Davis analyzed scat to determine where the elk originated.


A map of the elk’s journey from Tahoe to Sonora Pass.

About a dozen years ago, California Department of Fish and Wildlife (CDFW) biologist Nathan Graveline heard rumors that a sole elk had been spotted in a highly unusual location – the Stanislaus National Forest, between the Clavey and Tuolumne rivers. At the time, scientists didn't have the technology to confirm the reports.

“Nobody knew where the elk came from. We weren't able to piece any of that together,” said Graveline.

Last September, scientists got word of another unexpected elk sighting, this time just south of Lake Tahoe in the Crystal Basin Recreation Area. “When I heard there was possibly an elk back in the area, I thought, ‘We’ve got to jump on this. If we can get a good DNA sample, we can figure out where the elk came from,’” said Graveline.

They set up trail cameras and were able to get a photograph of the elk. They also collected scat samples, which they sent to Dr. Benjamin Sacks, director of the Mammalian Ecology and Conservation Unit at the University of California, Davis’ Veterinary Genetics Lab. Through DNA analysis, Dr. Sacks and Ph.D. student Taylor Davis determined that the elk probably originated from a herd in the northeastern part of the state.

“We first estimated likelihoods of the observed genotype originating from each potential population based on the frequency of the alleles in those populations. We then obtained a probability or origin for each population by dividing its likelihood by the sum of all likelihoods for all populations,” said Dr. Sacks.

The report of an elk near Lake Tahoe was unusual in and of itself — but six weeks later the story got even more interesting. Scientists conducting a helicopter survey reported seeing a bull elk near Sonora Pass. 

Scientists went to the location of the reported sighting and were able to collect scat samples, which they sent to Dr. Sacks’ lab for analysis.

“We did the genotyping and it turns out it was the exact same elk that was tracked south of Lake Tahoe,” said Tom Batter, a Ph.D. candidate in Dr. Sacks’ lab. 

It appears scientists had on their hands a trailblazing elk — a Rocky Mountain elk that traveled 40 miles in six weeks and ended up farther south in the Sierra than had previously been reported.

“That boy was on quite a quest,” said Shelly Blair, a unit biologist in El Dorado County. “He likely traveled over some pretty rocky terrain, depending on which route he took. He probably had to cross over Interstate 80 or the 395 corridor at some point. Without the DNA, it would have been a total mystery as to where the elk came from.”

Kristin Denryter, coordinator of CDFW’s Elk and Pronghorn Antelope Program, said the bull’s journey is likely evidence of population growth among elk or herd densities that exceed the carrying capacity of the habitat.

“We know there’s great potential for expansion by bulls, and this means there could be recolonizations happening. We want our elk to be expanding and figuring out new habitats and going to new places. A bull elk like this might be figuring out new migratory routes and allowing for migration to persist. If he’s taking this route, then other elk and wildlife could be doing the same in the future,” said Denryter.

As to what motivated the bull elk to travel so far off the beaten path, Graveline says it may have been looking for a mate or new territory.

“He went farther south than he would need to for food, so I don’t think he was driven by that. This is a younger bull, and sometimes they get pushed out of a herd by a more mature bull,” he said.

Denryter added, “Younger males that are not competitive for mates are more likely to go off on their own or get pushed out of the herd. There’s absolutely a chance he could turn around and head back the way he came, but he’ll likely keep moving to find a mate.”

Although the elk is described by scientists as young, its exact age is unknown. Elk typically live 10-13 years in the wild. As far as threats in the wild – mountain lions hunt elk, but deer are their preferred prey. This elk’s biggest threat would likely be poaching, said Denryter.

Scientists are excited about the possibility that elk are expanding their range, but it’s also their job to prepare for corresponding conflicts.

“It’s kind of a double-edged sword,” said Denryter. “There’s risk of disease if elk come into contact with livestock while creating new migratory routes, and they can compete with livestock for forage. They can also cause vehicle accidents. Understanding the movements of elk and other wildlife is important so we can address these potential conflicts.”

CDFW would like help from the public in tracking the movements of elk populations statewide. Elk sightings can be reported online on the department’s website.

“If you see an elk — especially in places where you don’t normally see one — definitely take a photo with your smartphone and let us know,” said Denryter. “Smartphone photos are geotagged which will help us confirm the location. The online form allows you to upload photos and share any interesting observations. It’s really helpful to have this information so when there are conflicts or regulatory changes proposed we have data to help make informed decisions.”

CDFW Photos. Top Photo: A bull elk

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Media Contact:
Ken Paglia, CDFW Communications, (916) 322-8958

A coast yellow leptosiphon seedling.


Residential development on the San Mateo coast threatens coast yellow leptosiphon’s habitat.


Coast yellow leptosiphon is a low growing annual from the Phlox family which typically blooms in April and May.

The world is closing in on coast yellow leptosiphon.

The endangered plant exists in only one known location on earth — an 1,800 square foot plot on Vallemar Bluff in Moss Beach, about 20 miles south of San Francisco. The low-growing annual from the Phlox family features bright yellow flowers with fused petals and typically blooms in April and May.

Erosion caused by rain, waves and other factors is making the bluff that the plant perches on less stable. One study showed that the bluff receded 48 feet between 1908 and 2014. Scientists believe it will continue to recede almost six inches per year moving forward. Climate change could accelerate the erosion process.

“The plant could be almost completely gone in the next 50 years due to bluff-top erosion alone,” said Cherilyn Burton, a senior environmental scientist in CDFW’s Native Plant Program.

Slightly inland from where coast yellow leptosiphon grows is a planned four-unit housing development. The project was approved in March 2019. Although the development project mitigates for direct impacts to the plant, it also eliminates an area that could have been used to help restore the species.

Then there are the indirect impacts caused by urban development. Some aspects of urban design, like installation of storm drainage and landscape irrigation systems, could alter water runoff patterns around the plant’s habitat. The new housing development could also mean increased use of fertilizers, pesticides and other chemicals which through runoff could flow into the plant’s habitat and harm the soil.

“An increase in human activity can cause soil and habitat disturbances, which creates conditions that can be favorable to the spread of non-native plants,” said Burton.

Growing among the coast yellow leptosiphon is freeway iceplant—a fast-growing, invasive species that dominates the landscape and outcompetes other plants for light, nutrients, water, space and other resources. Coast yellow leptosiphon is also threatened by non-native plant species like rough cat’s ear, hare barley and cut leaf plantain. It may also face negative impacts from non-native slugs which can be detrimental to the plant’s seedlings.

“There’s so much going up against this plant. We may have to get creative to save it,” said Burton.

If there’s a bright spot in coast yellow leptosiphon’s story, it may be the lack of opposition in getting it listed as a protected species. In 2016, the California Fish and Game Commission designated coast yellow leptosiphon as a candidate species under the California Endangered Species Act. The plant was officially listed as an endangered species in 2018.

Burton recalls the heavy workload that came with preparing her recommendation to the Commission, and her relief upon hearing the Commission’s vote.

“They voted on it right then – right after I gave my presentation. Sometimes the commissioners have questions. But this time there was silence, and then one of the commissioners said, ‘Well, I think we can all agree that this plant meets the criteria.’”

Options to save coast yellow leptosiphon are limited, but there are a few. Scientists are on the lookout for additional suitable habitat. However, most suitable areas already contain rare and sensitive plants to which scientists must consider potential impacts. If additional suitable habitat is found, there will likely be land use and management issues to be worked out.

“The biggest problem is there’s just not a lot of habitat left in the area, and it’s not clear how far away we could go before the microclimate or other conditions would be too different to be suitable,” said Burton.

Another conservation strategy could include long-term seed storage at a botanical garden or other suitable facility to preserve seeds for the future.

Meanwhile, one landslide at the bluff’s edge could have serious consequences.

“Because of its vulnerability and rarity, losing any portion of the plant’s population could result in extinction,” said Burton.

CDFW Photo. Top Photo:
CDFW scientists Jeb Bjerke, Cherilyn Burton and Bill Condon (retired) at Moss Beach in San Mateo County doing fieldwork to support coast yellow leptosiphon.

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

Mountain lion territory, San Diego County.


Justin Dellinger in the field, for the mountain lion study.


Mountain Lion after capture, before being released.

CDFW wildlife biologist Justin Dellinger has a most unusual job --  since 2015, he’s been capturing and collaring mountain lions in California’s back country. Justin aims to achieve something unique, which is the first-of-its-kind comprehensive population assessment of California’s mountain lions.

It’s a tough job that begins long before daybreak, in some of California’s roughest terrain. Justin works with a houndsman whose dogs track the lions by scent. When they pick up the trail, it’s Justin’s job to tranquilize the lion, take biological samples and fit it with a tracking collar before setting it free. But lions are elusive by nature, and there’s a lot of territory to cover. In between successful captures, Justin spend his time setting traps and cameras, fixing field equipment and hiking the state’s hills and mountains looking for tracks.

California’s mountain lion population is thought to be between 4,000 – 6,000.  Because lion habitat has been reduced by human encroachment in the most populous state in the nation, researchers like Justin are seeking any information they can to better understand where wildlife live, what they eat, how they deal with disease, and how they can thrive in the future.

To date, there’s just one corner of the state Justin hasn’t yet scoured as part of the project – the far northwest. That work is scheduled to start in November 2020, with the goal of incorporating the results of the study into the CDFW’s lion management plan by 2023.

Learn more about Justin’s work in the video below, and read about the early stages of the project in this July 2018 Science Spotlight about the state Mountain Lion Project.

CDFW Photos.

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Media Contact:
Tim Daly, CDFW Communications, (916) 201-2958

CDFW manages about 940,000 acres in over 200 properties statewide that are designated as wildlife areas or ecological reserves. Pictured is Elkhorn Slough Ecological Reserve in Monterey County.


Properties like the Carlsbad Highlands Ecological Reserve are acquired and managed to protect sensitive plant and wildlife species.

At the nearly 17,000-acre Yolo Bypass Wildlife Area near Davis, staff close off some areas to the public during certain times of year. The closed zones offer resident wildlife a reprieve from the many activities offered at the site such as hunting, wildlife viewing, and student education field trips.

CDFW working to improve negative effects of non-consumptive recreation on conservation

Editor’s Note: As we publish this article, California, the nation, and the whole world are gripped by the COVID-19 pandemic. To slow its spread and not overwhelm healthcare resources, distancing and stay-at-home orders have led to the delay of trout openers and other fishing events, and closure of parks, reserves and many other publicly accessible facilities. Stories are beginning to emerge of increased wildlife presence in park and reserve areas that are normally filled with people. We look forward to the end of the pandemic and its horrible devastation will be over very soon but we know it will be some time before we realize a return to “normal.” We hope to gain from this emergency more information on wildlife’s response to fewer visitors – data that may be able to help us improve our management of parks and reserves in a way that protects wildlife and their habitat while also providing reasonable recreation experiences. In the meantime, stay well, and stay home to save lives.

Do Not Feed Wildlife. Do Not Cut Switchbacks. Stay On Trail. 

If you’ve spent time in recreational areas, you’ve seen the signs. You’ve most likely complied with them. But you may not have a full understanding of why the rules are important.

A growing body of research is showing that non-consumptive recreation – i.e., activities like hiking, biking and bird watching, that don’t involve harvesting of resources – can have harmful effects on species, their habitat and efforts to protect them.

For example, one study showed that mule deer may experience increased predation risk when they shifted toward nocturnal activity in response to human recreation. Another study showed that human activity resulted in elk foraging less and showing increased signs of stress. Research has shown (PDF) that higher levels of human activity reduced habitat suitability for bobcats, gray fox, mule deer and raccoons. Human activity has also been linked to declines in reptile species.

Recreation has been cited as a factor in endangerment of plant and animal species on federal lands, and of all U.S. states, California has thegreatest number of listed species that are threatened by recreation. In a literature review led by Courtney Larson, a scientist for The Nature Conservancy, 93 percent of included articles found significant effects of recreation on wildlife.

“CDFW is tasked with managing the state’s diverse plant and wildlife species and the public’s use and enjoyment of them – so how do we also manage the effects of recreation? We have to bring environmental stewardship into the fold and find ways for recreation and conservation groups to work together,” said Ron Unger, a program manager in CDFW’s Habitat Conservation Planning Branch. “It’s important to set aside lands for both needs. Lands set aside for conserving declining and vulnerable species generally need to be restricted in terms of public access. Other, less sensitive sites need to be set aside so people can have a positive place to enjoy and appreciate nature and the outdoors.”

At the Carlsbad Highlands Ecological Reserve – a CDFW-owned reserve in San Diego County – land managers have had a tough time with mountain bikers and others building illegal trails. Over the past half-dozen years, bikers have illegally carved out about 17 miles of trails (the property has 2.1 miles of legal trails) and removed nearly 500 trail signs. CDFW had to step up enforcement to stop the illegal trail use.

“We don’t enjoy telling people they can’t ride here, but at the same time we have to make sure we don’t love these spaces to death – especially when the main reason the lands are acquired and set aside is to protect wildlife,” said CDFW Regional Manager Ed Pert.

At the nearly 17,000-acre Yolo Bypass Wildlife Area near Davis, staff close off some areas to the public during certain times of year. The closed zones offer resident wildlife a reprieve from human activity.

“It’s definitely a balance. We want the public to enjoy wildlife, but we also want to give wildlife a place to rest,” said Joe Hobbs, who manages the wildlife area.

CDFW Senior Environmental Scientist Shannon Lucas helps coordinate the department’s Natural Community Conservation Planning (NCCP) program, which issues regional permits that allow for development while ensuring habitat protection. She also oversaw grant funding for research on the effects of recreation on NCCP lands.

“These are areas that are intended to be preserved for their ecological value. We have a responsibility to analyze the effects of recreation on the species and habitats that contribute to conservation under an NCCP,” said Lucas.

CDFW is involved with research efforts aimed at gaining insight into how to best balance recreation with conservation. The department’s Human Dimensions of Wildlife Unit is currently researching the views of stakeholders, and future research will assess how to best communicate with stakeholders on the issue.

“We want to serve our constituents as well as manage the state’s natural resources for their ecological value. Once we understand how our stakeholders feel about the issue, we can communicate in a way that connects with their concerns,” said lead researcher Alex Heeren.

CDFW just released a special edition scientific journal featuring literature reviews and original research on the effects of non-consumptive recreation on wildlife. Ange Baker, editor-in-chief of California Fish and Wildlife Journal, chose the topic after soliciting ideas from CDFW employees.

“Research has shown that even mild recreation like hiking can have pretty significant impacts on some species. This is an especially important issue in California where CDFW manages about 940,000 acres of property designated as wildlife areas or ecological reserves. We decided to do a special edition to bring light to the issue,” said Baker.

Read the special edition journal (PDF).

CDFW Photo. Top Photo: Signage at Carlsbad Highlands Ecological Reserve in San Diego County is intended to help protect threatened and endangered plant and wildlife species by prohibiting incompatible recreation activities such as motorized vehicle, biking, and drones.

Media Contact:
Ken Paglia, CDFW Communications, (916) 322-8958

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