Recent accomplishments of CDFW's scientific community
Deer population estimates are an important element of the California Department of Fish and Wildlife’s (CDFW) management decisions regarding the species – including setting quotas for deer-hunting seasons, acquiring land and identifying habitat improvement projects. Historically, CDFW has relied upon helicopter surveys to obtain these population estimates, but such surveys can be problematic. While they are effective in open and largely flat areas, they are less so in tree-laden areas where deer are hidden from sight. They can also be extremely expensive.
Now, thanks to emerging DNA technology, scientists are exploring a less invasive, cost-effective alternative: Analysis of what the deer leave behind.
The use of DNA is not new, of course – CDFW has used hair or tissue samples to extract DNA and identify individual animals for years. But scientists are finding that the painstaking collection and analysis of deer droppings is particularly useful because it allows them to gather the necessary information without physically touching (or stressing) the animals. And that, one might say, is the “bottom line.”
Fecal DNA analysis is being used by wildlife biologists in the North Central Region as part of a six-year region-wide study of mule deer (Odocoileus hemionus) that will provide population estimates in areas where data has previously been lacking. CDFW scientists, in cooperation with UC Davis, will use the deer pellets to take a genetic “fingerprint” designed to help estimate deer populations.
Starting in 2016, a crew began setting transects for pellet collection in the standardized sampling locations (known to hunters as deer zones X6a/b, X7a/b and X8) which are located in Lassen, Plumas, Sierra, Nevada, Placer and Alpine counties. After starting points were randomly selected, habitat information and pictures were collected along with fresh pellets. After the pellets were removed from the area in an initial sweep, scientists revisited the transect once a week for three more weeks to collect new samples. Between July and September of 2016, biologists visited 43 different transects in the summer range and collected and analyzed 458 fresh pellet samples. Staff also captured 20 does and seven bucks and fit them with satellite collars that produced data that helped identify summer home ranges.
CDFW will also use DNA to identify individual deer to help gather buck/doe/fawn ratios. Biologists will then combine the DNA data with home range data from collared deer to calculate the estimated number of deer in the population. This year staff have already completed another 36 plots and collared 18 more deer. Another series of pellet collections is scheduled next year, with a goal of continuing until all 17 counties in the region have been sampled.
Although several DNA projects are occurring across the state, this project is the largest landscape-level study for deer in California. The study is funded through CDFW’s Big Game Account, a dedicated account that provides research and management funds for game species. The University of California will conduct the laboratory work and statistical analysis.
Camouflaged trap used to capture foxes for the study. CDFW photo by Jennifer Carlson.
Sierra Nevada red fox bounds back to its native habitat after capture and study. CDFW photo by Scientific Aide Corrie McFarland.
The Sierra Nevada red fox has been the subject of intensified study by CDFW over the past decade. As they are notoriously tough to track and even tougher to trap, there are many unanswered questions regarding this elusive animal.
In an effort to better understand this state-listed threatened species, an ongoing research project seeks to capture and affix GPS tracking collars to them. The data collected will help biologists better understand the size and characteristics of the fox’s home range, its denning and resting areas, and its foraging habits.
The species has been outfoxing researchers for some time -- to the point where in the 1980s, it was presumed to have vanished forever from its historically occupied habitat in the Cascade and Sierra Nevada ranges. In March 1993, thanks to the then-emerging technology of infrared trail cameras, US Forest Service employees detected a single red fox in the Lassen National Forest.
That discovery prompted a wider study of foxes and other meso-carnivores in and around Lassen Volcanic National Park. In the late 1990s and early 2000s, Dr. John Perrine of the University of California, Berkeley, captured five individuals, primarily in the park, and placed radio collars on them to study their home range (both summer and winter), food habits and resting sites. Unfortunately, two of the collared individuals died within a year and none of the females reproduced during the course of the study.
Years later, CDFW launched a new study to determine the foxes’ current distribution in northern California and to address potential impacts on the species from activities including recreation and timber harvest. Initial efforts in 2008 used scat-detector dogs to survey portions of Lassen Volcanic National Park and the adjacent Caribou Wilderness. Then, from 2009 to 2011, trail cameras and hair-snaring devices were employed to survey high-elevation habitats in the Cascade Range from Mount Shasta to Lassen Peak. Yet foxes were only detected in the Lassen Peak area.
CDFW biologists have continued to survey for foxes with trail cameras, hair-snaring devices and scat surveys. Scats and photos are often obtained along Lassen Volcanic National Park and Forest Service hiking trails, because, like many other animals, red foxes frequent trails as they move through their territories. Analysis of the DNA contained in the collected scats and hair identified 22 individuals from 2007-2016. Some of these foxes are long-lived – samples collected over time from the same individual indicate that five of those individuals lived at least five and a half years.
CDFW efforts to capture and collar Sierra Nevada red foxes since 2013 were unsuccessful – until early February 2018. The nearly two decade-long dry spell came to an end at last when CDFW captured a Sierra Nevada red fox, a male that weighed about 10 pounds. It was captured in a “log cabin” style trap on National Forest land just outside of Lassen Volcanic National Park, near the town of Mineral. The fox was collared and released at the capture location, and CDFW biologists have been impressed by the distances he has regularly been covering since (five to six miles per day) despite the rough terrain and high elevation.
“Persistence played a large role in our success, because there are many days when we do not have any fox detections,” said CDFW Wildlife Biologist Jennifer Carlson. “We also ramped up our efforts this year by hiring two scientific aids rather than just one, which allowed us to literally double our efforts by putting more traps out across the study area.”
CDFW hopes to capture as many as four more red foxes this year. Scientists are using box traps, cage traps and a “log cabin” style trap that researchers have used in other states to capture both red foxes and wolverines. Capturing foxes is not an easy task given the cold temperatures and snowstorms, but as the Lassen population may only consist of around 20 individuals, it is imperative for the department to learn as much as it can about this stealthy animal.
For more information, please visit the Sierra Nevada red fox page.
Top photo: Senior Environmental Scientist Pete Figura and Senior Wildlife Veterinarian Deana Clifford release a red fox study subject. CDFW photo by Corrie McFarland
These pregnant females will bolster the population of a newly established herd as well as provide an infusion of fresh genetic material to helps ensure their new herd’s health and long-term survival.
Outfitted with an ear tag and two tracking collars, this ram awaits delivery to a new herd where it’s hoped he will infuse the population with fresh genetics
Among the goals of the Sierra Nevada Bighorn Sheep Recovery Plan is the establishment of 12 viable herds across their historic range. CDFW’s capture and relocation efforts over the years have helped establish 14 herds today across 150 miles of their historic range.
These Eastern Sierra bighorn sheep are being prepared for their flight to a new home and new herds.
Can just seven Sierra Nevada bighorn sheep really make much of an impact on the species’ future?
CDFW scientists believe so, which is why they came away pleased with the results of their annual spring helicopter capture this past March. Limited to three days of work due to strong winds and bad weather, the effort resulted in the capturing, collaring and relocation of seven sheep to new herds high in the Eastern Sierra.
Although the final chapters have yet to be written, the saga surrounding the Sierra Nevada bighorn sheep, one of the rarest large mammals in North America, is shaping up to be a 21st century wildlife success story.
A unique subspecies found only in the Sierra Nevada, historic populations numbered in the thousands. Their steep population decline began in the 1800s as a result of competition from livestock grazing, unregulated hunting and the transmission of disease from domestic sheep. Drought and predation further hammered their numbers, which dwindled to about 100 animals in just three herds by the mid-1990s. State and federal officials declared them endangered in 1999.
Today, less than 20 years removed from those dramatic listings, there are 14 different Sierra Nevada bighorn sheep herds spread across 150 miles of the iconic mountain range. About 600 bighorn sheep are now eking out a living atop the Sierra’s highest peaks. Sierra Nevada bighorn sheep are present once again inside Yosemite National Park and Sequoia National Park after a 100-year absence.
CDFW’s role is itself unique as a state agency tasked with leading the recovery of a federally listed endangered species. Sierra Nevada bighorn sheep are recolonizing their historic range – with a major assist from CDFW’s twice-yearly captures, collaring and strategic “translocations.”
This spring, three males and four pregnant females were captured from two established herds and translocated to two newly reintroduced herds – one along their western range inside Sequoia National Park and another herd in Inyo County at the southernmost extent of their range.
“Whenever we start these new herds, we like to move a minimum of 20 females as well as additional rams over time,” explained Tom Stephenson, a CDFW senior environmental scientist based in Bishop and the leader of the Sierra Nevada Bighorn Sheep Recovery Program. “At that point, we feel the population has enough animals to begin growing at a high enough rate and also has sufficient genetic diversity.”
Before the animals are relocated, a CDFW team records their vital statistics. Ultrasound machines are used to measure body condition and determine pregnancy status. The animals are outfitted with identifying jewelry – color-coded ear tags, VHF and GPS collars that allow biologists to identify them and track their movements for years in some cases.
All the high-tech, intensive monitoring has paid dividends with new appreciation and understanding. Once believed to always migrate to lower elevations in the winter, CDFW scientists have learned that many sheep ride out the Sierra Nevada’s inhospitable winters at 11,000- to 14,000-foot elevations.
“They are really tough,” Stephenson said. “But they’re able to do that because they put on large amounts of body fat in the summer when they’re on quality habitat. They are essentially hibernating standing up in the alpine. They’ve got an environment up there that is wind-scoured so they can find some food. They’re not having to move around much, and they’re relatively free from predators when they’re up in those altitudes in the winter time.”
Not every sheep captured is relocated.
Helicopter crews this spring attempted unsuccessfully to capture rams in the northernmost part of their range, collar them and return them to their same herds. CDFW biologists are keeping close tabs on the Mount Warren Herd near Lee Vining in Mono County in particular and its proximity to domestic sheep grazing on public land. Sierra Nevada bighorn sheep are disease-free and CDFW biologists want to keep them that way.
While populations have met or exceeded some recovery goals, eliminating disease – or the risk of disease – remains a significant benchmark and key to delisting or down-listing the species from endangered status.<
“There are a lot of bighorn sheep populations throughout the West that continue to struggle with disease,” Stephenson said. “So we’ve worked really hard with public land managers as well as private individuals in the Eastern Sierra to try and ensure our bighorn sheep don’t come into contact with domestic sheep.”
CDFW photos courtesy of Andrew Di Salvo. Top Photo: A helicopter crew delivers four bighorn sheep to CDFW's base camp where vital statistics were recorded, blood was taken, and the sheep were outfitted with identifying ear tags and tracking collars.
It does not take a leap of faith to believe that CDFW scientists have gained the upper hand in bolstering the population of yellow-legged frogs in the High Sierra.
Over the past three decades, Sierra Nevada yellow-legged frogs have become imperiled in California due to the two-pronged impact of introduced (non-native) trout and chytridiomycosis, a disease that is affecting amphibians worldwide.
Past introduction of non-native fish, including rainbow trout and golden trout, to benefit sport fishing in the High Sierra took a heavy toll on the species. High-elevation lakes where these frogs once flourished were largely fishless until fish stocking came into vogue. As the years passed, scientists determined that these introduced fish were depopulating the frogs by competing for food sources (primarily insects) and by predation (trout ate both adult frogs and their tadpoles). Chytridiomycosis, which affects many frog species, also impaired the ability of the Sierra Nevada yellow-legged frog’s skin to exchange vital nutrients, which often leads to death.
As a result, Sierra Nevada yellow-legged frogs are believed to have vanished from approximately 92 percent of their historical habitat, and halting and reversing that decline has become an important goal of CDFW, as well as other state and federal entities.
“This is an animal that only lives in the Sierra Nevada,” said Sarah Mussulman, a CDFW senior environmental scientist. “It is one of our unique California species that lives in high-elevation areas, and as an amphibian it serves as an important link between the terrestrial and aquatic ecosystems. This link is especially critical in the low nutrient, granitic basins of the High Sierra, where frogs and tadpoles consume insects and algae and are themselves consumed by a variety of snakes, birds and mammals.”
CDFW recently completed two projects as part of its ongoing efforts to reverse the population decline of Sierra Nevada yellow-legged frogs.
The efforts took place at two sites: Highland Lake and Clyde Lake, located approximately seven miles apart on the Rubicon River in the Desolation Wilderness area of El Dorado County. The projects were completed with federal grant funds earmarked for the recovery of endangered and threatened species (the species is listed as threatened by the State of California and as endangered by the U.S. Fish and Wildlife Service).
Highland Lake, along with its outlet, an unnamed stream, and two small adjacent ponds, supported a small population of rainbow trout when the project began in 2012. Trout abundance had declined in the absence of stocking in recent years but sufficient natural reproduction occurred in the inlet to Highland Lake to sustain the population. CDFW began using gill nets to remove rainbow trout -- the descendants of fish planted in the lake by CDFW from 1935 to 2000 -- in 2012, in partnership with Eldorado National Forest personnel.
During a frog-monitoring survey at Highland Lake in 2016, approximately 800 adult frogs were observed, as compared to a 2003 survey in which only a few tadpoles were observed. Because the frogs have consistently survived in this area despite the presence of chytridiomycosis, scientists believe they have a good chance at persisting in the area for a long time.
“Highland really had a population explosion over the past five years and can be counted as one of the most successful projects of this type ever undertaken,” Mussulman said.
The project at Clyde Lake was smaller and had somewhat different factors.
Golden trout, which frequently have the same negative impacts on Sierra Nevada yellow-legged frogs as rainbow trout, including predation and competition for food sources, were planted by CDFW at Clyde Lake from 1932 through 2000.
Once stocking was halted, the golden trout proved less resilient then the rainbow trout at Highland Lake, due to habitat factors.
“Clyde Lake sits in a north-facing granite bowl bordered by 1,000-foot cliffs, and no flowing streams enter the lake,” explained Mussulman. “There was no spawning habitat, which is likely why golden trout did not persist there after stocking was halted.”
The stream flowing out of Clyde Lake and four nearby ponds did support a small population of golden trout after plants were halted. The fish in the stream and ponds, which are self-sustaining populations, are precluded from moving from the stream into Clyde Lake by a fabricated dam. In 2013, frogs and a few tadpoles were observed in the stream alongside fish, and CDFW began removing the fish from the stream with gill nets to provide additional habitat for the frogs.
Nine years of monitoring data collected by CDFW scientists indicate that the area’s Sierra Nevada yellow-legged frog population, while small, is slowly increasing. Surveyors observed more than 120 frogs in 2016, compared to a low of six observed in 2005. Moreover, in 2016, for the first time, dozens of tadpoles were observed in the newly fish-free lower reaches of the stream.
“It is great to see these populations recovering,” Mussulman said. “It is a great privilege doing this work that helps keep these frogs on the landscape.”
CDFW photos: Highland Lake in the Desolation Wilderness, and a Sierra Nevada yellow-legged frog
CDFW Environmental Scientist Brian Ehler measures the hind-foot length on a fawn captured near Medicine Lake for a mule deer study.
CDFW Environmental Scientist Brian Ehler measures the hind-foot length on a fawn captured near Medicine Lake for a mule deer study.
Driving up Interstate 5 through Siskiyou County in northern California, one cannot help but take notice of the looming, majestic land mass of Mount Shasta, the largest volcano in the Cascade system.
In this rugged region of the Golden State, mule deer are an iconic species, valued by recreationists and required by wild carnivores who prey upon them for nourishment. Mule deer are considered a “foundation species” because the large landscapes that are necessary for their survival can also be home to a vast array of other wildlife and plant species. But mule deer populations have dramatically declined in recent decades across many western ranges, and in Siskiyou County, this decrease has prompted researchers from CDFW and the University of California, Santa Cruz to partner on a multi-year effort to investigate the population dynamics of this high-profile species.
Since 2015, 51 adult female mule deer and 37 fawns have been captured in the Mount Shasta region. Biological samples, including blood and parasites, have been collected, physical measurements of body condition and age recorded and telemetry collars attached to each subject. Collars on adult deer provide a GPS location every hour and alert researchers when a mortality occurs. The collars also document movement details, including migration routes and the location of critical winter and reproductive ranges. The fawn collars feature location beacons that allow researchers to monitor both general movements and when a mortality has occurred. Once a mortality alert is sent from a collar, a search of the site and an examination of the carcass ensues to determine if the deer died from predation or other causes, such as disease or malnutrition. The collars have timed releases and are set to drop off the animal after 18 months. Researchers can then reuse the collars after retrieving them by following a GPS signal. This high-tech, high-resolution documentation of deer behavior is vital for prioritizing the conservation value of landscapes so they may be better protected in the future.
With the recent arrival of gray wolves to northeastern California, predators are a key focus of the mule deer project. Understanding the influence this large canid will have on natural prey species begins with establishing baselines of how current predators -- including mountain lions, bears, bobcats and coyotes -- are affecting prey in this region. Mountain lions, which rely on deer as the primary component of their diet, are a major focus of this study. Researchers have captured and affixed five adult mountain lions with GPS telemetry collars, allowing them to track and study rates of predation, feeding patterns and diet composition.
The analysis of fecal DNA combined with new statistical techniques is another way to study population density and composition across broad landscapes. DNA analysis allows researchers to determine the sex and identity of an individual deer, which is used to estimate densities and gender ratios. Researchers are collecting fecal samples throughout the mule deer’s summer range, in the hopes of reliably extrapolating estimates of density and sex ratios across the entire region.
This project, which began in 2015, is scheduled to continue into 2019, as researchers strive to gain further insight into the lives of mule deer and predators across this ecologically complex and breathtakingly beautiful region of the state.
California Department of Fish and Wildlife photos.
Top photo: Mount Shasta in winter.
“We’re getting more accurate and precise numbers for harvest than we’ve ever had before, which is critical for calculating the tag quota for the next year and conserving our deer populations for the future,” said Stuart Itoga, a senior environmental scientist with CDFW and the state’s deer program coordinator.
Until recently, accurate deer harvest data had proved elusive. Prior to 2015, only successful California deer hunters had to report their take and only about 30 percent of those actually complied. CDFW supplemented the harvest data with numbers collected from game processing facilities, an inefficient process that still left an incomplete picture.
“It’s Wildlife Management 101,” Itoga said. “You have to know what your population is, what’s coming in and what’s going out. We needed to have better numbers.”
Following the mandatory reporting requirement in 2015, submittal rates for deer tag harvest reports jumped to 50 percent. In 2016, a $21.60 non-reporting penalty took effect, which applies to the purchase of future tags, and boosted reporting to the all-time high.
Mandatory deer tag reporting data is just one of a number of new tools that has CDFW deer biologists excited about their ability to better assess California’s deer herds.
An innovative DNA study of deer feces promises to give biologists new information about the size and characteristics of the state’s deer population.
CDFW has also greatly expanded the use of deer tracking collars, thanks to improved technology. Since 2016, CDFW has affixed the relatively lightweight, remotely programmable, GPS tracking devices on 350 deer to learn more about their preferred habitat, in-state and out-of-state migration routes and sources of mortality other than hunting. Advanced camera technology also promises to improve the data collected from CDFW’s aerial and ground-based population surveys. A new computer model is being developed to incorporate all of these new data sources into more sophisticated, accurate and precise deer population estimates.
“It’s really an exciting time to be doing this type of work,” Itoga said. “We’ve always used the best available science, but with technology moving at the pace it’s moving now, we have tools available to us now that we didn’t have even five years ago.”
Management changes can happen more quickly as a result. For the upcoming 2017 deer hunting seasons, for example, deer tag quotas were cut in half in three highly desirable, Eastern Sierra X Zones – X9a, X9b and X12 – as a result of new data and field work that showed that migratory deer in these areas suffered from the long, intense winter.
“Winter survival was poor,” Itoga said. “Our hope is that if we reduce the harvest this year, the populations will have a chance to rebound and increase next year.”
The automated recorder model the scientists used. (CDFW photo by Brett Furnas)
Two avian researchers recently completed a groundbreaking study on the effects of climate change, based on the calls of California’s songbirds. By recording the sounds made by eight different songbird species, and tracking the dates they are most vocal and how frequently they sing, the scientists were able to develop a method to measure how the birds are adjusting to climate change.
CDFW Wildlife Ecologist Dr. Brett Furnas and William Jessup University’s Professor Michael McGrann analyzed data from two bird surveys, one done by CDFW and another led by William Jessup University, in the Klamath Mountains and Southern Cascades of northern California. Both studies used automated recorders to monitor bird sounds between 2009 and 2011. The results of their analysis, detailed in a research article entitled Using Occupancy Modeling to Monitor Dates of Peak Vocal Activity for Passerines in California, were published this month in a peer-reviewed, international journal of ornithology, The Condor: Ornithological Applications.
Furnas and McGrann’s study was prompted by the scientists’ concern that climate change could throw bird’s reproduction cycles out of sync with the seasons. Their work, which represents the first comprehensive assessment of songbird occupancy over approximately 15,000 square miles in California, earned high praise from Steve Beissinger, an expert on avian phenology at the University of California, Berkeley.
“Furnas and McGrann provide a textbook example of how to detect differences in the timing of nesting among bird species using information on the peak date of singing derived from surveys and automated recorders,” Beissinger said. “Their results support recent findings of a five-to-twelve day shift forward in the timing of peak singing by California birds in the nearby Sierra Nevada and coastal ranges in response to climate change.”
Because birds’ songs are correlated with their breeding behavior and are easily identifiable to species, the scientists found them to be a useful tool to provide new baseline data for the birds of northern California. Working together, they identified the precise dates of peak vocal activity for eight songbird species: Hutton’s vireo, hermit thrush, dark-eyed junco, Nashville warbler, MacGillivray’s warbler, yellow warbler, western tanager and black-headed grosbeak. In addition to gathering baseline data, Furnas and McGrann developed a method to track advances in the timing of vocal activity in the coming decades.
Male songbirds sing for several reasons -- including to advertise their territory or to find a mate with which to breed. When birds are at their most vocal, they are usually near the height of their breeding season, Furnas explained.
Much like the call of the imperiled “canary in the coal mine,” changes in the frequency or timing of these native birdsongs can serve as barometers of the cumulative impact of climate change.
“When the canary starts singing you know that there is a danger, such as a buildup of dangerous gasses in a mine,” Furnas explained. “When the birds in our study start singing earlier in the season, they are warning us that climate change is starting to disrupt complex ecological cycles that developed slowly over millions of years of evolution.”
One of the most interesting findings of the study so far is a hint in the baseline data that migratory birds may be at greater risk than non-migratory birds. “We found the highest singing activity for migrant birds spanned a shorter number of days than the highest singing activity for non-migratory birds,” Furnas said. “This could be because migratory birds have less flexibility to shift the timing of their breeding cycle. If they are prompted by increasing temperatures to migrate earlier in the year, they may arrive at their breeding grounds to find they don’t have enough insects to eat.
“Migratory birds have to compress a lot of activities into a shorter time period with less margin for error,” Furnas explained. “Think of it like scheduling a short holiday somewhere nice, but when you show up, bad weather cancels out a lot of your itinerary.”
This, in turn, negatively affects the very biodiversity that CDFW is responsible for monitoring.
“If all the species adjusted their ecologies similarly, perhaps that would be OK, but unfortunately, we expect that different insects and birds will react in different ways leading to a mismatch of conditions,” Furnas said.
Both CDFW and William Jessup University plan to continue bird surveys over the long term so that California has the information to support effective management of climate change and other conservation challenges.
Top photo: Singing hermit warbler, one of the species addressed in the study. (CDFW photo by Michael McGrann)
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