U.S. Navy Making Endangered Species History

 _{All photos were taken on San Clemente Island, by Joel Sartore, Joel Sartore Photography, with assistance from the dedicated Department of the Navy, Environmental staff of San Clemente Island.} 

In 2023, on San Clemente Island (SCI) off the California coast, the U.S. Navy quietly made Endangered Species Act (ESA) history when the  U.S. Fish and Wildlife Service  delisted five SCI species at once.

The San Clemente Bell's Sparrow (Artimisiospiza belli clementae), San Clemente Island (SCI) bush-mallow (Malacothamnus clementinus), SCI paintbrush (Castilleja grisea), SCI lotus (Acmispon dendroideus var. traskiae), and SCI larkspur (Delphinium variegatum ssp. kinkiense) were removed from federal listing in January 2023 because their populations have sufficiently recovered. 

“It is the largest group delisting in the history of the Endangered Species Act,” said Melissa Booker, San Clemente Island’s wildlife biologist.

The natural resource management effort is admirable, made more impressive by the mission under which this effort was made. San Clemente Island, situated 41 miles off the Southern California coast, provides the only ship-to-shore, air-to-ground, and boots-on-the-ground live firing range in the Continental U.S. In civilian terms, that means it is a place where troops can practice storming beaches, dropping bombs, and firing weapons – sometimes all at once. 

It’s important to manage the habitat not only for the endemic and protected plant and animal species, but also to maintain the landscape for essential training missions. The topography and habitats that occur on San Clemente – open grassland plateau, beaches, deep canyons, dense cactus, and scrublands – allow troops to train on a variety of terrains and conditions. 

Yet, with all of this intensive military activity, biologists and botanists who work for the military and myriad other agencies and nonprofit groups have simultaneously engaged in decades of resource management resulting in the recovery of these five federally listed species that occur on SCI, and they continue to work to protect dozens of other endemics found nowhere else. 

The success of the act [ESA] relies on recovery, and doing it in areas where we have overlays of active missions," said Kim O'Connor, Conservation Program Manager for the Commander Pacific Fleet. "There's a lot of coordination. And frankly, it's really a passion for us. We care about the natural resources, and we care about the mission."

The 1960 Sikes Act requires the Department of Defense to identify, monitor, and create recovery programs for the natural resources and ecosystems that occur on military-owned lands. At San Clemente Island, this mission means managing multiple unique ecosystems with a U.S. military mission that occurs nowhere else in the continental United States. 

But a law can’t create the kind of dedication needed for creating management plans and the cooperative relationships to successfully execute them. Such passion comes from within personnel who deeply care. 

"Take the SCI Larkspur, for example. In 1979, it occurred in only two places on the island, and in one of those spots there was a single plant," O’Connor said. She thinks about her predecessor out there in the hot sun putting a fence around that single plant. It had to feel hopeless.

And the challenges at that time were huge. The island had been used for ranching from the 1850s until the Department of Defense acquired it in 1934. Decades of grazing had left it bare of most native vegetation and home to invasive grasses and thousands of free-roaming feral goats, among other habitat degradations. 

However, once the last of the estimated 29,000 feral goats was removed from the island in 1991, the shrubs and plants began to recover, gradually bringing back the landscape that makes San Clemente Island unique among California’s Channel Islands. As the southernmost island in the chain, it encompasses a hybrid of the Baja Peninsula’s dry, desert habitat and the moist, more temperate habitat of islands farther north. 

The island’s native vegetation captures moisture from the fog and clouds that pass over the island almost daily. Pulling that moisture into the plants and soils below creates the habitat in which dozens of endemic species thrive. San Clemente has the highest endemism of flora and fauna in the California’s islands.

"As the habitat improved and the endangered SCI Larkspur spread, Navy officials found themselves having to consult with natural resources management in more areas of the island before initiating training missions. That made everyone’s tasks more complicated, but species recovery illustrates it’s worth it to get to the other side,”O’Connor said.

Now there are more than 19,000 SCI Larkspur plants spread over 74 areas.

Among other successes are the San Clemente Bell’s Sparrow, delisted in January 2023, and the SCI Night Lizard (Xantusia riversiana), delisted in 2014.

The San Clemente Bell’s Sparrow was first recognized as a subspecies of the Sage Sparrow during the 1800s, and at that time called the San Clemente Sage Sparrow. A 2013 taxonomy update for the Sage Sparrow split the species into two distinct birds – the Sage Sparrow and Bell’s Sparrow, with San Clemente Bell’s Sparrow, a unique subspecies.

 The bird was listed as threatened in 1977, along with six other species of flora and fauna endemic to the island. By 1984, only 38 Bell’s Sparrows existed on the island, and experts estimated it had a 96% chance of going extinct in 50 years, Melissa Booker said.  

On the plus side, Bell’s Sparrow is a very adaptable bird, and once the shrubs and other more vertical vegetation began to return after removal of the goats, the species’ nesting success improved, Booker said. Biologists also revamped their monitoring program after realizing the bird was adapting to other parts of the island for foraging and nesting. 

As a result, the Bell’s Sparrow population has grown to more than 6,000 birds, and has expanded from a range of 10,000 acres to 33,000 acres, nearly the entire island. 

The SCI Night Lizard (Xantusia riversiana reticulata) is another endemic species that dodged the extinction bullet under the military’s watch. This medium-sized lizard measures 5 to 8 inches from its snout to the tip of its tail and is widely dispersed over the island. It also occurs on Santa Barbara Island and San Nicolas Island, which also is managed by the military. But San Clemente Island provides about 90% of its range. At the time of its delisting in 2014, there were an estimated 21.3 million night lizards on San Clemente, according to the Federal Register. 

The SCI Night Lizard’s name isn’t totally accurate, Booker said. They are active during the day, but typically remain out of sight – under rocks or shrubbery – to avoid predators. They give birth to live young, and can live to be over 25 years old – a long time for a small reptile. 

“You have to admire these lizards,” Booker said. “They live over 25 years. And during drought or during fires, they go down into the ground and estivate (sleep). When the rains come, they are back.

And they have an interesting relationship with the Bell’s Sparrow," Booker added. Remote cameras have shown the lizards climbing into the sparrow’s nests, in search of food. So, while trying to protect the sparrow population, resource managers also had to respect the lizard’s needs. In the end, the improved habitat helped the ecosystem balance itself, with animals that eat the lizard keeping its brazen nest forays at a reasonable level. 

“Predator pressure is natural,” Booker said. “This is how it’s supposed to work.” 

Still working their way to recovery and delisting on or around San Clemente Island are six marine mammal species, four species of sea turtle, two plant species, two bird species, and one shark species. Add to that, the fact that San Clemente Island has dozens of endemic species and subspecies, along with new species being discovered – such as a recently noted land snail that DNA testing suggests is an as-yet, unnamed new species. 

Documenting this diversity is not only fascinating, it is important for the future," Booker said. "We are recovering habitat and sustaining the species we know to exist, but also looking to the future. It is my firm opinion that understanding our diversity and maintaining it will be paramount."

Climate change is the biggest variable SCI scientists face. Weather trajectories are uncertain, and climate models for the Channel Islands aren’t perfect. 

“There will be winners and losers that we cannot yet predict,” Booker said. “So if we can document our diversity now and manage to maximize maintaining diversity, we have hopes of keeping species that will survive under future scenarios.” 

Booker and O’Connor both said they feel good about the work they have done so far, and are optimistic about the work ahead. They have strong partnerships with area nonprofit groups and the U.S. Fish and Wildlife Service, along with a deep commitment and financial support from the Defense Department. The Department put more than $6 million toward natural resource management under O’Connor’s purview in 2022. 

In addition to the importance of the species outcomes, O’Connor said she hopes their efforts send a message to those lone scientists out there, struggling to fence off one plant or saving a single invertebrate. It may seem like a futile effort, but don’t give up, she said. 

“You don’t know where it’s going to go in 30 years,” O’Connor said. “You will get to the other side.” 

The endangered San Clemente Loggerhead Shrike (Ludovicianus mearnsi) struggles to maintain its population, even though it is one of the tough guys of the bird world. 

The Loggerhead Shrike is a songbird – a word that conjures images of colorful little feathered friends teetering on a branch, singing sweet songs. 

But the shrike is the bully of the bird yard – an astute hunter often called “the butcherbird.” This 9-inch carnivore with gray feathers and a black mask munches on grasshoppers, crickets, beetles, lizards, mice, and even other birds. 

Its infamy stems not so much from what it eats, but from how. The Loggerhead Shrike perches above the ground and drops on unwitting prey, breaking the neck of vertebrates with the “tomial tooth” on its beak. If the prey happens to be too large to take easily, the shrike will wrestle its quarry to a sharp twig, barbed-wire fence or other sharp object and impale it. In this way, the Loggerhead Shrike can cache a bird bigger than itself enabling them to dismember it for dinner or save it for later. 

However, the Loggerhead Shrike subspecies endemic to California’s San Clemente Island (SCI) is facing a threat far too big to impale on a fence: the decades of habitat degradation that shrunk the population followed by repeated drought cycles that appear to be preventing recovery, led to it being listed as a federal endangered species in 1977. 

More than 40 years later, it remains at the center of an aggressive program by the Navy’s Commander Pacific Fleet to help it recover. And this recovery must be done in concert with what the U.S. Navy needs to accomplish at San Clemente Island – training exercises that involve live fire.  Lots of it.  

It's the last Continental U.S. location where the Navy can engage in simultaneous live fire ship-to-shore, air-to-ground, and ground troop training. And it's the only place for the 3rd phase of Navy Seal training," said Melissa Booker, wildlife biologiest for SCI. "It has a unique role in the military."

San Clemente Island also has a unique ecosystem, she said. As the southernmost of California’s eight Channel Islands, San Clemente Island is a hybrid of the arid Baja habitat and the more moist habitats of the islands found farther north. It has grassland, canyon woodland, dune, and scrub ecosystems. 

Biodiversity thrives in the edges where different habitats meet, making San Clemente a 21-mile-long treasure trove of nearly 1,000 different species of plants and animals, including at least 47 species that are endemic – meaning they occur nowhere else. 

It is not uncommon for U.S. military bases – because of their large land masses that are used for specific mission needs – to provide some of the last open wildlands in the United States. The presence of endemic species isn’t a surprise, but because of their limited ranges, such species can become threatened or endangered without management plans that provide species protection while allowing the military to do its work.  

Integrated Natural Resources Management Plans for military installations must result in no net loss of the military’s mission on those lands. But that doesn’t mean the species conservation needs are ignored.  

Quite the contrary, San Clemente Island has shown that species can not only survive, but thrive alongside military missions.

The struggle with any species recovery on San Clemente Island is largely linked to vast habitat degradation caused by ranching and agricultural activity that occurred from the 1850s until 1934, when the Defense Department assumed ownership of the island. But the feral herbivore populations (pigs and goats) persisted after ranching ended. At the center of the problem was this large persisting population of feral goats that obliterated native vegetation, said Kim O’Connor, Conservation Program Manager for Commander Pacific Fleet. The island’s endemic shrubs are important to the overall health of the ecosystem because they capture and hold moisture from the frequent fog and low clouds that pass over the island and send that moisture into the soil. The military removed the last of the estimated 29,000 feral goats in 1991, and the ecosystem began to recover. “That’s not that long ago,” O’Connor said. “It’s pretty remarkable that 30 years later we have species being delisted."

Still, the SC Loggerhead Shrike is proving a challenge. Although the military worked to rid the island of feral goat and cat populations, partnered with mainland captive breeding programs to increase the wild bird population, and installed fuel breaks to protect habitat from fires caused by military activity, the shrike population still plummeted to just 7 pairs in 1998. 

"Officials moved the captive breeding program to San Clemente Island," Booker said, so “the birds could be held in the same conditions in which they will be released.” Keeping it on-island also helped prevent the introduction of mainland diseases. They also improved methods of release, resulting in released birds surviving and recruiting into the wild population.  

It seemed to work. By 2009, there were 82 pairs of Loggerhead Shrikes in the wild, and things were looking up.

Unfortunately, recent years of persistent drought have made conditions more difficult for the wild pairs to successfully raise their broods and survive, and the number of pairs in the wild dipped to just 20 in 2022, Booker said. Scientists believe that drought affects the shrike’s productivity and survival. Still, there is hope. Recovery is a marathon, not a sprint.

“We are very optimistic the rains this year will result in productivity increases and better survivorship,” Booker said. “The key is when the rats come back.” 

Invasive black rats decline during drought, but increase in numbers when the rains come. The hope is that the Loggerhead Shrikes will be able to incubate their eggs and have their broods fledge before the rats return to raid nests. The shrikes have a better chance of success if they are “out the door first,” she said. The Navy works to control the rats, especially where shrikes nest, but they cannot use poisons that would impact the shrikes themselves or other protected and endemic species like the Island Fox, so control is a challenge. 

Shrikes have preferred the southwestern end of the island where ship-to-shore bombardment occurs. Once in the central portion of this bombardment buffer zone, they are now clustered on the southeast side, where there is a large, vegetated buffer region between the mainland-facing side and the bombardment area as well as along the eastern side, north of the shore bombardment area. The Navy’s team of biologists releases birds outside of the bombardment area, to increase the population across the island, but shrikes, as it turns out like to nest near other shrikes. “If they see another (shrike), they’ll set up relatively close,” Booker said. “They cluster or what biologists call conspecific attraction.”

Recovery is a long process that requires diligence, patience, communication, and persistence among many stakeholders. The biologists from the San Diego Zoo and Institute for Wildlife Studies actually live on-island to run the captive breeding program, and release and monitoring program, respectively.  

“People give up what most of us would consider a normal life to live out here,” Booker said. 

The Navy with the U.S. Fish and Wildlife Service direct the recovery program and are committed to its success. The Commander Pacific Fleet has invested at least $50 million in the shrike recovery effort so far, taking all feasible management actions, Booker said. When the threat is drought, or extreme weather events, the road ahead is challenging. The Navy and biologists know how to remove non-native grazers, recover habitat, manage fire, raise and release birds, but we cannot control the weather. Still they are staying the course of the marathon. 

“Some people work their whole lives to save species and don’t get there. We are lucky to have the resources we have, the DoD structure we have,” she said. “And I can’t say enough about our partners. I have always had tremendous respect and gratitude for the San Diego Zoo and Institute for Wildlife Studies.”  

Biologists for the U.S. Navy monitor fox holes on the agency’s San Clemente Island training facility, but maybe not the kind typically associated with military maneuvers. 

These dens are home to actual foxes – specifically, the San Clemente Island Fox (Urocyon littoralis clementae), a species of concern that is covered under the Navy’s Integrated Natural Resources Management Plan. 

The San Clemente Island (SCI) Fox is a subspecies of the Island Fox that is endemic to six of California’s eight Channel Islands. The fox is the largest native terrestrial mammal to all of the islands it inhabits, making it a keystone species – one whose existence is tied to the success or failure of other species in its ecosystem. 

Fox populations on each of the six islands are considered separate subspecies that are endemic, or unique, to those islands, and two of those populations occur on military installations – San Clemente Island and San Nicolas Island.  

In 2004, four of the six Island Fox subspecies experienced catastrophic population declines and were listed as federally endangered under the Endangered Species Act. 

In what some may consider an unexpected turn, the two populations that were not in such peril are the ones found on San Clemente and San Nicolas. But it’s not all that odd. Military installations typically have vast land masses that are used for specific missions, and as a result provide some of the last open wildlands in the United States.  

The military is committed to protecting the endemic species on their lands by implementing management plans that provide protection while allowing the military to fulfill its mission. Such Integrated Natural Resources Management Plans must result in no net loss of the military’s mission. 

But that doesn’t mean plant and animal species' conservation needs are ignored. Quite the contrary. The military is charged by law with not only protecting species and habitat, but also having plans to help threatened or endangered ones recover. 

At the time of the 2004 listing, the SCI Fox constituted 45% of the total Island Fox population, and the San Nicolas Island Fox constituted 31%. That means 76% of the animal’s population existed on lands owned and managed by the Navy, and they aren’t considered threatened or endangered. 

But the Navy isn’t waiting for a federal listing. It considers the SCI Fox a species of concern due to its keystone species status and its decline on the other islands. It is far better to engage in protection before an animal is threatened or endangered.  

As an omnivore, the SCI Island Fox diet consists of a variety of plants, insects, mammals, and birds, adapting to whatever is available.  

At San Clemente, the fox occurs in its highest densities at the northern end of SCI and typically at its lowest densities at the southern end of the island.  Dune habitats support the highest fox densities followed by grasslands and scrub habitats.  The high densities of foxes at the northern end likely reflect their comfortable association with humans and adaptability, taking advantage of human food when they can get it. 

As evidenced by the high fox densities at the northern end of SCI, the fox seems to do all right around human activity, and there is plenty on the island, Booker said. In addition to the troop live fire training areas, which are separated with large land buffers, there are greenhouses for growing endemic species, facilities for the San Clemente Loggerhead Shrike captive breeding program, and bunkhouses and living quarters for everyone. In addition to all of the military personnel, there can be as many as 40 biologists on the island at one time. 

“There is a whole village of people who run the military ranges, galley, housing facilities, power plant, air field, port operations, etc., including the offshore areas,” Booker said. “It is the only Department of Navy fully staffed field station.” 

San Clemente’s Integrated Natural Resources Management Plan used to divide the island into 18 management units, with boundaries that were set with roads, canyon rims, or manmade fire breaks. While these units were created primarily to serve to control the spread of wildfires, they also provide delineated areas by which biologists tracked such species as the SCI Fox.  

However, over time it became clear that these delineated areas weren’t useful in getting accurate numbers because some species - like the SCI Fox – travel to various areas, Booker said. Fox monitoring has been redesigned three times in the past 17 years, each time leading to more accurate population estimates.  The Navy uses adaptive management, science and lessons learned from past data to inform its wildlife management programs.  This results in defensible data, better natural resources management, and often times long-term cost savings.  The Navy has added disease monitoring to its fox management to ensure new threats don’t impact the fox and addresses and maintains a fox hospital, aka “foxpital” to treat injured animals. The fox program on SCI is comprehensive as well as adaptive.  

Balancing the interests of various species doesn’t solely mean mitigating human interactions, but also those with other protected species in the ecosystem, Booker said. For example, the SCI Night Lizard, which was delisted due to recovery in 2014, will raid the nests of the San Clemente Bell’s Sparrow, which was delisted this year. And the SCI Fox will eat the SCI Night Lizard. They are dependent on each other, and as long as humans don’t interfere, will keep each other in check. 

“It is ecosystem balance. Prey and predators are requisite in virtually all natural systems,” Booker said. “If foxes were lost from SCI due to disease or some epidemic event, then it is possible lizard numbers would increase to a point where the sparrows were under too much predation pressure and their numbers would drop. If foxes and lizards were both lost then sparrows would likely over-populate and eat themselves out of house and home or be more vulnerable to disease,” she added. ”It’s nature's system of checks and balances.”