Coyotes—familiar residents of West Marin trails and yards—have long dined on small game, garbage and the occasional toy dog. New research is revealing that they also enjoy another snack: baby harbor seals.

People think of coyotes as land animals, said Frankie Gerraty of the University of California, Santa Cruz, who is conducting doctoral research in the Point Reyes National Seashore and other coastal sites to better understand the relationship between the canines and pinnipeds.

“Coyotes are potentially very important scavengers in sea environments,” Mr. Gerraty said. “They are super adaptable species and they’re really great at identifying and capitalizing on unique or new food sources.” 

Though coyotes have lived in harmony alongside pinnipeds on the beaches of Point Reyes for decades, wildlife biologists say their attacks on harbor and elephant seal colonies have increased over the last five years.

Last year at the Bolinas Lagoon, monitoring teams saw a coyote kill and eat a pup. In 2020, when harbor seal numbers dropped by nearly half at Drakes Estero—the most historically populous site—park wildlife ecologist Dave Press watched from afar as a coyote swam a channel to wreak havoc on a group of seals. 

According to park marine ecologist Sarah Codde, coyotes sometimes swim out to sandbars to snatch pups.

Coyotes are difficult to study through direct observation, so much is still unknown about their habits and how they fit into ecosystems, and numbers on their populations in West Marin remain unmonitored.

Coyotes are native to the Point Reyes peninsula and sightings were reported in the mid-1800s, according to naturalist Jules Evens. But they were hunted and became rare. An inventory taken by the United States Geological Society from 1998 to 2001 found just 15 coyotes in the park. 

Coyotes returned from the north in the 1980s and now their populations are expanding. Nearly 1,000 coyote sightings in the park in the past decade were registered on iNaturalist, a citizen science platform that allows people to record and share their observations.

Meanwhile, harbor seal populations are shrinking across the state, said Ms. Codde, who leads the park’s seal inventory and monitoring program. While the precise reasons are unknown, harbor seal abundance and distribution is typically dictated by disease, changes in food sources, rising sea levels—and disturbances to haul-out sites.

Populations are down in the seashore, which has the largest concentration of harbor seals in California. This year, during peak pupping season in May, the park’s monitoring program recorded its seventh below-average year for molting and eighth below-average year for pupping. Last year, the team tracked record-level low numbers of harbor seals. The current population for harbor seals in the Point Reyes area, including the Bolinas Lagoon, is 3,700, down from more than 7,000 in 2007. 

The growing presence of coyotes at beaches may be one factor for the decline at Point Reyes, because canine sightings and attacks across the seal rookeries are rising. But the scope of coyotes’ impacts is unclear.

“Unfortunately, it’s a big mystery,” Ms. Codde said. “I talk to other monitors in some of the smaller colonies in other parts of the state where populations are declining and nobody knows why.”

Elephant seal populations are healthier. An estimated 4,400 elephant seals visit the peninsula’s shores each year, a number that has grown by about 9 percent annually since the 1990s. They have had no terrestrial predators since bears were extirpated from the peninsula in the early 1900s. But as coyotes adapt, the canines could be more prone to attacking elephant seal pups, Mr. Gerraty said.

Teams are seeing more and more interactions between coyotes and elephant seals every year in the seashore. Coyotes have been observed eating elephant seal afterbirth, stillborn pups and carcasses and even attacking pups. On Drakes Beach, Ms. Codde has seen several pups with chunks missing from their back flippers as a result of coyote bites.

With populations of elephant seals booming statewide, there are more stillborn pups and afterbirth for scavengers like coyotes, especially when seals give birth in January.  

 “We caught one on camera actually biting the flippers until the seal got away,” Ms. Codde said. 

But coyotes are not considered a major predator of elephant seals because they aren’t causing a population decline, she added. 

“There’s some kind of interaction,” she said. “It’s a new mystery of what they are trying to do and what they are getting out of it.”

To gain insight into coyotes’ movement patterns, diet, genetics and social structure, in 2020 biologists with the National Park Service started attaching tracking collars and ear tags to animals in the Marin Headlands. 

Mr. Gerraty is using field cameras and genetic analyses to study coyote predation patterns at harbor seal rookeries at Drakes Beach, Agate Beach in Bolinas, Año Nuevo State Park in San Mateo County and Mac-Kerricher Beach in Mendocino County. 

“I think that disentangling the ways that those pinniped rookeries affect life on land is a really understudied but super fascinating topic,” he said.

He has installed between 10 and 20 cameras on these beaches, and he collects scat for DNA research. Now in the second year of a three-year data collection process, the project gets support from the park and the Tomales Bay Foundation for permits, camera setup and field navigation. 

Through a process known as fecal DNA metabarcoding, which shows what animals are eating, Mr. Gerraty is also studying coyotes’ dietary diversity. 

Seals are large and calorically rich parcels of nutrients and can make a huge difference for a hungry coyote, but they could come with costs. Marine mammals, especially elephant seals, are near the top of the oceanic food web, so their carcasses could contain high concentrations of toxins like mercury.

In the future, Mr. Gerraty hopes to work with the Golden Gate National Recreation Area and the University of California, Berkeley, to put collars on coyotes and obtain high-quality fur or blood samples that could reveal whether preying upon seals is transferring contaminants from the marine mammals to terrestrial ones.

“Knowing what [coyotes] are eating, you can learn a lot about what is available to them, or what food web pathways are most important,” Mr. Gerraty said.