Golf balls bounced nearby as Jonathan Young tromped across the fairways and beyond the rough of San Francisco’s Presidio Golf Course, an antenna held aloft, following an electronic signal. The scratchy beeping was a sure sign that coyotes lurked.

Young, the wildlife ecologist for the Presidio Trust, waded through heavy brush and poison oak in a forested area where the sound from the VHF transmitter got louder, revealing the hiding place of one of two canines he had affixed with radio collars.

“There she is,” he said, as the skinny, German shepherd-like animal broke out onto the rolling fairway, shooting wary glances backward.

Coyotes have moved back into San Francisco in recent years after being gone for the better part of a century, alarming residents who aren’t used to seeing wild predators roaming the streets, and sometimes killing small pets. Animal control officers have tried to ease concerns by assuring residents that, with certain precautions, it’s quite possible to coexist.

Amid the tension, experts don’t know exactly how many coyotes live in the city, and they don’t know much about their movements. That’s why, in May, Young launched the first comprehensive study of urban coyote behavior and ecology in San Francisco. The tagging and tracking program is part of an effort to educate the public about the creatures, which aren’t going away anytime soon.

Young has so far documented four adult coyotes in the Presidio, including one breeding pair with two or three pups. The animals mostly choose to live on the links, with golfers all around them.

“Coyotes and golf courses are like this,” Young said, holding up crossed fingers. “They really like the vantage points,” which allow them to see prey and potential predators over long distances.

The pilot study requires Young and his staff to trap as many coyotes as they can find, place colored tags on their ears and track them, using the collars’ built-in radio transmitters and GPS technology.

Young hopes to determine how many animals the Presidio can sustain, what percentage of pups survive, where young adults go when they disperse at 12 to 16 months of age, what they feed on, where they create dens and how many coyotes are killed by cars.

The idea is to avoid conflicts with humans and pets and identify abnormal behavior from disease or other causes. The ultimate goal is to inspire collaborative studies outside the Presidio and develop a citywide tracking system, including a database on family groups, dispersal habits, behavior and genetics.

“What people don’t understand, they often fear, so our goal is to push the information out to the public,” Young said. “We need accurate information.”

Creatures play dead

Young has captured one male and one female, using a spring-loaded cable loop that snags the animals’ legs. The trapped coyotes are not harmed, nor even tranquilized, as their habit is to submit and play dead as they wait for an opportunity to bolt. While the collars are put on, blood is drawn, measurements are made and plastic identification tags are attached to their ears.

The coyote that fled from the woods gave birth to three pups in April. During the day, Young said, she generally leaves her pups at their den, where they play all day, and periodically returns to drop off a dead squirrel, mouse or rat. He said one of the pups may have recently died, a common occurrence among urban coyotes.

The other collared coyote is a male, but it isn’t clear whether this coyote or another one with a chunk torn out of its ear is the father. Coyote packs have only one breeding pair, the alpha male and female.

Young trained his binoculars on a coyote lounging under a tree, quickly identifying it as Torn Ear. “The alpha is typically more aggressive toward subordinates,” he said, “so we’ll look and observe and see the behavior, but it can be a little challenging with the golf course and balls flying around.”

Coyote sightings and confrontations with humans have jumped over the past decade in the Bay Area. But the most remarkable change has been the migration from the suburbs into the city. San Franciscans have increasingly reported seeing the canines fearlessly sunning themselves on driveways, trotting across streets and poking around patios.

Wildlife experts say there are dozens of coyotes in the 47-square-mile city, but nobody has delivered a precise number.

Increasing population

“They are living here, they are thriving here, so the population is going to increase,” Vicky Gulbech, operations manager for San Francisco Animal Care and Control, said in a recent interview. “We are definitely seeing that and getting more calls.”

Coyotes are native to San Francisco, where the fossil record shows they were plentiful until the Gold Rush, but the yipping hordes were killed off in the city some 75 years ago. The first modern sightings were in 2004 in the Presidio, creating excitement and a good deal of puzzlement over how the creatures got there. Answers came when Golden Gate Bridge officials viewed video of a coyote dashing across the span in the dead of night.

Genetic testing of two coyotes that were shot by federal authorities in Golden Gate Park in 2007, after they attacked dogs, confirmed that the animals came from the north, but Young said coyotes have also migrated from the Peninsula.

All over the city

Since then, coyotes have been reported in neighborhoods and parks throughout southwestern San Francisco, in Bernal Heights, in Golden Gate Park and Stern Grove, at Lake Merced, and on Mount Davidson and the Olympic Club golf course. Experts believe the drought so reduced the primary prey of coyotes — mice, voles and rats — that they have been forced to look for food in neighborhoods.

There have been sporadic instances of aggressive behavior, including a few cases of coyotes charging pedestrians with pets. That usually happens, experts say, when coyotes try to drive a dog away from their den during pup-rearing season, from April through August.

The animals are opportunistic and, given a chance, will sometimes kill and eat small dogs and cats, but are not normally aggressive around humans. While family dogs kill an average of 20 people a year, there has only been one documented case of a coyote killing a human in the United States — the 1981 death of a 3-year-old who was dragged away from her house in Los Angeles County.

Reports of aggression typically involve the deliberate feeding of coyotes. Invariably, the feeders have said they they felt a kinship to the animals, which they believed were starving.

“These are wild animals that are perfectly capable of fending for themselves,” Young said, adding that coyotes are naturally skinny. The two coyotes he weighed in the Presidio weighed 25 and 29 pounds.

It is illegal to trap, relocate or kill wild animals like coyotes in San Francisco unless they are an imminent threat to humans. Moreover, leaving the animals to forage keeps populations of rodents and other mesocarnivores — like foxes, skunks and raccoons — in check, which in turn helps songbirds and ground-nesting birds.

Feeding causes problems

“Feeding makes them associate humans with food, and that’s when they begin approaching humans and getting aggressive,” Young said. “The ideal urban coyote is scared of humans all the time.”

City and Presidio officials are testing “hazing” methods, including paintball guns, flashing lights and noisemakers, to scare off the highly adaptable animals when necessary.

When he is not in the lab, Young visits the golf course or Mountain Lake four times a day on Monday, Wednesday and Friday, when the electronic collars are programmed to send out signals. He hopes his study will help dispel the notion that coyotes are vermin that don’t belong in an urban area.

“This is not something that is happening only in San Francisco. These animals are thriving in urban environments all across the country, Canada and even into Mexico,” he said. “We’re trying to be proactive. We’re trying to do something.”

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite