The brown bunnies that bounce and bolt in neighborhood yards aren’t what they seem to be. According to experts, these rabbits aren’t native, and could be pushing out the true indigenous species, the New England cottontail.

A recent study conducted by DEM's Division of Fish and Wildlife and US Fish and Wildlife Services found only one New England cottontail rabbit in the state. Now Roger Williams Park Zoo is partnering with the two organizations to restore populations of the once-abundant species.

New England cottontails have been a candidate for federal protection from the U.S. Fish and Wildlife service since 2006, but funding was never allocated to the reinstitution of the species until now.

Lou Perrotti, director of the Conservation Program at Roger Williams Park Zoo, is heading up the effort to reproduce and reintroduce the rabbits. In the former veterinary building of the Zoo, Perrotti has five New England cottontails being kept in captivity, four of which are females. The rabbits were shipped from eastern Connecticut, where there doesn’t appear to be a shortage of the bunnies.

Since late 2010, Perrotti has been monitoring the rabbits in captivity, trying not to domesticate them while maintaining their health in their captive setting.

"To try to rebuild a species, first, we have to learn if we can keep healthy individuals in captivity," said Perrotti in a statement. "We've learned that we can.”

Perrotti began breeding the rabbits, and soon five cottontails became 14.

Litters usually contain four to six rabbits, and gestation is normally 30 to 32 days. The nine offspring, ages three to four months, were successfully reared and weaned, and released into a one-acre, predator-proof enclosure at Ninigret National Wildlife Refuge on Nov. 11.

“We’re trying to harden them to their wild settings,” said Perrotti last week. “We try to keep them as wild as possible [in captivity], but I’m sure the adults have gotten used to their handlers”

The nine rabbits are being monitored daily, and Perrotti said they are doing well in their enclosure. Target numbers for the population still haven’t been nailed down and will be determined later in the process.

The US Fish and Wildlife Service (USFWS) said New England cottontails have dwindled because of a loss of habitat. Meagan Racey, public affairs specialist for the USFWS said the lack of young forests is a major problem for the rabbits, which prefer thick, scrubby brush. In the winter, the bunnies eat bark off of trees and prefer the mulberry, apple, raspberry and greenbrier varieties. In the spring, they typically eat green shoots and vegetation. New England cottontails do no burrow, but will occupy the burrow of something else.

Racey said some of the population problem is due to the natural aging of forests and the decrease in farmland. Without natural forces like floods or fires to destroy forests and allow them to re-grow, the landscape has matured into a setting that is ill fitting for New England cottontails.

Meanwhile, another species of rabbit, the Eastern cottontail, is thriving. Hunters introduced the Eastern cottontail in New England in the late 1800’s. The Eastern rabbit is indigenous to southern eastern states, but can thrive on the New England landscape.

“The two species have difficulty cohabitating,” said Perrotti, who said specialists are still trying to understand why.

The Eastern and New England cottontails are very similar in appearance, but Perrotti said it’s a “safe assumption” that the brown bunnies people often see on their lawns are Eastern cottontails.

Both rabbits are brown with white “cotton” tails, but the New England rabbit has black markings on the head and ears. Perrotti said the only true way to tell if the rabbit is Eastern or New England is through genetic testing.

“There are genetic differences between the two cottontails, but because New England cottontails are indigenous, they fill a certain place in the ecosystem,” said Racey.

The cottontails are a crucial part of the food chain, and Perrotti said because they are a prey species; their lifespan in the wild is typically three years.

Once Perrotti and his team have determined the New England cottontails bred in captivity are ready for life in the wild, they will be released on an island in Narragansett Bay. Perotti thinks the first litter will be ready by April, and from there, they will begin to breed more rabbits for release.

The USFWS is funding the bulk of the project, but the Zoo is also contributing.

“Resources, from money to time, are being pooled from different places, including federal, tribe, state, private landowners and partner organization contributions and grants,” said Racey. “These partners are working across state lines to be efficient and effective.”

As of now, the USFWS is not sure how much money is being pooled into the project as a whole.

“It can be expensive,” said Perrotti, who is unsure when their goal will be met and the project will end.

“I see it being a very long project,” he said. “We want to tread carefully, there’s really no race. However long it takes.”

Racey said ultimately the project would not only benefit the New England cottontails, but other species native to the northeast. Part of the project will work to restore habitats that are conducive to the New England species.

“We’re trying to spend money in the right way,” she said. “The work done will provide homes for a whole suite of native wildlife; keep in mind this work isn’t for just one animal.”

Currently experts believe there are no New England cottontails left in Vermont, and only about 40 in New Hampshire. Populations in the rest of New England are equally as sparse.

Despite his close work with the bunnies, Perotti said he hasn’t become attached to any of the animals he’s been studying.

“I never give something a name that doesn’t come when it’s called,” said Perrotti. “But I do think they’re cute.”