The Rabbit-Poop Census

To monitor the growth of the New England Cottontail population, scientists are collecting their droppings for DNA analysis.

A New England Cottontail (Linda Cullivan)

On a mild winter day in February 2012, the wildlife biologist Kelly Boland led a group of volunteers out the doors of Inn by the Sea, a hotel in the town of Cape Elizabeth, Maine, and onto the nearby snow-covered parkland. Equipped with latex gloves and plastic vials, the volunteers were on a strange mission: collecting the little brown piles of rabbit poop that dotted the otherwise gleaming white snow.  They carefully scooped the little pellets into the vials, usually two in each, before closing the vials tight and placing them into coolers to be shipped to a DNA-sequencing lab in New Hampshire.

At that point, the population of New England cottontail rabbits—the type behind the droppings her volunteers were searching for—had been declining for decades. They’d already been placed on Maine's list of endangered species, and they were a candidate for federal listing as well. And a few years later, the situation hasn’t improved much. “There’re maybe 300 rabbits in the entire state of Maine on a good day,” said John Litvaitis, a wildlife ecology professor at the University of New Hampshire. Other New England states aren’t doing much better. Litvaitis estimates New Hampshire’s rabbit population at about 100, Massachusetts at about 500, and Connecticut, the “cottontail stronghold,” at two to three thousand.

New England Cottontails are smaller than other varieties like Eastern Cottontails. They don’t run as fast and don’t change color for winter, meaning they remain very visible against the snow. They like young woods—stretches of low-growing shrubs under which they can hop, graze, and hide from predators—but their habitat has been shrinking. And as humans cut less wood for timber and get better at preventing forest fires, fewer trees die, which results in less young-tree growth and fewer places for cottontails to live. They also used to benefit from beavers that built dams on streams, causing floods which triggered growth of young vegetation. “But we don’t like beavers and we don’t like floods,” said Litvaitis. “So we eliminate them, and the rabbits’ habitats get eliminated with them.”

To continue as a species, the rabbits needed more places to live. A few months before Boland led her citizen-scientist group on a winter poop hunt, Inn by the Sea took over the maintenance of  an area of the adjacent Crescent Beach State Park, with a mission of turning it into a rabbit habitat (or, as they affectionately call it, a “rabitat”). That required eradicating invasive plants, including Japanese knotweed, a type of bamboo, and restoring the native vegetation. After trucks and bulldozers removed more than 500 shrubs and special fire-expelling machines burned their roots, the area was replanted next spring with plants that rabbits are known to love,  including raspberries, blackberries, and winterberry hollies, said Derrick Daly, the Inn’s gardener.  Many New England landowners and farmers went through a similar re-wilding of their properties, hoping to boost the creatures’ dwindling numbers.

But to see how well the efforts worked, scientists had to count the rabbits.

Poop proved a good population census tool. Before DNA sequencing, the only way to differentiate the long-eared individuals from one another and count them was to trap them and take their physical measurements, which caused the animals fair amount of stress. When DNA sequencing came of age, researchers started scraping rabbits’ ears for the samples, but that still required catching them. Today’s “stool test” is completely non-invasive—the animals just need to poop as usual, and scientists can ID them by the DNA from the feces.

But how does one get DNA from poop, which is not really part of the animal? Despite being only a transient substance that passes through the digestive tract, poo still delivers enough scrapes of the needed genetic material. When fecal masses move through the bowels, they snatch up a few actual rabbit cells along the way. “When the rabbit is eating a fibrous diet, those bits of plants pass through its gut and they scrape off small cells,” said Litvaitis. (This works the same way in humans—the reason doctors advise their patients to eat lots of fiber is because fiber scrapes off those potentially dangerous cells that may turn cancerous.) The rabbit cells end up on the outside of the pellets and allow scientists to identify the animal that laid them. And rabbits are prolific poopers, Litvaitis noted: “They put out a phenomenal number of pellets,” he said. “One rabbit can produce 500 to 600 pellets a day.”

Pellet-hunting is way more productive in winter than in summer, because snow preserves the rabbits’ tracks and makes the little brown piles very visible. The cold also helps keep the DNA intact. The most productive scat-hunting expeditions are those made within 24 hours of a snow fall, Litvaitis said, after the rabbits had a chance to run around and leave their pellets scattered. “You wait for a fresh snow, and then you find the tracks and follow them,” he said—and often, after a few feet, there will be a prize pile.

A pellet-collection kit (Lina Zeldovich)

Not all poop is created equal. The snowy landscape is open for all animals’ necessities, so before venturing out into the field, Boland’s volunteers have to learn their pooper-scooping ABCs. “The cottontails’ pellets are brown and round,” Boland said. “They look just like cocoa puffs.” The deer droppings sport a darker hue and are more oblong, with one little pointy end. “They sort of taper off on one end,” she explains.

But the scats of snowshoe hares and cottontails look the same, so the only way to distinguish them is by the tracks both species leave on the snow. That’s why the sample collecting kits come equipped with a little booklet featuring different animals’ tracks. Volunteers are also trained to wear gloves and avoid contamination—not by accidentally smearing themselves in poo, but by getting their own DNA onto the little orbs. “We don’t want human DNA in our samples,” Boland said.

When collected, the samples stay in coolers until they’re driven to the lab, where they undergo a lengthy DNA-extraction process.  The pellets get smooshed up into a solution and loaded into a centrifuge that separates the genetic material from everything else. The extracted DNA is broken down with special enzymes and put through a sequencing machine.

The testing serves multiple purposes. First, it lets researchers determine whether a given patch of land is occupied by New England cottontails or some other species. Second, it lets them identify and count each individual rabbit. And according to Adrienne Kovach, the associate professor of natural resources who leads the lab, it also allows them to study rabbits’ genetic diversity and how they move through the landscape.

With all the work, the cottontails’ future is still uncertain, and the prognoses vary.  In 2015, the Unites States Fish and Wildlife Service declared that because New England cottontails are rebounding well, they no longer merited inclusion on the federal list of endangered species. But not everyone agrees. Mollie Matteson, a senior scientist at the Center for Biological Diversity, a nonprofit organization that works to protect endangered species, believes that a place on the federal list would assure the rabbits a much better recovery. Without that status, their conservation depends on local funding and volunteer efforts.

Luckily, cottontails still attract citizen scientists. Boland has more pellet-hunting trips planned for later this season, and volunteers are signing up to scoop more poop. That process is actually much less unpleasant than one may think, she said, because the rabbit poo doesn’t have a high ick factor. “It’s not stinky, it’s not sticky, and it’s pretty dry,” Boland noted. “It smells more like grasses and twigs, because that’s what they eat.” It’s not the cuddliest way to interact with rabbits, but it may not be the grossest, either—and at any rate, handling the animals’ droppings now hopefully means there will be more of them in the future.