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New York City’s Citizens Are Collecting Coyote Scat for Science

© Ivan Kuraev / Urban Coyote Initiative


Local nature enthusiasts and high school students head out to city parks and pathways to help the Gotham Coyote Project collect dat, which will reveal the secrets of these new canid residents of the Big Apple.

by Ivan Kuraev
January 2017


“I’m always looking down,” says Mark as we walk side by side along a trail through Pelham Bay Park, in the Bronx. It’s a sunny and cool November day in New York City, and Mark’s eyes are scanning the ground as he speaks to me.

Mark Weckel is a biologist with the American Museum of Natural History, where he manages research into the behavior, diet and genetic history of coyotes in and around New York City. He seems a little distracted as he answers my questions, and his sentences are broken by long pauses that let me know his real focus is on finding his quarry. Today Mark and I are looking for scat – coyote poop – left behind by predators that have lived in this metropolitan park for the last twenty years.

Averaging thirty to forty pounds, coyotes aren’t small animals but they are great at staying unnoticed, and the best way to learn their habits is by studying what they leave behind.

Most neighborhood residents who pass us walking their dogs along the park trails have no idea that they are following paths that were crossed by coyotes only hours earlier. I don’t expect to see an actual coyote today, and neither does Mark, but he seems more optimistic than I am about finding coyote scat.

I don’t want to look like a rookie, so my eyes are also on the ground, scanning through several inches of dry leaves that cover the path ahead. Finding something among the leaf litter seems impossible. I am reminded of all the times that I have walked my girlfriend’s dog on autumn days and struggled to find its poop in a patch of fallen leaves, even if I had been looking at the very spot where the dog deposited it just seconds earlier. So how do we find scat in a 2,772 acre city park?

Luckily, Mark and I are not searching on our own – a team of eleven high school and college students assembled this morning to aid in the day’s hunt, along with eight adult “citizen scientists,” who are also contributing to the search effort. All of them are part of the Gotham Coyote Project, an organization that Mark founded in 2010 along with biologists Chris Nagy and Anne Toomey.

Today, the Gotham Coyote Project functions as an urban coyote think tank, regularly recruiting professional and amateur naturalists to collect data and report sightings of New York’s wild canids. The goal of today’s outing is to add to Gotham Coyote’s growing collection of coyote scat.

At their lab in the Natural History Museum, students and scientists working with the Project will dissect and analyze the scat in order to determine what prey items are on a New York coyote’s menu.

I’m walking side-by-side with Josh, who goes to high school in the city and regularly volunteers with Gotham Coyote, and he gives me some scat hunting advice.

“You have to think like a coyote. If we were coyotes, where would we poop?”

“Everything looks like a piece of poop,” I answer, downcast.

Dr. Mark Weckel shows students the area where they'll be doing field work. © Ivan Kuraev / Urban Coyote Initiative

Earlier this morning, the Gotham Coyote team assembled in the parking lot of Split Rock Golf Course on the edge of Pelham Bay Park, and after making our introductions, split off into smaller groups to search different areas of the park. My small group of citizen scientists was assigned to the Orchard Beach section of Pelham Bay Park, with Mark Weckel as our team leader. Olivia, Christopher, Josh and Tim joined my team as well – four teenagers who are seasoned scat-finders and nascent biologists.

The rest of the Gotham crew went to search another section of Pelham Bay Park with Chris Nagy and Anne Toomey. Chris and Anne have been studying New York’s coyotes together for eight years and are experts in the field, but their team has another advantage – scat sniffing dogs.

Ferdie Yao, a wildlife biologist and certified dog trainer, brought his own dog along with several of his canine understudies on today’s hunt. A large shepherd and two eager mutts zigzagged away into the woods when we last saw them, and I’m sure that by now their noses have found more scats than our eyes.

“Our group is not going to have a dog,” Mark said before we split off from Chris, Anne and Ferdie. “You just got me, and I tend to find scat one way or the other.” He paused, then added, “I might step in it.”

Citizen scientists and a scat-sniffing dog get ready for field work in New York City. © Ivan Kuraev / Urban Coyote Initiative
Dr. Mark Weckel shows students how to tell if the scat they've found belongs to coyote. © Ivan Kuraev / Urban Coyote Initiative

After an hour of walking as a group, winding through the leaves and feeling our eyes go cross from concentrating on the ground, Mark nudges Tim’s shoulder, then stops him and says, “Dude, I was giving that one to you!” Mark is pointing at the ground; in the middle of the path, clear of leaves, is a scat.

The whole group hunches over around the poop. Mark uses two twigs like chopsticks to turn over and examine the scat, which looks to me like it may have been left there by a dog sometime this morning, but Mark points out its shape.

“See that twist? Often you see that in a wild canine. I do not think that is dog,” he says with emphasis.

The twist Mark pointed out is caused by hair that is trapped in the scat. Pelham Bay Park coyotes are likely eating small mammals like mice and rats whole, and though flesh is digested, their hair and bones get expelled through the coyotes’ feces. Hair content, which is easy to spot for the trained eye, helps the Gotham team identify coyote scat in the field and tell it apart from poop left by domestic dogs.

By analyzing the individual bones and hair follicles from the scat in their lab at the American Natural History Museum, Mark and his team can identify the different mammal species that make up an urban coyote’s diet.

Mark places the scat in a brown paper bag, then labels it with a date and location. Since the Gotham crew split into groups earlier this morning, Mark has been texting with Chris to check on the other team’s progress. He looks up from his phone and smiles.

“So far it’s humans-one, dogs-zero.”

I want to see what happens to coyote scat once it is brought in from the field, so a couple of weeks after my Bronx outing with the Gotham Coyote team, I visit their lab in the American Museum of Natural History.

Mark meets me at Museum’s staff entrance, and I walk behind him as he leads me through narrow back hallways, closed to visitors and lined by metal cabinets and glass cases of specimens kept off public display.

There are skeletons of big cats, shelves holding large mammal skulls, and dented filing drawers labeled “Lepidoptera.” I want to slide all of them open and look at the butterflies and moths, pinned to cork, that must be inside. Different phyla of animals are arranged together, presented with care but without the embellishment of dioramas and oil-paint backdrops that adorn the museum’s stately exhibits.

We round a corner, then Mark opens an office door and welcomes me into the lab that’s used by the Gotham Coyote Project for their scat research. It is a narrow room, made narrower by a long table supporting two microscopes and a beige cabinet with pull-out drawers of mammal specimens: a whole skunk, a raccoon, an assortment of mice and voles, and an excess of brown and gray pelts.

At the far end of the room, Neil Duncan, the Museum’s Department of Mammalogy Collections Manager, stands up from his desk and walks over to shake my hand.

Neil supervises the scat analysis for Gotham Coyote, and his work involves breaking down samples and extracting useful evidence from the scat. Our introduction is brief, and Neil is visibly eager to share his work. He pulls a brown paper bag from a cardboard box filled with many more like it, then opens the bag and tips the contents on his desk. The coyote scat inside is several weeks old and so desiccated, I can hardly recognize it is poop.

“We start the process by separating the bones and fur from the scat matrix,” Neil explains.

What he calls the matrix is, well, the poo part of the coyote scat. It’s fully digested organic matter, and it mostly breaks down in water. Neil places the scat into a brown pantyhose, ties it off, then submerges it in a large bucket of water, clipping the pantyhose to the rim.

Neil leaves it to soak overnight, then washes what didn’t dissolve through the fabric over a sieve. By the end of the process, all that’s left of the scat is what wasn’t digested by the coyote – fur, bones, claws, beaks and teeth. This is the good stuff.

Bags of coyote scat collected in the field are brought into the lab at the American Museum of Natural History for analysis. © Ivan Kuraev / Urban Coyote Initiative
Neil Duncan, the American Museum of Natural History's Department of Mammalogy Collections Manager, looks through coyote scat samples during analysis. © Ivan Kuraev / Urban Coyote Initiative

Some of the students whom I met in the field with Mark and Chris, like Olivia, also work in Neil’s lab. The high-school students who contribute to Gotham Coyote’s research are part of the Museum’s after-school SRMP program, which Olivia affectionately pronounces as “shrimp.”

As members of the Student Research Mentoring Program, New York City’s young scientists can participate in one of many research projects being carried out in the Museum’s behind-the-scenes labs. Working with Gotham Coyote, SRMP students search for coyote scat in city parks, then look at the bones and hair from the scat through a microscope and compare what they find to reference samples in the Museum’s immense mammal collection.

“It’s real-time science in the field,” one student said to me about the SRMP program. “It’s not just on paper. All of high school is mostly just on paper and you don’t interact with the actual science.”

The ability to engage in both fieldwork and labwork in the city where they live allows these teenagers open access to science – wildlife biology is suddenly in their neighborhoods, just a walk or a subway ride away from their schools, apartments and corner bodegas. They can become scientists without having to ask their parents for rides or applying to remote internships.

Olivia isn’t really a student right now – she has taken a gap year before going to college, and has decided to devote two days a week to looking through coyote poop. Every Monday, Tuesday and Thursday, Olivia comes to Neil’s lab. She begins each scat analysis by looking at the size of the hair and bones from a sample to approximate the size of the animal that was eaten. Are they large bones? Then it’s probably a rabbit, or a raccoon, or even a deer. Small bones? That’s a little more complicated.

A high school student looks up rodent species in a text book in order to identify the bones found in coyote scat. © Ivan Kuraev / Urban Coyote Initiative

By looking at the structure of the bones, she can figure out if the prey was a mammal or a bird. When she narrows down the possibilities for who the victim could be – “Mammal, smaller than a squirrel, likely a vole species” – she can compare some of the found bones to those of known species in the Museum’s reference collection.

Looking through a microscope reveals small structures of individual bones and hair follicles that are invisible to the naked eye, and these can be used identify the genus or even the species of the prey.

“Finding teeth or claws makes it much easier,” says Olivia, “since each mammal species has distinctive teeth.” Still, sometimes making a positive ID of a coyote’s last meal just isn’t possible.

“We might not be able to ID the species,” says Neil, “but we can tell the order, or family, or say it was a mammal, and that may be good enough.”

Even an approximate identification helps the Gotham team figure out the breakdown of a coyote’s diet, and with such an opportunistic predator this is a significant accomplishment.

Based on the analysis of ninety-nine scats examined by the Gotham Coyote team and SRMP students, an urban coyote’s menu includes birds, mice, voles, squirrels, insects, raccoons, deer and even fruits and seeds. Olivia has looked through most of the ninety-nine scats herself, and her dedication has ensured that her name will be listed as a co-author in a future publication of Gotham Coyote’s results. This is a huge achievement for a teenage biologist, and goes to show the value of contributions from citizen scientists to Gotham Coyote’s research.

Olivia may be starting college in the fall, but in the meantime there is no shortage of work for her in front of the microscope. More coyote scat samples keep arriving in Neil’s lab on a regular basis. Mark picks up scat while hiking on weekends, and some people who are interested in the work of the Gotham Coyote Project even send scat in the mail, addressing it to the Museum of Natural History.

“I think the people in the mailroom hate me,” laughs Neil. “Sometimes they call and say, ‘You have to come and pick this up right now.’”

Bits of rodent bones found in coyote scat are identified in a lab at the American Museum of Natural History. © Ivan Kuraev / Urban Coyote Initiative
Bits of rodent bones found in coyote scat are identified in a lab at the American Museum of Natural History. © Ivan Kuraev / Urban Coyote Initiative
A piece of a rabbit jaw found in coyote scat is identified in a lab at the American Museum of Natural History. © Ivan Kuraev / Urban Coyote Initiative

Scat is a vital resource for learning about the coyotes that leave it behind. It’s easy enough to see bones and fur, but there is something else inside the scat that is well beyond the scope of our eyes, and it can reveal the identities, and even the family histories, of New York City’s coyotes.

Carol Henger is a PhD student at Fordham University, where she is studying DNA collected from the poop of NYC’s urban coyotes.

In her lab, Carol has a freezer the size of a standard kitchen refrigerator that’s packed with coyote scat, much of it samples collected by citizen scientists who work with the Gotham Coyote Project. The cold helps preserve the genetic code inside the scat, and that is Carol’s prize.

Most of the DNA contained within these scats belongs to the coyotes’ prey. However, if Carol uses a scalpel to scrape the surface of the scat, she can collect a small amount of coyote skin cells that were deposited on the poop as it left the animal’s body. She can then isolate the DNA that is contained in the nucleus of each skin cell – a process that takes about six hours – then suspend the extracted DNA in a liquid medium that helps preserve it. This sample contains the unique genetic code of an individual coyote. A tube containing the preserved DNA is then sealed and stored in another fridge, filled with hundreds more like it.

Carol is building a catalog of coyote DNA samples, and her mission is to create a genetic database of all coyotes living in New York City.

By noticing repeating sequences in sections of the sample DNA – non-gene-coding sections called ‘neutral markers’ – Carol can identify individual coyotes. So far, she has identified thirty-five different coyotes living in the Bronx. Using scarce bits of evidence left behind by secretive, alien predators, Carol can uncover their identities. When she finds the same coyote’s genetic sequence in two different scat samples, Carol can infer the boundaries of an individual coyote’s territory. If only a part of the unique sequence appears in another sample, Carol knows that she is looking at scat from a different coyote that belongs to the same family unit.

“I can’t tell if it’s parent-offspring or full siblings,” she says of samples that share about fifty percent of these repeating sequences, “but I can say, ‘look, these here share half of their DNA, so they are from the same family group.’”

This is known as first-order relatedness.

“You can also tell second-order relatedness,” adds Carol, “where they share a quarter of their DNA. That would be like aunt-uncle, niece-nephew, grandparent-grandchild.”

Of course, my immediate follow-up question to Carol is, “How many family groups have you found?”

“I’m still trying to decide,” she says, laughing.

“What I can tell you so far is it looks like there is a family grouping in each park [in the Bronx]. So, Pelham Bay has at least one family grouping, and Van Cortland, and then Riverdale. But I’m not sure how many individuals are part of that. And if it’s one family, could it be two different generations? So that’s what I’m trying to understand.”

It takes a long time to gain these insights from analyzing coyote scat. Carol is almost done with her degree, but it seems like she has an agenda for another four generations of Fordham graduate students.

“That’s my plan,” Carol says, smiling. “I want this to be the start, and for people to keep building on it. And I think that they will.”

What’s the future of her work? Carol opens her laptop and pulls up a map of New York City. On this map is a whole bunch of dots that are connected by either yellow or black lines. These dots represent the locations of found scat from coyotes that Carol has identified as members of two distinct family units.

Most of the black dots on the map are concentrated in Van Cortland Park, in the Bronx. Most of the yellow dots are in Pelham Bay Park. However, a couple of yellow dots are in out in Queens, connected to the Bronx by long yellow lines. A couple of black dots are also there, on the far edge of her map, miles away from their Bronx locus.

These points represent the coyotes that are leaving their family units to colonize new territories.

Their next frontier? Long Island.

PhD student Carol Henger works on coyote DNA samples in an effort to uncover the "family tree" of NYC's coyotes. © Ivan Kuraev / Urban Coyote Initiative

Coyotes are coming to Long Island – their arrival there is inevitable. By tracing the settler coyotes to their original family units, Carol and the future students who pick up her work will be able to identify the families that gave rise to the first generation of Long Island coyotes.

This is important because these settler coyotes will have been born in Bronx city parks, not in upstate New York forests. They will be city slickers, and the urban lifestyle and diet is the only kind they’ll know. Long Island has densely settled areas, but much of it is suburban and even pastoral.

Research from Chicago, where urban coyotes have been studied for nearly two decades, shows that city coyotes establish smaller territories compared to their wild cousins. Will coyotes that settle Long Island maintain small territories, just the way they would have if they stayed in the Bronx? Will they continue to eat the same diet as they did in the city? Or, will they learn new behaviors and teach them to their offspring? How will the behavior of city coyotes change when they start crossing sprawling backyards, soccer fields, farms and open beaches?

Seeing how urban coyotes adapt to a new environment can not only open a new chapter in our understanding of these animals, but also inform Long Island residents of how to get along with their new neighbors.

A few days ago, I visited Neil’s lab in the Natural History Museum again, to shoot close-up photos of some of the bones that he and his students have collected from coyote scat. As I was setting up my equipment, Neil said that he had some news for me.

A pair of coyotes was seen in Middle Island, a small town in the middle of Long Island, sixty miles from New York City. They were sighted at night, but it seems to have been a reliable report.

Mark is already planning a scat-searching blitz with his volunteers, and if they find any samples, Neil’s lab will analyze their contents to learn what these settler coyotes are eating on their journey East. Carol will use her DNA database to learn if these coyotes are related to family units breeding in the Bronx.

Coyotes have finally arrived on Long Island, and the Gotham Coyote Project is mobilizing all its resources to keep up.

The chase is on.


Follow our collaboration with the Gotham Coyote Project

Students install a trail camera on a tree in a local park in hopes of capturing coyotes on camera. © Ivan Kuraev / Urban Coyote Initiative

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