At the Louis Calder Center, scientists explore ecological mysteries and study society’s impact on the natural world.

To the casual observer, Fordham’s Louis Calder Center might seem to be just another quiet tract of Hudson River Valley forest. But for natural scientists, it abounds with opportunity. Explore the 113-acre biological field station in Armonk, New York, and you’ll find a bounty of ecosystems and animals, from the four-legged to the microscopic. At the heart of the preserve is a 10-acre temperate lake teeming with a diversity of aquatic life. Go high enough and, way off in the distance, you can see another big player in the preserve’s ecology: New York City, which begins only 16 miles away.

Its proximity has never been more relevant. “Humans and our cities are the most dominant forces of contemporary evolution now,” says Jason Munshi-South, Ph.D., a Calder-based biology professor who recently co-authored a paper in the journal Science on how species are evolving within cities. Other scientists at Calder study invasive species that arrive via big-city commerce. And they tackle many other mysteries: why some animals survive new threats while others don’t, how nutrients flow beneath the soil, or how insects transmit disease.

The center was born 50 years ago when the land was given to Fordham by the Louis Calder Foundation, named for the paper and pulp magnate who maintained a summer home on the property. Today, that home is Calder Hall, one of several buildings in which students and professors analyze DNA samples, inspect plant and animal specimens, hold classes, and generate knowledge.

Among many other public services, the Calder Center supports the nation’s longest-running study of ticks and Lyme disease, and its scientists work to illuminate society’s impact on nature at a time of growing concern about biodiversity and climate change.

It is also a crucial training ground: “The most important thing we do here is make scientists,” says Thomas Daniels, Ph.D., an expert in tick- and mosquito-borne diseases who has served as the center’s director since 2014.

On a sparkling autumn day late last October, FORDHAM magazine tagged along as undergraduates, graduate students, professors, and visiting scientists went about their work—gently probing, collecting samples, and explaining the science behind their work and its potential impact.

Evolution in the Big City

In recent years, Fordham biologist Jason Munshi-South, Ph.D., and his team of graduate and undergraduate students have become known for their studies of urban wildlife and pest species, most notably rats.

“The initial idea was to understand what a New York City rat is, from all ecological and evolutionary angles,” he says of one project, which grew to a global scale and has public health implications. “We’re using DNA to understand how they move around the city and how they’re related to other rat populations.”

In a first-floor lab in Calder Hall, doctoral student Carol Henger uses similar methods to study coyotes, animals that only recently moved into the city for the first time, Munshi-South says. She’s looking at DNA markers from coyote scat collected in Pelham Bay Park and elsewhere to infer how individual coyotes are related, what they’re eating, and how they’re dispersing.

Meanwhile, Nicole Fusco, another doctoral student in Munshi-South’s lab, sequences DNA to study gene flow among populations of salamanders.

Biodiversity and Climate Change

In the Calder Center’s Lord & Burnham greenhouse, constructed on the property nearly a century ago, doctoral student Stephen Kutos has been growing pairs of potted trees and studying how they pass water and nutrients back and forth via subsoil networks of fungus.

“Tree stumps have been found that are still alive hundreds of years after the tree was cut down, quite possibly because surrounding trees send them nutrients,” he says. With further study, he adds, it may be possible to restore the wild population of one type of tree he’s growing, the American chestnut, which was eradicated from the wild 100 years ago by blight.

Restoring the tree could help combat climate change, scientists believe, because the American chestnut can absorb and store carbon quickly.

In an adjacent greenhouse, several researchers work on an evolutionary study initiated by Fordham biologist Steven Franks, Ph.D., and focused on Brassica rapa (field mustard). As Franks demonstrated in an earlier study, the annual plant evolved earlier flowering within just five years to cope with drought conditions in California.

The Mystery of the Red-Backed Salamander’s Survival

Late in the morning, undergrads Dan Khieninson and Erin Carter and doctoral student Elle Barnes enter Calder forest in search of red-backed salamanders.

“You can find them anywhere in the forest as long as the soil’s moist,” Barnes says before the group navigates a steep decline to the forest floor.

She indicates several flat, weathered pieces of wood she’s left behind. “You’re more likely to find them under here.” The three researchers crouch down and soon locate several specimens.

They’re trying to discover why red-backed salamanders are not affected by the chytrid fungus that is devastating other amphibian populations.

“It’s not enough to just study the ones that are going extinct,” Barnes says. “There are solutions in the ones that will survive. What do they have that other amphibians are lacking?”

The answer lies in their microbiome, Barnes says. She, Carter, and Khieninson use cotton swabs on the salamanders’ bodies to collect samples of microorganisms that they can test against chytrid fungus in the lab. The impact of their research could extend beyond conservation biology, Barnes says: “The discoveries we make about disease and microbiomes can be applied to multiple systems, including humans’.”

A Closer Look at a Ubiquitious, Ecologically Valuable Species

Michael Kausch, a doctoral student in aquatic ecology, rows a boat out on Calder Lake to take some water samples he can later test for cyanobacteria at the lakefront McCarthy Laboratories. Meanwhile, inside the lab, his fellow doctoral student Stephen Gottschalk is working with their Fordham supervisor, John Wehr, Ph.D. Gottschalk is studying green algae in the Characeae family.

“They’re an important food source for birds, a habitat for insects, and they support fisheries,” he says.

So far Gottschalk has collected samples in nine U.S. states, and he’s been working at the New York Botanical Garden under the supervision of Kenneth Karol, Ph.D., to examine his samples on a molecular level.

He’s finding that what scientists once thought were just subtle differences among green algae are in fact ecologically important distinctions. “They’re designated as one species,” Gottschalk says, “but what it looks like to me so far is these are very regionally distinct.”

Mosquitoes, Ticks, and the Pathogens They Carry

Insect-borne diseases are a big part of the research focus at Routh House, the vector ecology lab at the Calder Center that’s jointly run by Fordham and the New York state health department. Inside the lab, scientists study samples of various species, such as the aggressive and potentially disease-carrying Asian tiger mosquito. Outside, they collect specimens and conduct surveillance projects.

“We set up mosquito traps all around the lower Hudson Valley,” says Marly Katz, a state employee and Fordham doctoral student. “All the mosquitoes end up here, where I identify them, and then we send a bunch [to the state health department]for disease testing.” She and her colleagues are also collaborating with Columbia University scientists to “map the Asian tiger mosquito,” she says, and determine if changes in climate are affecting its migration patterns.

While Katz checks a mosquito trap, research technician Richard Rizzitello collects ticks by dragging a white cloth across the ground and then pulling them off with forceps (he uses a lint roller to collect any larvae).

One Calder scientist, Nicholas Piedmonte, displays egg-to-adult samples of the blacklegged tick, which can carry the bacterium that causes Lyme disease.

“These are great for education and outreach,” he says, particularly in central New York, “where ticks are kind of a new problem.”

View a timeline of the Calder Center’s history. And watch a July 2017 video celebrating the center’s recent golden anniversary.

Where do they come from, and how do they get around? Fordham biologists produce the world’s first in-depth genetic study of brown rats, and investigate the mysterious, wily ways of New York’s biggest scourge.

New Yorkers love to hate their rats, shuddering whenever a pointy nose or a scaly tail peeks from behind a trash can or subway rail. So visitors to the First Street Green Art Park on New York’s Lower East Side were surprised one Saturday this past May when they came upon five street artists painting larger-than-life murals celebrating the city’s most reviled rodent—a rat giving the peace sign, a rat snuggled contently amid a vegetable ratatouille, a rat with an NYC baseball cap and a spray can, rats looking, well, cute.

The unusual project, “Street Art for Street Rats,” was intended to bring attention to the research of Fordham biology professor Jason Munshi-South, Ph.D., and his graduate students, who have spent the past four years trying to understand the species that, perhaps more than any other, has adapted itself to live side-by-side with humans in the urban environment.

“You’d think rats are so common, we’d know all about them, but in fact we don’t know very much about their ecology or evolutionary biology,” Munshi-South says.

Biologists don’t even know how many rats live in New York City. Estimates range from 250,000 to 2 million. Yet, argues Munshi-South, rats are as important to study as any other species, if not for their extreme resilience and adaptability, then for the insights into how we can fight back against the damage they cause and diseases they spread.

With the help of $670,000 in funding from the National Science Foundation, Munshi-South and his students have helped lift the veil of mystery to reveal the inner workings of New York’s rat population.

“The initial idea was to understand what a New York City rat is, from all ecological and evolutionary angles,” says Munshi-South. But the project soon expanded globally to examine where rats were coming from and how they got to New York. The lab put out a call to labs across the globe, and dozens of researchers from as far away as Japan and the Galápagos Islands sent in the genetic signatures of the rats in their neighborhoods—more than 300 samples in all. “It grew into an effort to understand the evolutionary history of rats all over the world,” he says.

A Long Global Journey

Other animals have adapted to live in cities—birds, mice, wild turkeys, and coyotes, for example, have moved into urban green spaces across the country. But rats may be the most successful at exploiting the human environment, says Matthew Combs, a Ph.D. student in Munshi-South’s lab. They’re also highly social animals that, once they establish a colony, reproduce and expand rapidly, learning from one another where to find the best sources of food—and which danger spots to avoid. “They are able to take advantage of all the resources we provide, even in the face of all our attempts to eradicate them,” Combs says.

In order to trace the journeys of rats around the world, the biologists in Munshi-South’s lab have availed themselves of recent advances in genetic research and data analysis.

“Anytime a population undergoes major changes, when it shrinks or expands or mixes with other lineages, it leaves a residue in the genome,” explains Munshi-South, who has been teaching at Fordham since 2013. To detect those residues, the lab uses a “big data” approach. Rats have some 2.7 billion base pairs in their genome. Using techniques developed for the Human Genome Project, the researchers are able to show through successive subtle gene variations which rats are related to which others, tracing their progression across both time and space.

The New York rat is known by many names, including the common rat and the brown rat. But its official name, the Norway rat (Rattus norvegicus), is a misnomer. Emily Puckett, a postdoc in Munshi-South’s lab who analyzed more than 300 rat DNA samples from 30 countries, discovered that the species actually originated in Mongolia, transitioning from forests to farms to villages as they adapted to human food sources—probably thousands of years ago, with the advent of agriculture. From there, they expanded both east to Japan and western North America, and west to Europe, where in the 1700s they stowed away on British ships bound for the bustling port of New York.

A Feisty, Unwelcoming Breed

To examine the history of rats closer to home, Munshi-South and Puckett got permission from the American Museum of Natural History to extract DNA from 100-year-old rat skulls and skins as a supplement to the samples they gathered from all over the city. They published their findings, the first in-depth study of its kind, in Proceedings of the Royal Society B, the flagship biological journal of the U.K.’s Royal Society.

While Munshi-South expected to see evidence of many waves of rat immigrants mixing in New York over time, mirroring the story of its human immigrants, that turned out not to be the case. In fact, all of the rats of New York can be traced to that initial wave in the 18th century, with little mixing with new arrivals since.

“We think that once rats get established and build big, healthy colonies, it’s hard for new rats to integrate and breed into the population,” he says. In other words, New York’s rats are so aggressive they fight off any newcomers. “That’s good news” for humans, he continues. “We are not at risk of novel diseases from a lot of new rats mixing with the local population.”

Combs has picked up the trail from there, looking at how rats are moving within New York. On any given day, he can be found setting and checking traps in every ZIP code of Manhattan, a difficult task given how adept rats are at avoiding danger. So far, he and his colleagues have caught more than 550 rats and produced genetic data for 250 of them since the start of the study.

“Most of the rats I trap are juveniles, only a couple weeks or a couple months old,” he says. “Those are the only ones foolish enough to walk into my traps.”

To find his quarry, Combs targets out-of-the-way spots behind trash cans and in the corners of parks, looking for telltale signs of burrows, pellets, or the greasy smudge marks from sebum, oil of their fur that marks well-traveled pathways. He often receives help from residents hanging out on sidewalks or stoops who are only too happy to tell him where the rats live in their neighborhoods—sometimes even letting him into their backyards to trap them.

Once he traps the rats, he brings them back to the lab where he extracts DNA samples and analyzes them for differences. So far, his research has revealed rats to be creatures of habit, rarely venturing more than 30 to 150 meters from their colonies. When they do stray, they tend to head north and south, possibly following the long, unobstructed paths of sewers and subway lines. As a result, a subtle north-south genetic gradient exists along the island, with a break in midtown.

“There seems to be an uptown group of rats and a downtown group of rats, with less movement around the midtown region,” says Combs. That break may be due to the neighborhood’s lack of residential buildings and green space, impeding their progress.

The next step in the research is to use computer models to ask what environmental attributes—such as water sources, open soil, sewers, and subway lines—determine how rats are distributed within the space. In addition, Combs will look at demographic patterns of rats’ human neighbors to see if, for example, rats are more prominent in socioeconomically depressed areas, as some research suggests.

Controlling Threats, Debunking Myths

In addition to its intrinsic value in understanding a species that lives so closely with humans, the project has public health implications. Rats can be a menace, damaging infrastructure and spreading diseases such as salmonella and leptospirosis to dogs and humans. If city officials are better able to understand where rats are coming from and how they get around, they can better control how they spread. Munshi-South has been collaborating with the New York City health department to help officials refine their strategy for exterminating rats. While much of that work remains confidential, Munshi-South says that part of the project is locating major reservoirs of rat colonies from which the rats might be spreading.

At the same time, Munshi-South’s lab has continued collaborating with researchers in other cities. Just as humans have built different urban environments, so too might rats adapt to them differently, following different patterns of movement in the open spaces of New Orleans, the parks of Vancouver, or the favelas of Salvador, Brazil. Researchers from all three cities have recently visited Fordham to compare notes and research techniques that will help tease out the ecological differences of rats, which may be just as pronounced as the cultural differences of the humans they live with.

The recent “Street Art for Street Rats” event was conceived by Combs as a way to help educate the public about the ecology of rats in all its complexity. The spark came when he ran into Jonathan Neville, a friend from his undergrad days at Hamilton College, who is a co-founder of the Centre-fuge Public Art Project, which works to “transform neighborhood eyesores” with vibrant murals.

While the artists were painting, Munshi-South, Combs, and others from the lab were on hand to teach passersby about how they use genetics to trace the journeys of rats around the city. And they debunked some common myths, such as the misconception that there are more rats than people in New York (actually, they say, there are 250,000 to 2 million rats, compared to 8.4 million humans) or that rats are able to squeeze their skeletons flat (though they can fit in tight spaces). Even so, they realize there are limitations to the average New Yorker’s tolerance.

“A lot of people do respect them and think they are fascinating,” says Combs, who likes their feistiness and adaptability. “But if someone thinks they are a scourge and is just interested in getting rid of them, I won’t try and change their mind.”

—Michael Blanding is a journalist and the author of two books, including The Map Thief (Avery, 2014).

Now, a Fordham professor just may have cracked one of them.

Henry Han, Ph.D., has developed a novel method of identifying the genetic activity unique to complex diseases such as cancer. This “signal” holds out hope of overcoming a key barrier to obtaining cancer diagnoses from the treasure trove of genetics information developed in recent decades, said Han, and could “totally change” medicine.

“It’s so hard to (separate) the ‘noise’ from the true signals in big data. Previously, people didn’t know how to do that,” said Han, an associate professor in Fordham’s Department of Computer and Information Science.

For years, scientists found that although they could identify the genetic markers for different types of cancer, those markers differed from person to person, hindering the development of reproducible diagnostics and treatment, Han said.

New technologies known as RNA-Seq offer a possible solution by producing dramatically greater amounts of data about genes and RNA within a cell. But the data is “noisy” and hard to analyze, in part because of its sheer volume and because of errors that were baked into the data by the technology used to produce it.

In tackling this problem, Han devised an algorithm that relies on wavelets—a subtle tool for differentiating among pieces of genetic information and eliminating what he calls “red herrings” in the data.

Working with researchers from Columbia University and the University of California, San Diego, Han applied this algorithm to RNA-Seq data and found three “common denominator” genetic markers across multiple cases of breast cancer and prostate cancer, among other findings.

His research has been supported by National Institutes of Health grants, and he is seeking further funding to work with doctors and turn his computations into treatments that catch cancer or other diseases earlier than ever—that is, before symptoms even show up.