The mutant wildlife adapting to New York City

In the 400 years since New York City's birth, the local wildlife has adapted to a life of fast food, pollution and isolation.

At a top secret location in Manhattan, within a large public park, is a tiny patch of moist hillside. Flecked with shade from a grove of young maple, oak, and black cherry trees, the area is bordered by a busy road and sits just across the street from a school. And yet, stalking the slope's meadows of moss and wildflowers, lounging among decaying logs and fallen leaves, is a population of New York City's most obscure inhabitants.

This is predator territory, and here lives a killer so rare and little-known, only a handful of New York City's eight million or so residents have ever seen one. "They will eat anything they can stuff into their mouths. They'll eat each other," says Ellen Pehek, a retired ecologist who spent 21 years working for the NYC Parks & Recreation's Natural Resources Group. With strong, crushing jaws and thick legs, these hunters have a muscular, almost-reptilian physique that evokes Komodo dragons. "If they were six feet (1.8m) long, we'd be running from them," she says.

The hunters in question are northern dusky salamanders, and they easily fit into the palm of a hand. Though they are rarely seen or thought of – even by park officials, according to Pehek – they are thought to have been living in this very spot for the best part of a century. 

As New York City has grown up around them, the little amphibians have continued to eke out a living on an area of land significantly smaller than the footprint of any of the iconic skyscrapers now found just a short distance away. "I would say it [the hill] is maybe 75 yards [68m] across, and maybe 40 yards [37m] high," says Erik Baard, Chair and Executive Director of HarborLAB, an environmental education organization that gives free kayaking tours of NYC.

New York City is famous for its worldly, subway-riding pigeons and epicurean rats – such as Pizza Rat, who went viral for hauling a large slice of margherita pizza down a flight of stairs on the subway. But there are less familiar urbanites to be found too, ones which were in residence long before Western civilisation showed up. Coyotes routinely visit Central Park, where precious orchids bloom in the ground. Comb jellies pulse through the East River under Manhattan Bridge. And each spring, from Brooklyn to Queens, the prehistoric, tank-like forms of horseshoe crabs haul themselves up onto beaches to mate and lay their eggs.

Though some of these organisms are continuing life as normal, it would be impossible to remain unaffected by the approximately one million structures that have popped up over the last 400 years, or the bustle of a cultural and economic metropolis. In fact, New York City's native wildlife is evolving, and fast. Some occupants have already diverged so much, they have developed unique physical and genetic characteristics.

In 1945, Carl Gans was out for a walk in Manhattan. While ambling down a hill – Pehek likes to think he was on his way to visit a local university – the young German-American herpetologist stumbled upon a population of northern dusky salamanders. Desmognathus fuscus is a species that needs ultra-pure water, shade, and personal space – particularly from humans. But there they were, in a public park, in a major city. And they were thriving.

Soon Gans had published his discovery in a scientific paper. He noted the exact location where the salamanders had been found – with the street, and details of their habitat – and called for them to be protected. But nothing happened. Eventually the sightings dried up, and after a while, most scientists believed that they had vanished from the area forever.

Then came Pehek. It was 2005 and she couldn’t help wondering, was it just possible that the salamanders might have managed to cling on, despite over half a century of further development? "I assumed not," she says, "but I grabbed a couple of people and we went out there."

The salamanders' favourite New York City haunt is what's known as a "seepage" – a miniature wetland that exists on a shallow slope, which is kept continuously moist by groundwater that flows over its surface. The dusky salamanders' Manhattan hill has its own little stream bordered by rocks, and the surface is coated with a thin layer of fallen leaves and mud.

"It was so fragile that if you stepped on it, you would slide down the slope," says Pehek. She doesn't remember finding the first northern dusky salamander of the day, because there were so many. "It was so exciting… we just kept finding them over and over," she says. The team even found a mother and her young, who had just hatched out of a little cluster of white eggs.

At one point, the dusky salamander was the most common variety in New York City. But now they are extremely rare, and Pehek has found just a handful of solitary populations. Pehek likes keep their locations a secret, to avoid any accidental trampling by curious members of the public.

By thoroughly scouring suitable sites, eventually she identified another group in the Manhattan park, around a mile (1.6km) from the first area – but separated by two bridges carrying fourteen lanes of traffic. The others were discovered in streams within public parks on Staten Island.

As it turns out, this insular existence has been having a profound impact on their genetics. In 2013, Pehek teamed up with colleagues from City University New York, including the geneticist Jason Munshi-South – who now leads a laboratory at Fordham University, New York – to examine how inbred New York's urban dusky salamanders had become.

The researchers found the two Manhattan communities had entered a significant genetic bottleneck – a sharp reduction in genetic variation as a result of the population being so small. While these can occur due to global challenges such as climate change – it's thought that drought and glaciation reduced our own species to just 1,000 individuals early in our history – in the salamanders' case, the genetic squeeze is thought to be down to man-made infrastructure.

Namely, the Washington and Hamilton bridges, which constitute an impassable barrier for even the most adventurous northern dusky salamanders. Each of Manhattan's two populations might as well be divided by icy mountain ranges or vast oceans – they exist in near-total isolation. One has become so inbred and homogenous, they just have one version of most of their genes, a highly unhealthy situation known as "allele fixation". Compared to more common species of salamanders tested in rural areas, even the Staten Island group has low genetic diversity. 

By continuing to exist in such a fragmented habitat, Manhattan's northern dusky salamanders have embarked on a journey that could eventually lead to them becoming a new species. Pehek explains that they have already separated from other populations – though not yet enough. "It's a long shot," she says, but if they survived, eventually Desmognathus Manhattani could become a reality.

And you don't need to go far to find evidence that other New York City residents are also rapidly diverging from their countryside counterparts. As it happens, you don't even have to leave the salamanders' public park.

The white-footed mouse has lived in what is now New York City for more than 18,000 years. Towards the end of the last Ice Age, as the glacier that once covered the region began to retreat, the species reclaimed its old territory. It has been there ever since. Each evening, as night descends on the city, these wary little mammals – with oversized, button eyes and dull brown fur – emerge from their burrows in the small pockets of forest that remain.

One late afternoon in the 1990s, Stephen Harris was out for a walk in Central Park West – appropriately, he had just left the Museum of Natural History – when he spotted white-footed mice scurrying along one of the large, rocky outcrops that formed the edge of the park.

Then Harris looked across the other side of the street to a sidewalk, and there were yet more mice of a different kind, digging through trash cans. These ones were regular house mice – a species that is not native to the US, but originated in Southeast Asia. They live alongside people across the globe, surviving on scraps of human food or foraging for seeds and grains, and are thought to have first arrived in the United States in the 16th Century.

As Harris looked from one to the other, he was struck by the parallel lives of these two city-dwellers, which were both surviving the hustle of urban life just a few metres away.

"There's this idea that, as you urbanise an area, there are urban avoiders," says Harris. "So the native flora and fauna that move away as humans come in – large predators, bears, things like that." Then there's the urban exploiters, opportunists who rely on people – a group which includes pigeons, cockroaches, house mice and rats. "And then there's the urban adapters. That's the really interesting group," he says. 

Harris explains that white-footed mice fall into the latter category. "It was in Manhattan before European settlers arrived, and it's still there now. But it's living in these spaces that we sort of forced on it. So what is that doing?" he says. Harris views New York City's parks as analogous to Galapagos Islands – evolutionary laboratories where it's possible to watch in real-time as organisms adapt to their environments and start to diverge.

After incubating the image of the white-footed mice at the edge of Central Park in his mind for decades, eventually Harris embarked on a series of experiments to investigate if they were any different from their rural cousins – did they carry mutations that weren't present in the countryside?

For one 2017 study, together with Munshi-South, he analysed the genomes of white-footed mice from three sites in New York City – Central Park, New York Botanical Gardens, and Flushing Meadows – and compared them to mice from rural sites around 62 miles (100km) away. The researchers found evidence that the urban white-footed mice were indeed evolving, with mutations in genes that regulate how fats and carbohydrates are metabolised.

"So it kind of makes sense. You know, they're in this new green space [public parks] with reduced native seeds and fruits that they would normally eat, but an abundance of human food waste," says Harris. He calls it the cheeseburger hypothesis – these once-wild mice are now subsidising their diets with human takeaways.

In research that has not yet been published, Harris analysed DNA present in droppings from white-footed mice living in Central Park to see exactly what they had been eating. He discovered some surprising signatures: tomato – and dog. In the absence of tomato plants growing in Central Park, Harris is fairly confident that he knows where this signature is coming from. Like New York City's rats, it seems the white-footed mice have developed a predilection for pizza. However, the dog was more of a surprise.

"Now, the mouse isn't eating dog," Harris reassures. "But there are dogs in the park. And the dogs have a high-quality diet… the mice might be digging through the dog faeces and eating fruit from that," he says.

Other research has found that urban life is even changing the shape of the mice's skulls. With their new Super-Size-Me diets of soft foods like cheesy chips, white-footed mice in Manhattan and the Bronx tend to have shorter jaws – a result of doing less chewing as they are developing.

Intriguingly, this quirk is mirrored in humans too. Modern diets require significantly less mastication than those of our ancestors, and as a result our jaws have become smaller and our teeth more crowded.

Like New York City's salamanders, the region's white-footed mice are also extremely isolated – another factor that is contributing to their divergence. In urban areas, these populations have forested, parkland territories that are separated from the rest by impassable deserts of roads and buildings. As a result, they tend to have lower genetic diversity.

In fact, the impact of this habitat severance is so stark, the history of New York City is literally written into the white-footed mouse's DNA. One study found that the metropolis' population first became genetically isolated from their country-mouse cousins around four centuries ago – a timeline that coincides perfectly with the founding of the city. Today, each park within the city has mice with their own distinct genetic signature.

Despite this, Harris explains that New York City's mice might experience some genetic mixing with outsiders, and therefore they're unlikely to become a new species. "Even if one individual mouse makes it down from the Catskill Mountains, that is enough gene flow to stop it short of speciation," he says. But they are already diverging, he adds. "It's very feasible that a unique urban population of mice that might one day warrant its own conservation status or something like this."

Aside from genetic isolation and a change of diet, another major challenge of life near a city is pollution. In the Hudson River, this was particularly extreme between 1947 and 1976 – a period when General Electric facilities dumped vast quantities of polychlorinated biphenyls (PCBs) into its waters. 

The legacy of this era of pollution lingers on. Around 200 miles (321km) of the Hudson is classed as a "Superfund" site – a place contaminated with toxic material that is still in the process of being cleaned up today. Many pollutants are still there, lurking in the river's sediment. It also contains some rather unusual fish.

Atlantic tomcod are small, grey fish with white bellies and cute googly eyes – like miniature versions of the Atlantic cod that humanity is so fond of eating. They spend most of their time at the bottom of the water column, rooting out crustaceans and other seafood delicacies from the sediment. Unfortunately, this means that they also end up exposed to high levels of whatever toxins happen to be there.

"In the 1980s, there was a lot of concern in the US about the high prevalence of tumours in fishes that live on the bottom, at contaminated sites," says Isaac Wirgin, an associate professor at New York University's School of Medicine. In two-year-old tomcod fish, rates of liver cancer were around 90%. "And if you're in a clean place, they found that there's almost no tumours," he says.

However, despite the tumours, the tomcod were doing remarkably well in the Hudson's PCB-infested waters. Where other species were wiped out, they hung on. Their livers had the highest levels of PCBs known in nature, yet they were alive. How?

In 2011, together with colleagues from oceanographic institutions across the US, Wirgin analysed the genomes of Hudson tomcod and compared them to those from elsewhere. "And it turns out the molecular mechanism was in a single gene," he says. Regular tomcod have a receptor – the aryl hydrocarbon receptor2 – which binds strongly to PCBs, resulting in all kinds of toxic effects. However, New York's special mutant population had receptors that didn't bind to it as well, allowing them to coexist with these pollutants relatively unscathed.

This was lightning-fast evolution, and it created a population of fish that are unique to New York. But despite the species' impressive feat of adaptation, there are still other perils ahead.

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Currently, the Hudson River supports the southernmost population of tomcod in the United States. But as the climate gets warmer, there are concerns the extra heat may become too much. "People are very concerned that the tomcod are on the way out, they not only have exposure to these toxic PCBs, but they're thermally challenged during the summer months," says Wirgin.

And other city-dwellers may be struggling, too.

On one of Pehek's most recent trips back to visit Manhattan's northern dusky salamanders, she discovered a scene of utter devastation. The little hill that they have occupied since at least 1945 had been inundated with runoff from a stormwater overflow and was strewn with rubbish and debris. "Obviously there was a torrential stream of water that came down over the habitat and brought a lot of sediment and plastic bags," she says. "So that was very disturbing." Pehek could find very few salamanders on that visit. 

But Pehek says she has found it very difficult to convince anyone to care. She believes that, for many years, the little community of amphibians has inadvertently benefitted from benign neglect – the scrap of land they live on is so steep, it's been allowed to remain wild and unnoticed. But this is a double-edged sword. She still worries about them, she says.

New York City's native wildlife has already survived centuries of change. The public parks that exist today are mostly man-made landscapes constructed in the late 19th Century – in some cases, every tree, hill and large rock was painstakingly planned. Before then, the city was a swampy patchwork of buildings and farmland. But still, the local species never entirely disappeared. Now, after 400 years of living alongside humans, many have been nudged onto new evolutionary paths. But though they seem to be adapting, they could still be at risk.

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