A rat eats on the platform at the Herald Square subway station in New York City.

Is it pizza?Credit: Gary Hershorn/Getty

The rats of New York City are nothing if not adaptable. They eat pizza, hot dogs — even salads — and inhabit nearly every corner of the five boroughs, from subway tunnels to playground sandpits.

Their genomes are now offering clues to rats’ ability to conquer cities such as New York, where there are thought to be about 2 million of the creatures. In a study1 posted to bioRxiv this month, geneticists identified dozens of genes involved in diet, behaviour and movement that might have helped New York rats to thrive.

“As both an evolutionary biologist and a New Yorker, I can’t help but be amazed by the ways that rats have adapted to urban environments,” says Arbel Harpak, a population geneticist at the city’s Columbia University. He co-led the study with evolutionary biologists Jason Munshi-South, at Fordham University in Armonk, New York, and Pleuni Pennings, at San Francisco State University in California.

Before looking for the trademarks of evolution in New York’s rats, the researchers first had to catch them. Between 2014 and 2015, Mushin-South’s team, which specializes in urban evolution and ecology, collected nearly 400 brown rats (Rattus norvegicus) from across the city, luring them to traps with a mix of bacon, peanut butter and oats. The researchers then sequenced the full genomes of 29 of these rats — all from Manhattan — and compared them with the previously sequenced genomes of rats from rural northeast China, the presumed ancestral home of brown rats2.

Genetic variation

Harpak’s team then looked for regions of the genome containing variations that were likely to be so beneficial to New York City rats that they quickly became common among local populations. The evolutionary process — known as selective sweep — has also happened in humans, for instance to spread gene variants that allow some humans to digest milk as adults.

The scan produced a list of dozens of genes that harboured the signature of a selective sweep in the rats. The genes include some associated with diet, behaviour and mobility — potentially reflecting the challenges, and delights, of life in the Big Apple. While it’s tempting to speculate that CYP2D1, a gene the team identified that may be important for detoxifying plant compounds, could help the city rats to enjoy kale salads, scientists can’t yet say how these genomic hallmarks influence the animals’ biology.

Harpak sees his team’s list as a starting point for future research. Tests in transgenic lab rats could, for instance, explain whether changes to a gene that is involved in growing new neurons altered the behaviour of the rats, or whether other genes the team identified linked to the metabolization of carbohydrates and sugar might have influenced the rats’ diets.

It’s intriguing that some of the genes the researchers identified are implicated in brain wiring, says Andrés Bendesky, an evolutionary geneticist and neuroscientist at Columbia. Researchers have hypothesized that animals might adapt to new environments by changing their neural circuitry, but Bendesky says no one has yet shown this.

Changing times and changing places

Harpak says he and his colleagues hope to determine when the selective sweeps occurred by looking at DNA from nineteenth-century New York rats. They plan to catch rats from other cities to see if their genome has evolved in the same way as that of New York City rats.

On the basis of one recent experience, evolutionary biologist Hopi Hoekstra expects there will be at least some differences in the genetic adaptations of rats from other cities. About a month ago, Hoekstra, who is at Harvard University in Cambridge, Massachusetts, tried to trap a rat in the basement of her home. “I was like, ‘This rat picked the wrong house.’,” says Hoekstra, who studies the genetics of wild rodents. “I’ve been trapping rats for 25 years.”

After weeks of failing to catch the culprit, she called in an exterminator, who told her she was using the wrong bait for Cambridge’s rats, which prefer Dunkin’ Donuts pastries and Slim Jims, a dried-sausage snack, over the peanut butter-laced traps she was setting. The exterminator filled the hole that Hoekstra’s rat was using to enter her basement, but he is now collecting Cambridge rats for DNA analysis. “When the paper came out, it just clicked. Of course there were differences. The local exterminators know they are different,” says Hoekstra.