New York City Has Genetically Distinct ‘Uptown’ and ‘Downtown’ Rats

New York City is a place where rats climb out of toilets, bite babies in their cribs, crawl on sleeping commuters, take over a Taco Bell restaurant, and drag an entire slice of pizza down the subway stairs. So as Matthew Combs puts it, “Rats in New York, where is there a better place to study them?”

Combs is a graduate student at Fordham University and, like many young people, he came to New York to follow his dreams. His dreams just happened to be studying urban rats. For the past two years, Combs and his colleagues have been trapping and sequencing the DNA of brown rats in Manhattan, producing the most comprehensive genetic portrait yet of the city’s most dominant rodent population.

As a whole, Manhattan’s rats are genetically most similar to those from Western Europe, especially Great Britain and France. They most likely came on ships in the mid-18th century, when New York was still a British colony. Combs was surprised to find Manhattan’s rats so homogenous in origin. New York has been the center of so much trade and immigration, yet the descendants of these Western European rats have held on.

When Combs looked closer, distinct rat subpopulations emerged. Manhattan has two genetically distinguishable groups of rats: the uptown rats and the downtown rats, separated by the geographic barrier that is midtown. It’s not that midtown is rat-free—such a notion is inconceivable—but the commercial district lacks the household trash (aka food) and backyards (aka shelter) that rats like. Since rats tend to move only a few blocks in their lifetimes, the uptown rats and downtown rats don’t mix much.

When the researchers drilled down even deeper, they found that different neighborhoods have their own distinct rats. “If you gave us a rat, we could tell whether it came from the West Village or the East Village,” says Combs. “They’re actually unique little rat neighborhoods.” And the boundaries of rat neighborhoods can fit surprisingly well with human ones.

Combs and a team of undergraduate students spent their summers trapping rats—beginning in Inwood at the north tip of Manhattan and working their way south. They got permission from the New York City Department of Parks and Recreation, which gave them access to big green spaces like Central Park as well as medians and triangles and little gardens that dot the city. And they asked local residents. “More often than not, they were very, very happy to show us exactly where they had rats.” says Combs. A crowdsourced map of rat sightings also proved very helpful.

Rats, although abundant, are not easily fooled into traps. They’re wary of new objects. To entice them, the bait was a potent combination of peanut butter, bacon, and oats. And the team placed their traps near places where rats had clearly crawled. They looked for rat holes, droppings, chew marks on trash cans, and sebum marks—aka the grease tracks rats leave when they traverse the same path to the garbage over and over again.

For the DNA analysis, Combs cut off an inch or so of the rats’ tails. (Over 200 of these tails are still saved in vials in a lab freezer.) The team also took tissue samples for other researchers interested in studying how rats spread diseases through the urban environment. And some of the rats they skinned and stuffed for the collections of the Yale University Peabody Museum of Natural History, where they will join stuffed rats from 100 years ago.

Combs is now writing his dissertation on the ecology of New York’s rats. He’s looking at how a number of characteristics—natural features like parks, social factors like poverty, physical infrastructure like the subway system—account for the spatial distributions of rats in Manhattan.

The point of all this, ultimately, is to help New York manage its rat problem, which is annoying as well as a genuine public-health hazard due to rat-borne diseases. In July, New York Mayor Bill de Blasio announced a $32 million war plan against the varmints. The New York Times noted wryly that when it came to rats, “There have been 109 mayors of New York and, it seems, nearly as many mayoral plans to snuff out the scourge. Their collective record is approximately 0-108.”

After two years of trapping rats, Combs has come to respect the enemy. At the end of our conversation, he launched into an appreciation of rats—their ability to thrive on nearly anything, their prodigious reproduction, and their complex social structure, in which female rats will give birth all at the same time and raise their offspring in one nest. “They are, quote-unquote, vermin, and definitely pests we need to get rid of,” he says, “but they are extraordinary in their own ways.”