The Black Death first swept through Europe in the mid-1300s, killing tens of millions of people. But it didn’t stop there—the plague-causing bacterium Yersinia pestis hid inside the bodies of black rats (Rattus rattus) and continued to cause smaller outbreaks as fleas transmitted it from rats to humans for hundreds of years afterward. Then in the mid-1700s these outbreaks largely stopped. The timing coincides with the introduction of brown rats (Rattus norvegicus), which spread from Asia and outcompeted black rats almost as soon as they set their little clawed feet on the European continent.
This brown rat takeover happened not just in Europe but also in the Americas as these pests stowed away on ships headed across the Atlantic Ocean. Today the brown rat is most prevalent in eastern North America but is beginning to gain more of a foothold in the western part of the continent, too.
“Brown rats show up, and it’s just like a ghost town for black rats,” says Eric Guiry, a molecular zooarchaeologist at the University of Leicester in England. But although the two rodent species are ubiquitous pests and critical vectors of disease, scientists know very little about how they took over North America. To piece together this history, Guiry and his colleagues performed molecular analyses on 311 rat bone samples from archaeological sites across eastern and southeastern North America that are dated from the 1550s to the early 1900s. Their findings, published April 3 in Science Advances, show fundamental differences between the two species and provide clues for how one species came to dominate the other.
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Until now, reconstructing a rat timeline had proven tricky. From historical accounts we know that brown rats arrived from Europe by 1776, around the time of American independence. But though archaeologists have unearthed troves of rat bones from various dig sites going back even earlier, they can’t say with certainty when those rats lived. Radiocarbon dating is too imprecise to be helpful in this period of history, Guiry explains. And brown rats have an inconvenient habit of burrowing into the ground, so their presence at an archaeological site could be caused by contamination after the fact.
To get around this problem, the researchers collected many samples from shipwrecked rats. “If you find a black rat in a shipwreck, you know it has to date to that time period,” Guiry says. This is “quite [an] innovative approach,” says Johannes Krause, an archaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who has studied the history of brown rat introduction in Europe and has encountered similar problems from burrowing brown rats in his own work.
Some of the sunken samples came from the remains of the La Belle, a ship that ran aground off the coast of Texas in 1686. Among the wreckage, which was rediscovered in 1995, archaeologists found three bronze cannons, pottery and jewelry, a human skeleton—and “a really large number of rat remains,” says study co-author Susan deFrance, a zooarchaeologist at the University of Florida who studied the La Belle wreck in the 1990s. Samples that had been unearthed from seven ships that sank between 1559 and 1760 allowed the researchers to determine that brown rats first arrived on the continent earlier in the 1700s than historical records indicated.
Next, to understand how these rat species expanded and duked it out on land, researchers analyzed remains from coastal sites from Louisiana to Nova Scotia, including the 1600s Jamestown colony and a site in New Orleans that may have inspired the folk tune “House of the Rising Sun.” First, the researchers identified brown and black rats using a relatively new technique called collagen peptide mass fingerprinting that traces small differences in the structure of collagen in different species’ bones. This technique is less expensive and more straightforward than DNA analysis, deFrance says: “If you’d done ancient DNA [analysis] for all of this, the cost would have just been astronomical.”
Then, to determine the rats’ dietary habits over the centuries, the researchers looked at the varieties of carbon and nitrogen found in their bones. Different isotopes of these elements are more likely to be present in an animal’s body depending on its position in the food web. While the information scientists can glean here is limited, the researchers were able to conclude that the brown rats and black rats had “fundamental differences” in their dietary preferences: brown rats ate more animal protein than black rats.
Their different dietary habits means that the two species likely weren’t competing for the same ecological niche. “Yet still the [black rat] disappears,” Krause says. “That was the biggest surprise” of the molecular analysis findings, he says.
Why the brown rat “steamrolled” over the black rat “remains a completely open question,” Guiry says. One leading theory is that the brown rat’s aggressive nature and larger size helped it edge out the black rat. But this can’t explain everything—there are places in the world where the black rat dominates instead, Guiry says. He would love to see a similar study conducted on a single city, which could give scientists more granular information about how this transition happened, at least in one location.
And there’s no shortage of rat bones to make that happen, Guiry says. “I was able to find most of these rats through hearsay,” he says, adding that there are countless more samples across the globe. He is currently putting together a similar analysis from sites in Europe to track how these populations arrived from Asia. “I think there’s a lot more to be found here. This is really just scratching the surface.”