Shedding light on the Black Death

Seven hundred years ago, millions of Europeans were wiped out by a disease we still don't entirely understand. The Black Death might seem like a pretty open-and-shut case at this point: It was caused by plague-bearing fleas that hitched rides on the rats that infested a grim and grimy medieval world. The End.

But that simplified version only makes sense if you overlook some important facts about how the plague (which still exists) operates today. "The Black Death killed between 30 and 50 percent of the affected population," says Sharon DeWitte, assistant professor of anthropology and biology at The University of South Carolina. "Modern plague, at most, kills between 2 and 3 percent, and that's even in areas without access to modern medicine."

What's more, DeWitte says, recorded symptoms from the Black Death don't entirely match up with those of modern plague. And the Black Death seems to have spread through populations faster and killed much faster than its modern cousin. The differences are striking enough that some scientists, including DeWitte at one point, have suspected that the Black Death might not have been caused by plague at all. But genomic reconstructions of ancient DNA suggest the two are one. So what changed? Ultimately, that's the question that makes last month's discovery of a new Black Death cemetery in London so important.

Given the vast numbers of people who died in the Black Death, there are relatively few burials that can be absolutely confirmed as containing Black Death victims, and only Black Death victims. DeWitte could only think of three when I spoke to her. But it makes sense. To put it simply, in the midst of a horrific catastrophe nobody was really thinking about how to makes sure the data would be nice and tidy for scientists to find hundreds of years later. Medieval writers didn't necessarily record information that would have helped archaeologists identify a Black Death cemetery. What's more, it wasn't even totally normal to bury nothing but Black Death victims together in one place. "A lot of them were just incorporated into existing cemeteries," DeWitte said.

That's made it difficult to know whether Yersinia pestis — the bacteria that causes the plague — really is present in Black Death victims. This work is already hampered by the degradation of DNA over the centuries. Finding tiny Y. pestis is hard enough, even in people who were killed by it. Mixed burials add the extra complexity of not knowing whether the body you're working on actually died from Black Death, to begin with.

Because of that, the best work in this field comes from England, where we have good documentation of a few places that were set aside specifically for victims of the Black Death. The newly uncovered cemetery might be one of those places — at any rate, there was definitely a recorded Black Death cemetery that would have been in about the same location.

If that turns out to be the case, then the bones of the people buried there could help scientists fill in the gaps on the Black Death.

In 2011, a team led by McMaster University paleogeneticist Hendrik Poinar became the first to reconstruct a full genome for Black Death era Yersinia pestis.

This was not a full and complete genome drawn from a single bacterium inhabiting the body of a single victim. Instead, the genome was patched together from bits and pieces of DNA in remains taken from London's East Smithfield cemetery. The small chunks were lined up to create a whole, similar to the way you make a panoramic photo by combining a series of different shots. Hendrik Poinar calls it a "draft" of the genome, rather than a smooth, polished work of biology.

The draft tells us a couple of things. First, the Y. pestis of the Black Death era is related to modern Y. pestis. In fact, it's probably the ancestor of all the strains of Y. pestis that exist today. Second — and this is the weird part — there is really not much difference between the old Y. pestis and the new. It boils down to about 100 genetic changes, few of which seem to have given the bacteria enough of an evolutionary advantage that they spread widely through the population.

Genetically, Y. pestis has barely changed. Its infection profile in the real world, though, has changed massively. That suggests that at least some of those small alterations in the genome must have been extremely important. But which ones? And why? To answer those questions, you could reverse-engineer the evolution of Y. pestis in the lab. "We'd have an opportunity to test those changes, one at a time, and find out," Poinar said. "… If we could do it in a form or fashion that wouldn't terrify people."

But, you know, good luck with that.

Instead, what would be really helpful is some burials from later outbreaks of the Black Death. Poinar's draft genome comes from bodies that date to the 14th and early 15th centuries. And his draft of the Y. pestis genome suggests that this bacterium might have a relatively slow rate of evolutionary change. During outbreaks, though, when there are more bacteria multiplying and they have more hosts to multiply in, change can happen faster.

"Now, if the new burial dates to the Great Plague of London, around 1665, I'd really like to see that," Poinar said. That outbreak was less deadly than earlier ones, killing "only" about 20 to 30 percent of the people who contracted it. If you could compare the DNA of Y. pestis of the 14th century with that of Y. pestis of the 17th, you might begin to see which changes ultimately made the bacteria less of a killer.

That, however, remains to be seen. So far, 13 bodies have been found at the new cemetery site. Those, unfortunately, are of the same vintage as the ones in East Smithfield. But, if the new cemetery is the recorded Black Death cemetery that experts think it is, then we know it was in use all the way up through the 1500s. Find the right bodies, and you might be able to get a peek at how Y. pestis was tamed.