DNA from hunter-gatherer teeth reveals secrets of ancient plague

**Benjamin Thompson** (0:23)
Welcome back to the Nature Podcast. This week, investigating plague outbreaks in ancient hunter gatherers and a prototype dark matter detector.

**Nick Patrick Howe** (0:34)
I'm Nick Patrick Howe and I'm Benjamin Thompson.

**Benjamin Thompson** (0:45)
Plague, a disease caused by the bacterium Yersinia pestis has devastated humanity, causing the deaths of millions of people over millennia. But not much is known about ancient plague, something a new paper in Nature is shining a light on. Now, there are actually a few different types of plague, and they're transmitted in different ways. But the one that everybody immediately thinks of is bubonic plague, transmitted by the bites of fleas. It's the cause of the Black Death, a pandemic that tore through Europe and parts of Asia in the Middle Ages.
But evidence suggests that Yersinia pestis only gained the ability to be transmitted this way about three and a half thousand years ago. There have been much older cases of plague discovered in human remains, dating back well over five thousand years. What this older plague was like though is something of a mystery, and researchers have been debating things like its genetics and how severe it might have been. This week though, a team of researchers have been trying to answer some of these questions. They've been looking at evidence of ancient plague infections in hunter-gatherers living in a resource-rich area around the enormous Lake Baikal, in what is now Siberia. To find out more about what they found, I spoke with one of the team, Rury Macleod, from the University of Oxford, here in the UK.
Rury laid out to me a little bit more about the sites and where the remains were found.

**Rory Macleod** (2:17)
This is a great place to be a prehistoric hunter-gatherer, and so we see really, really long-term presence of humans living around Lake Baikal. We're looking at four burial grounds that have been reused by these hunter-gatherers. This is around about 5,500 years ago for the oldest site. The oldest pair are Uxtida 1 and quite close to that is Xumulika, and then Pratsky Kamin and Serovo.

**Benjamin Thompson** (2:41)
And these sites are separated by hundreds of years.

**Rory Macleod** (2:43)
Yes. So these sites are separated by centuries. And so what was quite exciting about this large cemetery, Uxtida 1, was that there was a real mystery around about the mortality profile of the individuals that the archaeologists excavated at that site.
A lot of teenagers basically, a lot of adolescents, a lot of older children, far more than you would usually expect for a cemetery of that size. And so it was clear that something was causing this high mortality of these younger people. So it was super exciting when we managed to find such widespread evidence for infections of plague amongst these individuals.

**Benjamin Thompson** (3:16)
And you were researching these people, and you did, as you say, find evidence of plague infection. How did that come about?

**Rory Macleod** (3:24)
So for the most part, what we were doing where we were taking teeth from the archaeological remains of these individuals, taking a very, very small amount of the tip of the root of some of these teeth, and grinding that down, powderizing that to be able to dissolve it and extract purified DNA to look for evidence of these individuals' own genomes, as well as anything that they might have been infected with, like plague. So across these individuals, we got a 39% detection rate of plague. So obviously, a lot of the time, pathogen DNA doesn't preserve very well. It's a very, very small component of the DNA that we'd expect to get in these remains. And so frequently, we find that we have negatives, quite high negatives for some diseases. Just as a comparison, we have lots of sequencing data from medieval plague pits in London. There's one at Smithfield site, and there they obtained a detection rate overall of 20%.
But that's within a medieval plague pit, where you'd expect 100% of the people pretty much to be infected with plague. So really the fact that we're getting 39%, five and a half thousand years ago, thousands of years before this medieval plague pit is an incredible result in itself, and would be consistent with pretty much everybody potentially having died of plague.

**Benjamin Thompson** (4:31)
So broadly, then, you have these four burial sites separated into pairs in terms of how old they are, with a gap in between them, suggesting the outbreak of this disease happened more than once.

**Rory Macleod** (4:43)
That's a big question. Is it something that's been maintained in the Baikal population over a few centuries, or is it just spilling over again from a wild animal reservoir? And I think it's almost certainly spilling over again. We can see that there are slight differences in the mutations present between these two strains, and if it's spilled over once, then it can spill over again from the wild rodents that are around about Lake Baikal.