Benjamin Vernot: Digging for DNA in cave dirt

Benjamin Vernot: Image courtesy of Benjamin Vernot

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Benjamin Vernot: Digging for ancient human DNA in cave dirt

Moving on from direwolves, giant kangaroos and Siberian unicorns to our own species, I caught up with Dr Benjamin Vernot - a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Rather than studying bones, he’s been digging for DNA in more unlikely places in order to unearth the stories from our ancient ancestors.

Benjamin: The idea basically is that we study human history by looking at the DNA from bones mostly. Right. So if we want to study ancient human history. But for large parts of our history, there's no bones for us to look at. We look in a cave. We know that Neanderthals lived there and there just was no Neanderthal bones in most ancient caves. And so if we want to study them, we're really limited by the dozen or two dozen or so bones that we can find. And the idea was basically that these people lived in these caves, they made stone tools that cut themselves, they shed their skin and you have DNA and everything that comes out of your body has DNA in it. Right. And that stuff accumulates on the floor of the cave. And maybe, maybe, maybe the DNA is still there. And it turns out that it is. And so by getting that DNA, we can study the genetics and the history of the people who lived in those places, even if they didn't keep their dead people around in the caves also.

Kat: It seems kind of logical because I know in recent years there's been a lot of excitement about this idea of environmental DNA and people, you take soil and you look at what's in there and it's like, oh, yeah, there's going to be stuff in there from a long time ago, potentially. So, I mean, how long ago we're talking about and also what kind of DNA, what kinds of things are you looking for? Presumably when you scoop up some soil, take DNA out of it and then have a look.

Benjamin: Yeah. So you can go back pretty far. I mean, the oldest that we have from our lab is about two hundred and fifty thousand years old, but that's from Denisova Cave in Siberia, which has really good DNA preservation, even in bones and things like that. Other labs have gotten much older DNA even from permafrost cores. And at that point, those things have been frozen for seven hundred thousand years or five hundred thousand years, something like that. But no, the DNA preservation is sort of similar to what you would see in bone. So we can get things from Europe where it's harder to get things from Africa or the tropics. 

Kat: And what kind of DNA are you looking at? What sort of sequences can you find when you start to analyse this?

Benjamin: Yeah. So previously what we had done is looked at mitochondrial DNA, this is the DNA that you inherit just from your mother and from your grandmother and your great grandmother. And so it really only tells you about this one lineage going backwards in time. And for human history, it's actually not that helpful. It's not that informative to know about the mitochondrial DNA. I may have the same mitochondrial DNA as someone who I'm not even remotely related to. Right. And so what we did in this project is we move that to nuclear DNA, which is the rest of your genome, and that you inherit from both parents and all four grandparents and all eight great grandparents. So it represents the full tree going backwards. And by looking at the nuclear DNA, then you can really get a much richer picture of someone's ancestry.

Kat: So tell me about the most recent study that you did. Where were you looking and who were the people that you were digging their DNA up? 

Benjamin: Yeah. So since this was the first time we did this, we wanted to kind of have some verification that it would work. So we did it in three different caves. And for two of those, we actually already have DNA from bones from those caves. So we can compare the DNA we get from the sediments to the DNA from the bones and say, OK, this method works, right. We can actually replicate the same histories that we get from the bones in the sediments. And then, of course, where we want to do this is where there's no bones to be found and there are no Neanderthal bones. 

Benjamin: So we went to this cave in Spain where we know that Neanderthals lived for about fifty thousand years. So this huge time period, as long as Europeans have been in Europe. Right. Essentially. And yet there are no Neanderthal bones there. It's from a time period when there aren't really any bones from the surrounding area either. And so we just didn't know anything about these people who lived there. But we know that they made tools, et cetera, et cetera. And those are all in the cave. So we were able to get Neanderthal DNA from really the entire time period that these people lived there. And what we found may not sound so incredible because what we found is that there were not just one group of Neanderthals living there, but two groups of Neanderthals living there. 

Benjamin: But for me, it's really nice because we could really get DNA from essentially every few thousand years going all the way through this fifty thousand year period, we can really identify the precise time where the one population was replaced by the other population. You know, then we can look and say what else is going on in the world around at that time period? It sort of allows you a much finer resolution there

Kat: And what was going on. So there was a population and they went away, died out, got replaced? What can you tell about the dynamics of that situation there?

Benjamin: Yeah, so having sold it like that, I then have to follow up with; I don't really know. 

Kat: Yeah, you got to follow through.

Benjamin: I know. Yeah, but I think that at this time period there was there were big climate changes happening to the world was getting cooler. So it could have been that the previous Neanderthals died out because it was too cold or because the things that they hunted went away, moved away. It could have been that they just moved. We don't really know where they went, but we do know that shortly thereafter they were replaced by a newer group of Neanderthals. 

Benjamin: One thing that was interesting about this is that we saw a similar pattern happening across Europe. So we didn't just look at the Neanderthals that we got the DNA from the caves. We also looked at other Neanderthals. And we see at the same time period that the Neanderthals that are leaving or dying out or something's happening to them at this cave in Spain, that this is happening elsewhere in Europe and then they're being replaced by these younger Neanderthals. So it could be that what was happening in Spain is actually a more universal thing happening in Europe. 

Kat: What kind of level of granularity can you get in the analysis? Can you see family relationships? Can you distinguish individuals or is it a bit like, here's just kind of a mess of DNA and we can make some patterns within it?

Benjamin: It's kind of several of those things. So my expectation going in was one hundred percent that it was just going to be a mess of DNA. You know, I mean, if you think about it, you have groups of Neanderthals living in this cave, working in this cave. You're not going to expect to be able to identify individual people. Right? It's just going to be a mess of the DNA. So for my methods, that's actually OK, because we think about populations. So if we have DNA from a population, that's also OK. But actually several of the sediment samples really look like they only have one person in them. We can't be sure. Right. But we can say that they only have one type of mitochondrial DNA in it. So at least they have to be brothers and sisters or something like that, and that their DNA comes from people of one sex. Right. So all male, all the same mitochondrial DNA. I think the simplest explanation is that it comes from one individual, but it could have come from two brothers or a mother and daughter or something like that. 

Kat: It's incredible to think that just with this technique of scooping up a handful of dirt looking at DNA, you're potentially getting an insight into just a single individual that lived so long ago. I mean, how does it make you feel when you look at this data and start to imagine these people? 

Benjamin: Yeah, I mean, it's crazy. And for me, the thing that it really brings to mind is I wonder what happened. Right? I wonder why that DNA from that person is there. One of the big open questions is where the DNA comes from. We can imagine all sorts of ways that it might have accumulated from their skin cells. Maybe they spit on the ground. Maybe the baby pooped on the ground. Maybe they'd cut themselves and bled or something. But, you know, it would just be cool if we could tell what actually happened. Where did that DNA come from? Give it a little more personality. Right. 

Kat: So Neanderthals are one branch of our human ancestry. And then we've got other ones. We've got Denisovans and potentially kind of weird, shadowy ghosts in the human genome. So presumably this kind of technique we can then use to look at other places where ancient humans and the precursors of humans might have lived. 

Benjamin: Yeah, for sure. We're limited, as I said, to DNA preservation. So, for example, we know that the hobbit, this Homo floresiensis lived in Indonesia and that's a hot place. It's going to be really challenging to get DNA out of there. But one thing that's actually very nice about this is that it is you can imagine. So you have Homo floresiensis and there's just a few bones from this hobbit. And it may be sort of scientifically questionable or ethically questionable to drill those bones up and try to get DNA out of them because you don't have a very high expectation of success. 

Benjamin: Right. But it is totally fine to take some dirt and try to get DNA out of it. And so I think that not only will we be able to expand the locations and the places where we're able to look for our ancestors and look for our relatives, but we're going to be able to do so in maybe a bit more systematic way and not have to destroy those precious things in the process. 

Kat: It does seem to me that particularly in the past couple of years, this field of human origins from a field that's looking at basically individuals that died many, many, many thousands of years ago. It's an incredibly alive field and there seems to be new finds, new fossils, new DNA, new evidence coming out all the time. It's a very much living field. What have been some of the most exciting recent discoveries to you? We've seen the so-called Dragon Man going on, what's going on? What is the latest from the field of human origins?

Benjamin: Yeah, I mean, there's almost so much that it's hard to keep up with and my perspective is the DNA perspective and so many of the really cool things this year are actually new bones that I'm sure that people will then be trying to get DNA out of as well. But this Dragon man is really cool. I think that with the Dragon Man, I think this is a Denisovan. I'm pretty convinced that we have finally found a Denisovan skull and that the authors just didn't want to go out and say that without having very, very conclusive evidence for this.

Benjamin: We know very, very little about Denisovans but we know that they had a really large population and we know they didn't live in Europe, which sort of means they had to live in Asia. Right? Because there's not really many other places for them to live. We only have a few bones from Denisovans, a few very, very large molars. So we know that they had really large molars and we have one tiny piece of a skull cap and that skull cap is also really thick. So essentially, the only physical thing we know about them is that they had big teeth and a thick skull.

Kat: Chunky. 

Kat: Yeah. And that they lived in Asia. Right? And their bigger teeth and bigger skulls than humans or Neanderthals. And then we find, Chris Stringer and colleagues, find the skull in Asia that has huge molars and a thick skull. I mean, this is a Denisovan I think. Right? But one will have to get some protein or DNA from it to really try to figure that out. But now this is really, really awesome to have an actual skull from a Denisovan is great.

Kat: I find it so absolutely fascinating. I've been to a couple of conferences on human origins and genetics and it's like mind blowing the discoveries that we're making even very recently. So what's coming next for you? What's the next project you're trying to get your teeth into, the next bits of dirt that you're going to dig up in sequence? 

Benjamin: Well, I mean, there are so many places. One of the reasons that we started this is because there are so many caves where you just don't have any human remains. You see transitions between, say, Neanderthals and modern humans in Europe and Asia. And you don't know exactly when that happened. You see transitions and tool technology where the tools change and you don't know if it's that Neanderthals learn something new or Neanderthals died out and humans arrived with a new tool technology.

Benjamin: And if we knew even just the answer to that question, if we were able to say, in this cave, we see a change in the tool type and we see a DNA change that occurs with that, or we don't see a DNA change that occurs with that. Right? Let's say that you find that the new tools arrive and Neanderthals are still making them. I mean, then that means that Neanderthals learn from humans. Right? And that would be a huge find. So these are the sorts of questions that I really look forward to trying to answer.