Genetic analysis reveals how the Neanderthals went extinct

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0:41And it's fair to say really, isn't it, that we are obsessed with our extinct relatives? We are. Well, we're obsessed. We feel an affinity with especially the Neanderthals and the Denisovans, our close relatives. And it's not just that we carry some of their DNA with us, which we do, and we'll get into that. But it's the idea that not really that long ago there were other species of humans around. But that's the joy of this, of DNA work, that it brings what was out of reach into the realm of science and analysis. Yeah. And that's what we're getting into today on The World, the Universe and Astronauts of New Scientist.

1:17I'm Dr. Rowan Huber. And I'm Dr. Penny Sarchet. We're joined today by science writer Mike Marshall and news scientist staffer Ali George. Welcome to the pod. Let's start by talking about this new work. Mike, can you talk us through what we know about the decline of the Neanderthals and where and when this was exactly happening? So we knew that the Neanderthals went extinct around about 40 ,000 years ago. And what this new study sort of does is kind of fill in the gaps of what was happening in the last few tens of thousands of years of their existence. So the climate was cooling and faced with that, the Neanderthal population shrank and also sort of wound up being.

1:56and when I say shrank, I mean like geographically so, so they wind up confined to what's now southwest France. Not a bad place to be. Yeah, one of my favourites. Later on, the climate warmed up and the Neanderthals started roaming more widely again. But in that shrinkage of the population, a lot of their genetic diversity had been lost. So those widely dispersed groups that we see later all had quite similar DNA despite living hundreds of kilometres apart. And that's not a good thing for the survival of a species, is it, to have a very little genetic diversity? It's kind of the dreaded genetic bottleneck.

2:32Yeah, and any sort of conservation biologist today will tell you that that is a major risk factor. You know, if there's not many of you and you're all genetically kind of similar, then there can be harmful mutations accumulating and any kind of like little accident, any sort of little misfortune that befalls you can prove to be critical. Whereas if there were loads of you, maybe you'd absorb it. and so yeah the fact that the neanderthals were in these small and isolated groups that may well have been one of the factors that contributed to them disappearing uh 40 000 years ago so this is kind of uh you know the the end to a very long story because the neanderthals had lived in europe and asia in fact for hundreds of thousands of years and previous studies of their dna had sort of said oh yeah something had happened to them genetically towards the end so we knew that the late neanderthals and that's roughly those who lived after about 60 000 years ago were quite genetically similar to each other and they were quite different from those who came before that no one was quite sure exactly why and how that had happened so what some a team of geneticists did is to get mitochondrial dna from 10 neanderthals from sites scattered across europe you know belgium in the north, Serbia and the southeast.

3:49And they compared those 10 new genomes to 49 existing mitochondrial genomes, 49 that had already been read. What they could see was that the Neanderthals who lived between 60 ,000 and 40 ,000 years ago were all very genetically like. They seemed to belong to the same lineage, and this lineage had originated about 65 ,000 years ago. So if you looked at older neanderthals you could see you know lots of other genetic lineages lots of variety but all pretty much all of that had vanished so that sort of suggests that there's what had been what we call population turnover for some reason all those old genetic lineages had been uh sort of stripped from the population and there was just this one main one that was left so population turnover mike is that basically means that the populations just vanish it can mean like literally that some of these groups just died out.

4:42Sometimes this can also happen just through interbreeding. So if there's some genetic variants that prove to be advantageous for some reason, they might sort of sweep through a population and kind of replace all the old ones. But the fact that so much of the genetic diversity disappeared, that does suggest to me that at least some of these groups genuinely were dying out without leaving. There's a long tail, isn't there? The writing's been on the wall for the Neanderthals for a long time. if they lingered with this very low diversity for quite a long time, there was maybe no coming back from that.

5:16I think so. I mean, another way to look at it, of course, is that they were there for 400 ,000 years, which is longer than we've managed as a species. So in one respect, they were very successful. But I do think that there's some truth in that, that, yeah, there was always this lurking problem of the small and isolated populations. but it probably took some additional factors sort of coming in, like additional pressures to sort of finally push them over the edge. And so to understand this a bit more, the team have married some of their genetic data to archaeological data, haven't they, to sort of map it onto what we know from what we found?

5:53Yeah, that's right. So they sort of have this database of Neanderthal sites spanning tens of thousands of years, and what they can see is this geographical contraction. So Neanderthals previously are sort of found all over Europe, way into Asia as far as Siberia. But those sites have gradually become uninhabited. And the only ones that we see them living in sort of after about 75 ,000 years ago or so are in southern France or thereabouts. So, yeah, there's been this huge geographical contraction, which you can see in the archaeological record. And then a bit later on in the last 10 ,000 years or so of their history, you can again see them roaming a bit more widely, you know, out as far as Eastern Europe and so forth, but still quite isolated.

6:37So if we've got this picture then of, they were very successful, they were all over Europe, but gradually, you know, populations were replaced. And then we had the climate got a lot less nice. People got, Neanderthal people got pushed into this kind of refuge in southwestern France, genetic diversity shrunk, and that sort of set things in train for their extinction. What was happening to us homo sapiens at this time? Were we going through the same thing in Europe? Why are we still here? So some modern humans actually were in Europe at this time. So the big migration into Europe of modern humans sort of comes after about, from about 45 ,000 years ago, but there were some earlier groups that came in.

7:18And it does seem that a lot of the early ones didn't survive. So a few of them have had their ancient DNA sequence, so we can see what their genomes look like. And they don't seem to have contributed to later populations. There's no evidence of them having any sort of descendants passed on. Wow. So we were resupplied effectively by... Well, we had population turnover. Yeah, absolutely. And probably for quite similar reasons. So there's this one particular sort of modern human culture called the LRJ, which is found in Northern Europe around about this time. But again, they seem to have been very isolated.

7:57It seems to have been a very small population in terms of numbers, but yet they were living from Britain to Poland. So again, those have been pretty small groups that weren't in an awful lot of contact with each other. And again, vulnerable. This episode is brought to you by Welch's Fruit Snacks. Big news for your kids' lunchbox. Welch's Fruit Snacks are now made without any artificial dyes. A snack parents can feel good about and the same delicious taste kids can't get enough of. All made with no artificial dyes. Try Welch's Fruit Snacks today. Okay, let's bring Alison in now, Ali. Because I know you've got a favourite Neanderthal, Thorin, and Thorin, he bucks the trend that we've been talking about in terms of the sort of flatlined genetic diversity, doesn't he?

8:45Yes. So, yes, as you say, he's my favourite Neanderthal. So a bit of a background about him. His fossil remains were discovered at a remarkable site called Grotte Mandran, I think it's pronounced, in France in 2015. and he's named after the dwarf king of Tolkien's The Hobbit. Finding any Neanderthal remains is pretty exceptional and even more exceptional, the dating showed that Thorin was one of the last Neanderthals in that he was living around, say, 43 ,000 years ago, just before they went extinct. Even more remarkable, his genome could be sequenced and this showed that he was part of an extremely isolated group, an unknown lineage that had seemed to have lived in isolation for about 50 ,000 years.

9:37That's an extremely long time with no sort of breeding with other Neanderthal groups and the tools they used were different. So it really does suggest that this tribe somehow clung onto existence for an incredibly long time in really extreme isolation. And this is all outlined in a wonderful book called The Last Neanderthal by the paleoanthropologist called Ludovic Slimac, who is the person who discovered Thorin. So how then does this isolated population that Thorin was part of, how does that fit with this new study showing that the last Neanderthals emerged from this refuge population in the southwest of France after this cold snap?

10:20Was he and his group part of that refuge population? Thorin is the exception to the rule of all the other late Neanderthals in that his group didn't fit that pattern at all and they really were a separate lineage and so whilst all the other Neanderthals were having this population turnover Thorin's group pretty much carried on as they'd always done on their own, not mingling so the new study sort of emphasises what we already knew about the extreme, extreme isolation of Thorin's group Wow, they're a really grumpy bunch of dwarves that hid themselves away in the mountains. But why did they do? I mean, we can't speculate, but it does seem extreme, doesn't it?

11:04Like, almost hard to believe that there could be no intermixing. Yeah, well, actually, Ludwig Slimac, the paleoanthropologist I mentioned a few minutes ago, has some really interesting thoughts that relate to what Mike was saying about the earlier incursions of modern humans. he actually thought that seeing this other species maybe shocked them and made them sort of close down even more. And, I mean, let's face it, they've lived for at least 50 ,000 years in this isolation. It worked for them until it didn't, and it worked for them for a very long time. So maybe that's what they needed to do at the time and not mingling.

11:43I could be wrong here, but am I right in thinking that around this time, maybe earlier in Africa, there were diverse populations of Homo sapiens and they were interconnecting and breeding and moving all over. It's quite, is that an accurate picture? And it's quite extreme to think, well, the other picture in Europe was one of extreme isolation and it's quite a contrast, isn't it? Well, I suppose Thorin's group weren't necessarily representative of all the other Neanderthals who were mixing a bit more. But on the other hand, it was a vast area with not very many people in it. So mixing was much more difficult than in Africa.

12:20While we're talking about mixing, Mike, there has been some new stuff about interbreeding, hasn't there, that you've worked on. Tell us a bit about that. Yeah, that's right. So we know that modern humans and Neanderthals interbred and the big interbreeding seems to have been between about 50 ,000 and 43 ,000 years ago, somewhere loosely in the eastern Mediterranean. And the new finding is to do with, well, who's doing the mating? And genetic evidence suggests that it was usually the Neanderthals that were the fathers and the modern humans that were the mothers. There seems to have been some kind of sex bias in the way that the interbreeding was happening.

12:57And the reason that we suspect that is basically to do with the human X chromosome. So human females would have two X chromosomes and a human male would have an X and a Y. The human X chromosome has almost no Neanderthal DNA on it, despite all the interbreedings. So the other chromosomes, you can find bits and bobs of Neanderthal DNA sort of here and there because of this endocrine. But the X chromosome is weirdly devoid of it. And the researchers who looked at this basically drew up a list of reasons why that might have been. And they went through all of them one by one and sort of ended up putting crosses again and saying, no, this doesn't explain it.

13:34This doesn't make sense. It can't be that. and the only thing that they they found that could make sense was just a mating preference that for some reason one group or the other or both had a preference and we can't we can't we can't say if it was the neanderthal males that had a preference or the human females that had a preference or both or what but some kind of a preference there was non-random mating between them in that way as instead yeah instead of just random any old way which which is what you might expect but there it does seem to have been some kind of a pattern. Ali, do you have any other thoughts on Neanderthal genetics?

14:10Well, again, I think I'm going to say something which sort of goes against what Mike was saying because I was part of a story, I was talking to geneticists and I've come across evidence of a completely different mating habit. So in the last era of the Neanderthals, they were interbreeding with modern humans, we know that. But whilst there's signs of Neanderthal DNA in the modern humans from these recent interbreedings, there's no sign of the DNA going the other way, like the modern human DNA from recent interbreeding going into the late surviving Neanderthals that we've sequenced so far. So there's this largely one directional gene flow from Neanderthals to modern humans and not the other way around.

14:58So there's lots of reasons why that might be. and one of them that Ludovic Slimac thinks is that Neanderthal women were joining modern human groups but the reverse didn't happen so that doesn't really fit with what the pattern Mike was talking about so any thoughts Mike? Only like a mild skepticism about what I originally said so I said that the researchers sort of knocked said we don't think any of the other possible explanations for this hold up and i'm not entirely sure that they're right and when i certainly when i spoke to another geneticist from a different group she's she was sort of rocking her head from sort of side side going it could be but i'm not entirely convinced so it could be for example that there's um that some of the neanderthal dna just really didn't work on the human x chromosome that does sometimes happen and so it got selected against by evolution in which case that would be nothing to do with a mating preference, it's just a genetic and biochemical thing that's happening.

15:58And it is also true that in earlier episodes of interbreeding, there must have been human males involved because for one thing, the Neanderthal Y chromosome, the chromosome that's only found in males, got completely replaced by modern human Y chromosomes something like 200 ,000 years ago so clearly at some point um neanderthal females and modern human males were interbreeding so it may be that it's just a bit complicated but it does i think we can probably say it's not just like completely random like sort of 50 50 there does seem to be some patterns at work here i just think we don't quite understand what they are yeah i mean but the thing is that just remind ourselves how fast this whole field has moved.

16:42So it was only 2010 that we even sequenced the first Neanderthal genome. And now we're arguing about, you know, what, there's been 60-odd individuals sequenced. There'll be many more. When we get those, we'll start to maybe answer some of these questions or get a clearer picture. But the speed of what... And the things we're able to talk about now is incredible, isn't it? If you'd asked me any of these questions 10 years ago, I would just have thrown my hands up in absolute despair and said I haven't got the faintest clue. But it's actually possible to have a cogent, uncertain argument about it.

17:17Yeah. Actually, in 2011, I interviewed Svante Pabo, who led the Neanderthal Genome Sequencing Project, and he had some really interesting thoughts about all this. I went back and looked at the interview, and I quote him here. He said in 2011, just a year after the draft sequence of the Neanderthal genome was published, he said, we will be able to follow changes in the genome across time before and after glaciation to discover their population history. And within a blink of an eye, that's already happened. It's quite incredible. That must have sounded so far fetched back then, but he was right.

17:55Yeah. And also he's discovered the Denisovans from a little bone in a cave in Siberia. So the whole world opened up of all these undiscovered humans and things they did. And Ali, something I've always wondered about is the what if of what if they had survived until now alongside us. And you asked that to Parbo, didn't you? What did he say? Well, he said that if Neanderthal carried on for just 2 ,000 more generations, they would still be here with us, which is quite mind bending to think about. But he also sort of mused on what that might mean. He said, would they be living in suburbia or would they live in a zoo?

18:36Perhaps racism against Neanderthals would have been even worse than the racism we experience in the world today because they were quite different in appearance from us in some respects. or would having this is more optimistic would having another form of humans around have allowed us to have been more open minded and not make the enormous distinction that we make between say us and other animals today no one can know but it's really interesting to think about what do you think Rowan would we have fully interbred with them or would we have driven them out I'm not that optimistic about what would have happened I feel like they'd probably be if they were they may be living in a reserve you know like like i've been thinking about cheetahs have been talking because they went through a huge bottleneck and i think there was only maybe one pregnant female cheetah survived and all cheetahs we have today came from that one female um and that so their diversity was also and is also incredibly low and they only survive on reserve so maybe that's what would have happened to neanderthals that that even feels optimistic i don't even think they'd have survived I have a way worse opinion of the human species than Svante Pabo evidently does.

19:48The only thing is if they had managed to cling on in a really remote place, say in the Arctic or something, and made it through to today when hopefully we're a bit more enlightened, that's one optimistic way of looking at things. Thanks, we'll leave it there. Thanks to our guests Mike Marshall and Alison George, and thanks to you for watching and listening. Do give us a follow to get more of the content and we'll see you soon. Bye for now. Bye.

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