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One tiny bone, from the finger of a child has provided the evidence for a previously unrecognised hominin. Oxford University Professor of Archaeological Science Tom Higham introduces us to the mysterious Denisovan.



Denisova Cave is in the Altai region, about halfway across Russia, and the Altai region is a really fascinating place. To get there, you fly into Novosibirsk, the biggest city in Siberia, and then you drive for about 11 hours.

And if you look at this picture, you’re looking down here at the camp of Denisova. So this is the camp down at the bottom here on the banks of the Anuy River, which is near where this site was discovered.

When the Russians first found the site in 1978, they had to get in there by helicopters and tramping. It was a really out of the way place, there were no roads, but in true Russian style, they’ve created not only a road but also a chalet-like camp that you can go and stay in.

Now the site itself is just along this river, about 250 metres away from the camp, and it consists of a large entrance hole and a smaller hole at the side. The site has been excavated since the mid-1980s. It’s more than 7 or 8 metres have been excavated down. And as you go into the main gallery here – this is a 3D reconstruction – on your right-hand side, down at the base of there is the main gallery, so just down where you’re looking at is the main area of the site. But the key stuff is to the right of this. And as you come into the so-called east gallery and you look down – this is about 7 or 8 metres down here – and you go down, just through here where these ladders are, this is where some of the key fossil evidence has been discovered that tells all about these interesting individuals called Denisovans.

In 2008, this tiny finger bone was excavated in the east gallery, which is we think 50,000 years plus. And this is the finger bone of an 8 or 9-year-old girl, and the phalanx is exceptionally well preserved in terms of DNA and collagen. And this is because the site of Denisova Cave has a very, very low temperature all year round. It’s rather like a fridge – it’s the perfect place for DNA preservation. And in fact, this finger bone had more than 70% of its DNA still in it endogenous. Most bones that are analysed in this period have less than 1%. Most of the DNA is bacterial and contaminating, but this bone had 70% endogenous. The bone only weighed 29 milligrams, but it produced a nuclear DNA sequence 99.9% extracted, done dozens of times to produce the same result. It’s a better genome than the Neanderthal genome that took so long to make just because of the preservation state.

So what does it tell us? So amazingly, when the DNA was analysed, it showed that this wasn’t a Neanderthal and it wasn’t a modern human, it was something else, this mysterious third hominin. And it was initially given the name Hominin X, but then later it was decided to name it Denisovan after the cave. But of course you can’t give it a formal species name on the basis of a tiny fragment like that because you have to describe the bones when you report a new species. But intriguingly, this individual sits outside Neanderthal and modern human DNA. So this is kind of a family tree. In the grey here, all modern humans outside and including Africa – all people – and then in the blue here at the bottom, Neanderthals – so we have a common ancestor 380 to 400,000 years ago – and then at the very bottom, this little Denisovan individual, which again shares a common ancestor a little bit before that, about a million years ago perhaps. So if we zoom down here, you can see Denisovans sitting just off our close cousins. So if you imagine how this might pan out, so we’re talking about an individual that is as far away from a Neanderthal as we are from a Neanderthal.

And intriguingly, of course, it was discovered in 2011 that the Denisovan individuals had interbred with modern humans as well, so that not only was there a Neanderthal interbreeding or gene flow event, but there was also gene flow from Denisovans into modern humans. And fascinatingly, the groups that we see in the modern world that have Denisovan DNA include people in eastern Asia, in Melanesia and in Australia.

This is the kind of summary diagram which gives you a kind of a rundown of the complex nature of what we’re now terming the leaky replacement model. So what you can see here are modern humans in the blue here and Denisovans here in the middle in yellow and Neanderthals over there. And this is a kind of a family tree of evolution. And you can see here that there are evidence for gene flow coming in these red arrows.

The picture is becoming extremely complicated but nonetheless very fascinating.

The Science Learning Hub would like to acknowledge:
Professor Tom Higham, University of Oxford
The Allan Wilson Centre for Molecular Ecology and Evolution
Photos of Denisova camp site and cave entrance, Professor Tom Higham, University of Oxford
Animated 3D model of Denisova Cave in the Altai Mountains, Trimetari Consulting, Saint-Petersburg, Russia
Denisovan finger bone, courtesy Max Planck Institute for Evolutionary Anthropology
Human family tree diagram, © The Trustees of the Natural History Museum, London
Figure showing human family tree with map, The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Johannes Krause, Qiaomei Fu, Jeffrey M Good, Bence Viola, Michael V Shunkov, Anatoli P Derevianko and Svante Pääbo. Nature, 464, 894-897 (8 April 2010). doi:10.1038/nature08976
Figure showing a possible model of gene flow events in the Late Pleistocene, The complete genome sequence of a Neanderthal from the Altai Mountains. Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer et al. Nature, 505, 43–49. 02 January 2014. doi:10.1038/nature12886