Ancient DNA reveals what our prehistoric relatives Denisovans looked like


For the first time, scientists have reconstructed the face of Denisovans who lived alongside humans – and even interbred with them – some 100,000 years ago, before they went extinct. 

The reconstructions are the first glimpse into what our elusive relatives actually looked like, given that everything we know about Denisovans comes from a single pinky bone, three teeth, and one lower jaw, found only in two caves in Asia.  

Now, Israeli researchers have developed a new method of reconstructing fossils based on ancient DNA, and have used it to reveal the looks of our long-lost relatives.

They extracted the DNA from the little finger of a woman, who lived between 74 and 82 thousand years ago. 

‘We provide the first reconstruction of the skeletal anatomy of Denisovans,’ says author Liran Carmel of the Hebrew University of Jerusalem. 

‘In many ways, Denisovans resembled Neanderthals, but in some traits, they resembled us, and in others they were unique.’

The first reconstruction of what ancient Denisovans looked like show that they resembled both humans and Neanderthals, but that they also had some unique features, such as a large dental arch and very wide skulls. This pictured reconstruction is of a juvenile female Denisovan who lived sometime between 82,000 and 74,000 years ago

The first reconstruction of what ancient Denisovans looked like show that they resembled both humans and Neanderthals, but that they also had some unique features, such as a large dental arch and very wide skulls. This pictured reconstruction is of a juvenile female Denisovan who lived sometime between 82,000 and 74,000 years ago

This is one of the first reconstructions of what our ancient relatives Denisovans looked like (pictured)

Neanderthals (pictured) were closely related to Denisovans, both of them are now extinct

The researchers identified 56 anatomical features in which Denisovans (left) differed from modern humans and/or Neanderthals (right), 34 of them in the skull. For example, Denisovans had wider skulls and longer jaws than Neanderthals

Denisovans are more related to Neanderthals than they are to humans. So, the team expected them to resemble Neanderthals.

The new reconstructions, based on DNA from a finger bone of a juvenile female who lived sometime between 82,000 and 74,000 years ago, now show Denisovans did indeed resemble Neanderthals, but they also shared features with humans.

And in some aspects, they were unique. For example, they had a large dental arch and very wide skulls.

‘We were particularly excited to find those anatomical traits where Denisovans differed from both modern humans and Neanderthals,’ Carmel told MailOnline.    

Overall, the researchers who reported their findings in the journal Cell, identified 56 anatomical features in which Denisovans differed from modern humans or Neanderthals, 34 of them in the skull. 

To do so, they’ve used chemical modifications that influence gene activity without changing the underlying genetic sequence of As, Gs, Ts, and Cs, the so called DNA methylation.

The researchers first compared DNA methylation patterns between the three hominin groups to find regions in the genome that were differentially methylated. 

Next, they looked for what those differences might mean for anatomical features based on what’s known about human disorders in which those same genes lose their function.

Earlier this year archaeologists discovered the first evidence of Denisovans - the ancient human ancestor that bred with humans - outside their small Siberian cave. Half a mandible - the jaw bone - found in a cave in China proved the extinct race populated the Tibetan Plateau around 160,000 years ago

Earlier this year archaeologists discovered the first evidence of Denisovans – the ancient human ancestor that bred with humans – outside their small Siberian cave. Half a mandible – the jaw bone – found in a cave in China proved the extinct race populated the Tibetan Plateau around 160,000 years ago

Between 300,000 and 100,000 years ago tens of thousands of Neanderthals and Denisovans lived in fragmented populations scattered around Europe and Asia

Between 300,000 and 100,000 years ago tens of thousands of Neanderthals and Denisovans lived in fragmented populations scattered around Europe and Asia

‘By doing so, we can get a prediction as to what skeletal parts are affected by differential regulation of each gene and in what direction that skeletal part would change – for example, a longer or shorter femur,’ Gokhman says.

To test the method, the researchers first applied it to two species whose anatomy is known: the Neanderthal and the chimpanzee. They found that roughly 85% of the trait reconstructions were accurate in predicting which traits diverged and in which direction they diverged.   

The findings show that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record. The approach may ultimately have a wide range of potential applications.

‘Studying Denisovan anatomy can teach us about human adaptation, evolutionary constraints, development, gene-environment interactions, and disease dynamics,’ Carmel says. ‘At a more general level, this work is a step towards being able to infer an individual’s anatomy based on their DNA.’ 

Both Denisovans and Neanderthals are thought to have interbred with humans, and some of us still carry their genes. 

‘Denisovan DNA exists to this day in people of the pacific, Australia and East Asia – it can teach about how these admixture events affected modern humans,’ Liran told MailOnline.

‘We already know that these Denisovan DNA regions helped Tibetans to adapt to high altitude, and possibly Inuits to adapt to life in the arctic. There is definitely a lot more to be discovered with regard to how Denisovans shaped modern humans,’ Liran said.

WHO WERE THE DENISOVANS?

Who were they?

The Denisovans are an extinct species of human that appear to have lived in Siberia and even down as far as southeast Asia.

Although remains of these mysterious early humans have only been discovered at one site – the Denisova Cave in the Altai Mountains in Siberia, DNA analysis has shown they were widespread.

Scientists were able to analyse DNA from a tooth and from a finger bone excavated in the Denisova cave in southern Siberia.

The discovery was described as ‘nothing short of sensational.’

The individuals belonged to a genetically distinct group of humans that were distantly related to Neanderthals but even more distantly related to us.

How widespread were they?

Researchers are now beginning to find out just how big a part they played in our history. 

DNA from these early humans has been found in the genomes of modern humans over a wide area of Asia, suggesting they once covered a vast range.

They are thought to have been a sister species of the Neanderthals, who lived in western Asia and Europe at around the same time.

The two species appear to have separated from a common ancestor around 200,000 years ago, while they split from the modern human Homo sapien lineage around 600,000 years ago.

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Last year researchers even claimed they could have been the first to reach Australia.

Aboriginal people in Australia contain both Neanderthal DNA, as do most humans, and Denisovan DNA.

This latter genetic trace is present in Aboriginal people at the present day in much greater quantities than any other people around the world.

 How advanced were they?

Bone and ivory beads found in the Denisova Cave were discovered in the same sediment layers as the Denisovan fossils, leading to suggestions they had sophisticated tools and jewellery.

Professor Chris Stringer, an anthropologist at the Natural History Museum in London, said: ‘Layer 11 in the cave contained a Denisovan girl’s fingerbone near the bottom but worked bone and ivory artefacts higher up, suggesting that the Denisovans could have made the kind of tools normally associated with modern humans.

‘However, direct dating work by the Oxford Radiocarbon Unit reported at the ESHE meeting suggests the Denisovan fossil is more than 50,000 years old, while the oldest ‘advanced’ artefacts are about 45,000 years old, a date which matches the appearance of modern humans elsewhere in Siberia.’

Did they breed with other species?

Yes. Today, around 5 per cent of the DNA of some Australasians – particularly people from Papua New Guinea – is Denisovans.

Now, researchers have found two distinct modern human genomes – one from Oceania and another from East Asia – both have distinct Denisovan ancestry.

The genomes are also completely different, suggesting there were at least two separate waves of prehistoric intermingling between 200,000 and 50,000 years ago.

Researchers already knew people living today on islands in the South Pacific have Denisovan ancestry.

But what they did not expect to find was individuals from East Asia carry a uniquely different type.

 

 



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