DNA from an unknown ancestor of humans is in people today

DNA from an unknown ancient ancestor of humans that once bred with Denisovans still exists among people today, study reveals

  • Researchers from the US developed a new tool to analyse ancient DNA
  • Three per cent of the Neanderthal genome can from an ancient human group
  • This genetic transfer is thought to have occurred some 300,000 years ago
  • Also, one per cent of the Denisovan genome came from an unknown species
  • This ancient ancestor of humans may have been Homo Erectus, the team think 

DNA from an unknown ancient ancestor of humans that once bred with Denisovans still exists among the genomes of people today, a study has revealed. 

The different branches of the human family tree have interbred and swapped genes — a processes known as ‘introgression’ — on numerous occasions.

DNA sequencing of Neanderthals and Denisovans have provided insights into the nature of the interbreeding events and the moment of ancient humans. 

For example, around 50,000 years ago, a group of humans migrated out of Africa to Eurasia, where they interbred with Neanderthals and swapped DNA fragments.

Experts from the US found that some three per cent of the Neanderthal genome came from interbreeding with another ancient human group 300,000 years ago.

DNA from an unknown human ancestor that bred with Denisovans some 300,000 years ago still exists among the genomes of people today, a study has revealed (stock image)

In their paper, computational biologist Adam Siepel of the Cold Spring Harbor Laboratory and colleagues developed a special algorithm for analysing genomes.

This software can identify segments of DNA that originated form other species — even in cases where the gene flow was minimal, took place thousands of years ago and came from an unknown or unclear source.

The work is exciting, Professor Siepel said, as ‘it demonstrates what you can learn about deep human history by jointly reconstructing the full evolutionary history of a collection of sequences from modern humans and archaic hominins.’

The researchers used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans.

Alongside finding that a small proportion of the Neanderthal genome came from ancient humans, the team also determined that one per cent of the Denisovan genome appears to have come from an unknown and more distant species.

Moreover, up to 15 per cent of this ‘super-archaic’ genetic material has likely been passed down into modern humans who are alive today, the researchers said.

While it is not clear exactly from which species these fragments of DNA originated, the team suspect that they may have come from Homo Erectus, an ancient hominin species that first emerged around two million years ago.

‘This new algorithm that Melissa has developed — ARGweaver-D — is able to reach back further in time than any other computational method I’ve seen,’ commented Professor Siepel.

‘It seems to be especially powerful for detecting ancient introgression.’

 Alongside finding that a small proportion of the Neanderthal genome (red) came from ancient humans, the team also determined that one per cent of the Denisovan genome (blue) appears to have come from an unknown and more distant species (orange). Moreover, up to 15 per cent of this ‘super-archaic’ genetic material has likely been passed down into modern humans who are alive today (green), the researchers said

The findings add to the many previously known cases of gene flow between ancient humans and their relatives.

Moreover, given the number of introgression events, it seems likely that interbreeding occurred whenever two groups overlapped in time and space, the researchers commented.

The ARGweaver-D algorithm may also prove a useful tool to study other species which have undergone significant interbreeding episodes — such as occurs among wolves and dogs.

The full findings of the study were published in the journal PLOS Genetics.

WHO WERE THE DENISOVANS?

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.

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.

DNA analysis of a fragment of pinky finger bone in 2010, (pictured) which belonged to a young girl, revealed the Denisovans were a species related to, but different from, Neanderthals.

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. 

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.

DNA analysis of a fragment of a fifth digit finger bone in 2010, which belonged to a young girl, revealed they were a species related to, but different from, Neanderthals.

Later genetic studies suggested that the ancient human species split away from the Neanderthals sometime between 470,000 and 190,000 years ago. 

Anthropologists have since puzzled over whether the cave had been a temporary shelter for a group of these Denisovans or it had formed a more permanent settlement.

DNA from molar teeth belonging to two other individuals, one adult male and one young female, showed they died in the cave at least 65,000 years earlier.

Other tests have suggested the tooth of the young female could be as old as 170,000 years.

A third molar is thought to have belonged to an adult male who died around 7,500 years before the girl whose pinky was discovered.

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