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.
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.’
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.