Excavation in the East Gallery of Denisova Cave, August 2010
The piece of bone was found in Siberia's Denisova cave

In a remarkable discovery of interbreeding between different types of ancient humans, scientists have found a 90,000-year-old bone fragment from a young woman who had a Neanderthal mother and a Denisovan father.

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig extracted and analysed DNA from the 2cm piece of long bone excavated at Denisova cave. The cave is a celebrated palaeontological site in the Altai Mountains southern Siberia, near the border with Kazakhstan and Mongolia, where extreme cold has helped genetic material within human remains to survive for tens of thousands of years.

To their astonishment, the DNA analysis showed a genome that came unambiguously from someone who was a first-generation Neanderthal-Denisovan hybrid. There was a substantial genetic gap between these two hominid groups whose evolutionary divergence began about 400,000 years ago. Their ancestral lineage had separated from Homo sapiens — ancestors of modern humans — 500,000 years ago.

“We knew from previous studies that Neanderthals and Denisovans must have occasionally had children together,” said Viviane Slon, an author of the study which is published in Nature. “But I never thought we would be so lucky as to find an actual offspring of the two groups.”

“When I first saw the results I was convinced that they had screwed something up in the lab,” said Svante Pääbo, senior author. But checking and rechecking convinced him and his team — and then Nature’s reviewers — that the conclusion was correct. The arrangement of chromosomes in the newly sequenced genome showed unambiguously that the DNA must have come from someone with a Neanderthal mother and a Denisovan father, rather than a population with a mixed Neanderthal-Denisovan ancestry.

Scientists extracted and analysed DNA from the 2cm piece of long bone

Neanderthals have been famous as a separate human type since their fossilised remains were first discovered in Germany in the mid-19th century. Scientists disagree about whether they should be regarded as a distinct species or just a sub-species of Homo sapiens. Denisovans, in contrast, were unknown until 2012 when researchers at the Max Planck Institute revealed their existence by analysing ancient DNA from a bone fragment and two teeth found in Denisova cave.

Six years later, “Denisovans are still known only from bone fragments and teeth from one cave in Siberia while Neanderthals are relatively well represented from fossils across western Eurasia”, said Chris Stringer, human origins specialist at the Natural History Museum in London.

But the genomic history of Denisovans is better known through DNA analysis, which shows that they tended to move eastward through Asia while Neanderthals spread west through Europe. Both groups interbred with each other and later with ancestral modern humans who came in from Africa and migrated across regions populated with these earlier inhabitants of Eurasia — and eventually became the only people on the planet.

Asians today have a small percentage of Denisovan DNA in their genome, while Europeans have a little Neanderthal DNA. In 2015 it turned out that an ancestral modern human who lived in Romania 40,000 years ago had a Neanderthal great-great-grandparent.

Further analysis of the hybrid hominid’s genome showed that her Denisovan father had at least one Neanderthal ancestor further back in his family tree.

Different human types “may not have had many opportunities to meet”, said Prof Pääbo. “But when they did, they must have mated frequently — much more so than we previously thought.”

“As we learn more about the genomes of other species of mammals and birds, it seems that many closely related ones do interbreed when they get the chance, as this has the benefit of increasing their genetic diversity,” added Prof Stringer. “Nevertheless, Neanderthals might have overlapped with the Denisovans . . . for over 300,000 years, so the fact that their lineages remained largely separate must indicate the existence of some geographic, genetic or behavioural barriers to more widespread mating through that time.”

The next step in the Leipzig team’s research will be to use the latest ultra-sensitive techniques for detecting DNA to analyse sediments from the floor of Denisova cave, to look for a pattern of Denisovan, Neanderthal and modern human occupation over the past 100,000 years.

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