Denny (Denisova 11): A Neanderthal-Denisovan Hybrid Child

Denny is the nickname of Denisova 11, a girl who lived in Siberia roughly 90,000 years ago and whose genome, published in 2018, showed that her mother was a Neanderthal and her father a Denisovan. She is known from a single fragment of bone about 2.5 centimetres long, found in Denisova Cave in the Altai Mountains of Russia. Denny was the first known first-generation child of two distinct groups of ancient humans, and she offered rare direct proof that such groups met and had families together.

Background: Denisova Cave and the Denisovans

Denisova Cave lies above the Anui River in the Altai Mountains of southern Siberia, close to where Russia meets Kazakhstan, Mongolia and China. Russian archaeologists have excavated its layers for decades, recovering stone tools, ornaments and many thousands of animal bones spanning several hundred thousand years.

In 2010 a team led by Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig sequenced DNA from a small finger bone found in the cave. The DNA did not match Neanderthals or modern humans. It belonged to a previously unknown population, named the Denisovans after the cave. Remains of Neanderthals were also found there, showing that both groups used the site at different times.

The cave is unusually good for preserving DNA because it is cold for much of the year. That made it possible to recover genetic material from fragments far too small for anatomists to identify.

Finding a hominin among bone scraps

The fragment that became Denisova 11 was excavated in 2012 from one of the cave’s deeper layers. Like most bone pieces from the site, it was broken and could not be recognised as human or animal by its shape.

In 2016 Samantha Brown, then a student working with Katerina Douka and Thomas Higham at the University of Oxford, screened about 2,000 unidentified bone fragments from the cave using collagen fingerprinting, a method known as ZooMS (Zooarchaeology by Mass Spectrometry). The technique reads small differences in the collagen protein preserved in bone, which vary between animal groups. Only one fragment produced a hominin signature: Denisova 11.

Mitochondrial DNA, which is inherited only from the mother, was then extracted and turned out to be Neanderthal. At that stage the researchers assumed the bone had simply belonged to a Neanderthal.

What the genome revealed

The Leipzig team, led by Viviane Slon and Svante Pääbo, went on to sequence the nuclear genome, which carries DNA from both parents. The results were published in the journal Nature on 22 August 2018.

At many positions in the genome, Denisova 11 carried one gene version typical of Neanderthals and one typical of Denisovans, in roughly equal proportions. This is the pattern expected in a first-generation hybrid, that is, the direct child of one parent from each group. Combined with the Neanderthal mitochondrial DNA, it showed that her mother was a Neanderthal and her father a Denisovan.

The thickness of the bone wall suggested she was at least 13 years old when she died. The genome showed she was female, and the researchers nicknamed her Denny.

The parents

The DNA held further surprises. Denny’s mother was more closely related to Neanderthals who lived later in Croatia, at Vindija Cave, than to an earlier Neanderthal known from Denisova Cave itself. This suggests that Neanderthal populations moved between western and eastern Eurasia over tens of thousands of years.

Her father’s Denisovan genome also contained traces of Neanderthal ancestry from an earlier mixing event, several hundred generations before. In other words, Denny was not an isolated case: contact between the two groups had happened more than once in the Altai region.

Significance

Before Denny, mixing between ancient human groups was inferred indirectly, from fragments of foreign DNA scattered through genomes many generations later. Studies had already shown that modern humans outside Africa carry Neanderthal DNA (see Neanderthal interbreeding), and that some living populations, especially in Oceania, carry Denisovan DNA.

Finding a first-generation hybrid among only a handful of ancient genomes sequenced at the time suggested that interbreeding may have been fairly common whenever these groups met. Pääbo, who received the Nobel Prize in Physiology or Medicine in 2022 for his work on ancient genomes, and his colleagues noted how unlikely it would be to find such a person by chance unless mixing happened often.

Denny also shows how much can be learned from tiny, unremarkable fragments. The combination of protein screening and DNA sequencing has since been used at other sites to identify human remains that would otherwise have been overlooked.

Myths and facts

• Myth: Denny proves Neanderthals and Denisovans were one species. The finding shows they could have fertile children, but they were genetically distinct populations that had been separated for hundreds of thousands of years. Their classification is still debated.
• Myth: scientists have Denny’s skeleton. Only one small piece of a long bone from an arm or leg survives. Her appearance is unknown.
• Fact: the bone was found before anyone knew what it was. It sat among animal bone scraps for several years before collagen screening identified it.

Timeline

• c. 90,000 years ago (range roughly 80,000 to 120,000): Denisova 11 lives and dies in the Altai region.
• 2010: DNA from a finger bone in Denisova Cave reveals the Denisovans.
• 2012: The bone fragment later called Denisova 11 is excavated.
• 2016: Collagen fingerprinting identifies it as hominin; mitochondrial DNA shows a Neanderthal mother.
• 22 August 2018: Nature publishes the genome showing a Neanderthal mother and Denisovan father.
• 2022: Svante Pääbo receives the Nobel Prize in Physiology or Medicine for his ancient-genome research.

Why it matters

Denny turned an abstract genetic inference into the story of a single person. She showed that Neanderthals and Denisovans met, formed families and raised children together in Siberia some 90,000 years ago, and she helped establish that the history of human populations was one of repeated contact and mixing rather than isolated lineages.