A single bone, a new history
In 2012, Russian archaeologists excavating Denisova Cave in Siberia's Altai Mountains found a bone fragment 2.5 cm long. Cataloged as Denisova 11, the piece of a long bone was initially unidentifiable among over 2,000 other fragments. Years later, a technique called Zooarchaeology by Mass Spectrometry (ZooMS) identified the bone's collagen as belonging to a hominin. Radiocarbon dating showed the individual, a girl nicknamed 'Denny', died approximately 90,000 years ago. The bone's thickness indicated she was at least 13 years old. The fragment was discovered in a section of the cave designated as layer 11. This archaeological layer also contains stone tools and decorative objects, including bone beads and pendants.
The bone was sent to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for genetic analysis. A team led by paleogeneticists Viviane Slon and Svante Pääbo sequenced its genome, a feat that would earn Pääbo the Nobel Prize in 2022 for his work on ancient DNA. The results were unexpected. The analysis of mitochondrial DNA (mtDNA), which is inherited from the mother, showed a Neanderthal lineage. The nuclear DNA, inherited from both parents, was a near-equal mix of Neanderthal and Denisovan. This made Denisova 11 the first and only known first-generation hybrid of two distinct archaic human groups.
Reading the genome
The genome of Denisova 11 shows at the lives of her ancestors. Her genetic makeup is direct evidence that Neanderthals and Denisovans interbred. While previous genetic studies of modern humans had suggested this, Denny is the physical proof. The analysis revealed her parentage and more. Her Denisovan father also carried some Neanderthal DNA from ancestors who lived 300 to 600 generations before him. This shows that interactions between the two groups happened on more than one occasion.
The genetic story of her mother is also complex. Her mother's DNA was more closely related to Neanderthals found thousands of miles away in Vindija Cave, Croatia, than to an older Neanderthal who had lived in Denisova Cave itself. This suggests that Neanderthal populations migrated east and west across Eurasia thousands of years before they disappeared. Denisova Cave is the only known location where Denisovans, Neanderthals, and early modern humans all lived, although not necessarily at the same time. The discovery of Denny in layer 11 confirms it was a place where these different human populations met.