The woman may have been just a teenager when she died more than 50,000 years ago, too young to have left much of a mark on her world. But a piece of one of her bones, unearthed in a cave in Russia’s Denisova valley in 2012, may make her famous. Enough ancient DNA lingered within the 2-centimeter fragment to reveal her startling ancestry: She was the direct offspring of two different species of ancient humans—neither of them ours. An analysis of the woman’s genome, reported in this week’s issue of Nature, indicates her mother was Neanderthal and her father was Denisovan, the mysterious group of ancient humans discovered in the same Siberian cave in 2011. It is the most direct evidence yet that various ancient humans mated with each other and had offspring.
Based on other ancient genomes, researchers already had concluded that Denisovans, Neanderthals, and modern humans interbred in ice age Europe and Asia. The genes of both archaic human species are present in many people today. Other fossils found in the Siberian cave have shown that all three species lived there at different times. But the new finding “is sensational” just the same, says Johannes Krause, who studies ancient DNA at the Max Planck Institute for the Science of Human History in Jena, Germany. “Now we have the love child of two different hominin groups, found where members of both groups have been found. It’s quite a lot of things happening in one cave through time.”
Viviane Slon, a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who did the ancient DNA analysis, says when she saw the results, her first reaction was disbelief. Only after repeating the experiment several times were she and her Leipzig colleagues—Svante Pääbo, Fabrizio Mafessoni, and Benjamin Vernot—convinced. That a direct offspring of the two ancient humans was found among the first few fossil genomes recovered from the cave suggests, Pääbo says, “that when these groups met, they actually mixed quite freely with each other.”
The bone fragment’s characteristics suggested it came from someone who was at least 13 years old. After pulverizing small samples, extracting DNA, and sequencing it, Slon and her colleagues found that its owner was female, and that her genome matched that of Denisovans and Neanderthals in roughly equal measure. Moreover, the proportion of genes in which her chromosome pairs harbored different variants—so-called heterozygous alleles—was close to 50% across all chromosomes, suggesting the maternal and paternal chromosomes came directly from different groups. And her mitochondrial DNA, which is inherited maternally, was uniformly Neanderthal, so the researchers concluded she was a first-generation hybrid of a Denisovan man and Neanderthal woman. The evidence “is so direct, we almost caught them in the act,” Pääbo says.
A closer look at the genome suggests her father also had some Neanderthal ancestry, possibly several hundred generations back. And the woman’s Neanderthal genes are closer to those of a Neanderthal found in Croatia than those from remains found in the Siberian cave. That suggests distinct groups of Neanderthals migrated back and forth between western Europe and Siberia multiple times.
Along the way, apparently, they freely spread their genes to outsiders. That highlights the question, Krause says, of why Denisovans and Neanderthals nevertheless remained genetically distinct groups. “Why don’t they come together as one population if they come together from time to time?” Geographic barriers probably played a role, he says, but researchers need more fossils with ancient DNA, from multiple sites, to understand the true legacy of these prehistoric couplings.