Viviane Slon among Nature's annual Top Ten
Nature magazine includes Max Planck researcher in its list of top ten personalities that most influenced science in 2018
Starting with a tiny piece of bone, the French researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig discovered that the parents of a girl born about 90,000 years ago were a Neanderthal (mother) and Denisovan (father). This genetic information provides insights into the history of humankind.
When she first saw the results of the genetic analysis, paleogeneticist Viviane Slon could hardly believe it. 'What went wrong? Did I make a mistake?' she recalls thinking. 'Could I have accidentally mixed two samples together?'
The reason for her skepticism: if the findings were correct, the tiny bone belonged to a 13-year-old girl with mixed ancestry - a Neanderthal mother, and a Denisovan father. Scientists had long suspected that there had been intermingling between the two species. DNA traces of both lines had been found in both early humans and in people living today. But there had been no evidence of such an encounter.
Slon stuck with it. She took six more samples from other places on the bone and kept getting the same result: The tiny splinter contained almost the same proportion of Neanderthal and Denisovan DNA. Her article in “Nature” is now considered the first evidence of a direct descendent of these extinct human groups.
Early humans from the Denisovan cave
In 2012, her doctoral supervisor, Svante Pääbo, had decoded the entire Denisovan genome. In a cave in Siberia’s Altai mountains, the scientist had found a tiny fragment of a finger bone. The DNA sequences showed that the specimen was from a type of human that was previously unknown. Along with the Neanderthals, the Denisovans, named after the location of Pääbo’s find, are considered the nearest extinct relatives of modern humans.
Viviane Slon visited the cave for the first time during a symposium. She remembers the high ceilings of the three chambers well. 'It is beautiful there', she says. Before that, she had only seen photographs and drawings of the location, and she considered herself particularly fortunate to be able to see it with her own eyes: 'From eye level to the ground, where excavations were begun, it is easy to pick out various archaeological strata in the space of several metres.'
Analysis of the fossils from this cave showed that the Denisovans branched off from a common ancestor of the Neanderthals around 390,000 years ago. They are thought to have lived around 40,000 years ago at a time when the Neanderthals were slowly becoming extinct. But many questions about these mysterious prehistoric humans remain unanswered. 'How many of them were there? How similar were they to the Neanderthals or to modern humans?' asks Slon, like many other researchers. So far, few fossil remains of Denisovans have been found.
A sophisticated technology allows the collagen content of countless bone fragments to be analysed and fragments that come from humans to be distinguished from those that come from non-human mammals. Samantha Brown, a colleague of Slon’s, analysed hundreds of such bones from the Denisova cave until she finally identified one as hominin. Slon then extracted the DNA from the bone and discovered that the mitochondrial genome was within the Neanderthal variation. This genetic material is passed on only from a mother to her child. 'But this didn’t necessarily mean that this individual, whom we named ‘Denisova 11’ or ‘Denny’ for short, was a Neanderthal', Slon says.
A 'hybrid', a colleague suggested jokingly
In order to get a complete picture of the lineage, it was important to examine the genome in the cell nucleus. Nuclear DNA is inherited from both mother and father. That is why Slon checked to see whether Denny's DNA had more Neanderthal-like or Denisovan-like genetic variants. It turned out that the girl, who was about 13 years old, had almost the same share of each. 'I remember someone mentioning a ‘hybrid’ when I first reported the result in a group meeting. Off the cuff and almost jokingly – that’s how unlikely it seemed,' Slon says. Some of her colleagues laughed.
But the intuition proved correct. Intermingling of Neanderthals and Denisovans was probably more common than previously assumed. 'Only a handful of these early homini have been sequenced so far, and we have already found evidence of a first-generation offspring,' Slon says with pride. 'That’s a pretty high rate.'
What is fascinating about analysing genomes of mixed ancestry is what can be discovered about two populations by separating the Neanderthal portion from the Denisovan and comparing the result with the previously sequenced Neanderthal and Denisovan genomes. 'We expected Denny’s mother to be closely related to another Neanderthal from the cave,' Slon said. 'Instead, it turned out that she had closer genetic similarity to a Neanderthal who lived in Croatia.' The father also had ancestors who were Neanderthals.
There was migration even then
That is why paleogeneticists began to compile the results of multiple studies and trace the timelines of migration on a map. It quickly became clear that Neanderthals, at least at one point in their history, moved thousands of kilometres between eastern and western Eurasia.
There is still much to be discovered, and methods are becoming increasingly sophisticated. Slon is currently working with other bone fragments from the Denisova cave and sediments from other excavation sites. Although there are many prehistoric excavation sites in Europe and Asia containing tools and other objects ancient humans used, skeletal remains are exceedingly rare.
A team of scientists in Leipzig headed by Matthias Meyer and Viviane Slon have therefore been searching for new ways to acquire prehistoric human DNA. From sediment samples from seven archaeological excavation sites, they have sifted out tiny DNA fragments of various mammal types – including our extinct human relatives. In cave sediments from four excavation sites, the researchers have also found Neanderthal DNA, even in layers and excavation sites where no bones have been discovered. And in sediments for the Denisova cave in Russia, they have found genetic material from Denisovans. 'These new insights will enable us to discover who the previous inhabitants of many archaeological excavation sites were,' Slon says.
The recognition from Nature magazine marks what has so far been the high point for Viviane Slon and her painstaking detective work. 'I am very happy to have received this honour, which motivates me to continue to do research in this field,' Slon says.