A new analysis of a finger bone used to study the Denisovans – a mysterious group of ancient humans discovered in 2010 – offers clues to a decade-long mystery surrounding one the most important human fossils ever found.

The study describes a piece of the tip of a right-hand little finger that was separated from the rest of the finger bone after it was excavated 11 years ago. A digital reconstruction of the complete finger bone, or phalanx, reveals that the Denisovan’s fingers were far more similar to those of modern humans than previously thought.

“I’m happy that we could get something out,” says Eva-Maria Geigl, a palaeogeneticist at the Institute Jacques Monod in Paris, who led the study. “So far there was nothing, as if the phalanx was lost.”

Her team sequenced DNA from the missing fragment to show it matched the rest of the fingertip bone, and used photographs to digitally reunite the two pieces. The work was published on 4 September in Science Advances . ¹ .

“It’s not going to revolutionize our knowledge of Denisovan morphology, but it adds a little piece,” says Bence Viola, a palaeoanthropologist at the University of Toronto in Canada who was part of the team.

Denisovan discovery

The mystery surrounding the lost piece began in a remote valley at the foot of the Altai Mountains in southern Siberia, where Russian archaeologists excavating Denisova Cave discovered a finger bone belonging to an ancient group of humans in 2008. Anatoly Derevianko, who is an archaeologist at the Russian Academy of Sciences Institute of Archaeology and Ethnography in Novosibirsk and was leading the dig, decided to divide the little-finger bone and send the pieces to two labs to see whether DNA could be extracted from either half.

Svante Pääbo, an evolutionary geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, received one of the fragments. After his team sequenced its DNA and discovered that it belonged to a lineage distinct from modern humans or Neanderthals, Pääbo and several colleagues flew to Novosibirsk in January 2010.

That’s when Derevianko told Pääbo's team that he had divided the bone in two and sent the other half to Edward Rubin, a geneticist at Lawrence Berkeley Laboratory (LBL) in California, whose team had been competing with Paabo’s to sequence Neanderthal DNA.

“We freaked out a bit,” remembers Viola, who joined Pääbo on the trip. “We had no idea there was this second part.”

Worried about getting scooped, Pääbo's team raced to report their discovery. They published the fossil’s mitochondrial genome in March 2010 and, several months later, the first complete nuclear genome of a Denisovan . Their studies showed that Denisovans were a group of extinct hominins more closely related to Neanderthals than modern humans, and that they lived in the Siberian cave – and probably across Asia – more than 30,000 years ago.

The 2010 discovery transformed the cave into one of the world’s most important archaeological sites . Researchers have since found more ancient human bones in the cave, including the stunning discovery of a first-generation hybrid which had a Neanderthal mother and Denisovan father.

But Viola – who has analysed nearly every Denisovan fossil from the cave – says he never forgot about the second finger bone fragment. “I’ve been wondering the whole time what the other half would have looked like,” he says. "All I knew is that it was in Berkeley."

Revisiting old bones

According to Geigl, Rubin, who left LBL in 2016 for industry and could not be reached for comment, sent his half of the fossil to her lab in 2010. Pääbo's team had already published the fossil’s mitochondrial genome – a short stretch of maternally inherited DNA that harbours limited ancestry information. But Geigl hoped to obtain nuclear DNA from the fossil, which could indicate much more about its relationship to humans and Neanderthals.

Initial efforts to extract DNA from the bone failed, so Geigl’s team worked on developing other methods. But after Pääbo's team published the Denisovan nuclear genome, Rubin asked for the fossil to be sent back. Geigl returned the fragment in 2011, but was able to sample its DNA and take detailed photographs first.

Geigl sat on the data for years, but in 2016 she decided to publish them at the suggestion of Pääbo. Her team sequenced the mitochondrial genome of the sample and discovered – unsurprisingly – that it exactly matched the sequence Pääbo's team published in 2010. But a digital reconstruction of the complete finger bone held a surprise: its slim shape was more like those of modern humans than the stout fingers of Neanderthals, even though Denisovans and Neanderthals are closer relatives. The few other Denisovan remains that have been discovered, including large molar teeth, tend not to resemble those of modern humans.

“Given the limited skeletal remains definitively associated with Denisovans, this is an important discovery,” says Tracy Kivell, a palaeoanthropologist at the University of Kent, UK, who was not involved in the study. The slender shape of the Denisovan finger also suggests that Neanderthals’ burlier fingers may have evolved as a result of strenuous use of their hands, she adds.

While the story of the missing fragment has become clearer, its current whereabouts are still unknown. According to Derevianko, Rubin sent the sample to the ancient-DNA lab of Eske Willerslev at the University of Copenhagen and the Danish Museum of Natural History in 2011 or 2012. Willerlsev did not respond to requests for comment by Nature ’s news team.

Pääbo's team had to grind up their piece of the bone to produce a high-quality genome sequence, and Geigl is unsure if the half she analysed is also gone. “It’s like a Sherlock Holmes story,” she says.