A pinky finger bone, some teeth, and a lower jaw. That’s all the physical evidence we have of the mysterious Denisovans, an extinct group of hominins closely related to the Neanderthals. Remarkable new research offers a physical reconstruction of the Denisovans based on genetic evidence, providing our first potential glimpse of this ancient human species.
A paper published Thursday in Cell has accomplished the seemingly impossible: a reconstruction of Denisovan anatomy using genetic information. The new work, co-authored by archaeogeneticists Liran Carmel and David Gokhman from the Hebrew University of Jerusalem, suggests the Denisovans possessed several distinguishing physical characteristics that set them apart from both Neanderthals and anatomically modern humans, including a broad, projecting face, an exceptionally weak chin, and wide hips.
“The paper by Gokhman and colleagues is a pioneering piece of research, which at first glance seems almost like science fiction,” Chris Stringer, a physical anthropologist from the Natural History Museum in London who wasn’t involved with the new research, wrote in an email to Gizmodo. “This is exciting work, pushing the boundaries of what can be gleaned from ancient genomes.”
Science fiction is right. Very little is known about Denisovan anatomy owing to the paltry amount of available physical evidence.
The first confirmed fossil of the species, an 80,000-year-old pinky finger bone fragment, was found in Siberia’s Denisova Cave in 2010. Aside from that, scientists have uncovered some molars and a 160,000-year-old mandible.
That’s obviously not much to work with in terms of reconstructing a full anatomy, but these fossils showed that Denisovans had molars unlike those found in Neanderthals or modern humans (specifically differences in size and the shape of cusps and roots), their jawbones were robust, protruding and with no apparent chin, and the shape of their fingers was startlingly similar to ours (an observation that suggests Neanderthals evolved distinctive fingers, while modern humans and Denisovans retained their fingers from a common ancestor).
Mercifully, the finger bone fragment, which belonged to an adolescent Denisovan female who was around 13.5 years old when she died, yielded some precious DNA, allowing scientists to confirm the Denisovans as a distinct species, though one closely related to the Neanderthals.
As the story goes, modern humans and Neanderthals branched off from a common ancestor about 800,000 years ago, and later the Denisovans branched off from the Neanderthals between 390,000 and 440,000 years ago, which is why they’re referred to as a sister species to the Neanderthals. To be clear, all three of these hominin groups belong to the Homo genus, so technically they’re all humans.
Not surprisingly, therefore, the new Denisovan reconstruction includes some very Neanderthal-like features, including the long face and wide pelvis. But the Denisovans followed their own evolutionary path after breaking away from the Neanderthals, exhibiting a longer dental arch (the horseshoe-shaped arch to which our teeth are attached), and a wider skull.
Going into the project, the HUJ researchers thought it highly likely that Denisovans would resemble Neanderthals more than modern humans, but the team was “particularly excited to find those anatomical traits where Denisovans differed from both modern humans and Neanderthals,” Carmel told Gizmodo in an email.
To reconstruct the young Denisovan female, the researchers took the DNA extracted from her pinky finger, along with DNA from two Neanderthals, many modern humans (both ancient and present-day), and chimpanzees, allowing for a robust comparative analysis involving dozens of samples. To discern distinct anatomical features, the researchers used a genetic technique known as DNA methylation mapping — a process that required three years of “intense work,” said Carmel.
“DNA methylation refers to chemical modifications that affect a gene’s activity but not its underlying DNA sequence,” explained Carmel. The HUJ team “first compared DNA methylation patterns among the three human groups to find regions in the genome that were differentially methylated.” Next, they looked for “evidence about what those differences might mean for anatomical features — based on what’s known about human disorders in which those same genes lose their function,” he said.
“By doing so, we can get a prediction as to what skeletal parts are affected by differential regulation of each gene and in what direction that skeletal part would change — for example, a longer or shorter femur,” explained Gokhman in a press release.
Explaining the technique to Gizmodo, Stringer said the observed methylation patterns were “translated into predictions of how those patterns would affect certain developmental pathways, using genetically linked abnormalities in modern human anatomy as a check on the areas of the body affected, and where possible, the direction of change compared with the norm.”
In total, 56 anatomical features were flagged as being distinctly Denisovan. To evaluate the accuracy of their technique, the researchers also reconstructed the anatomy of a chimpanzee and a Neanderthal, which was then compared to their known anatomy. Incredibly, the researchers achieved 85 per cent accuracy, which is the same level of confidence they attribute to the Denisovan reconstruction. As a positive sign it works, the reconstruction matched the Denisovan mandible almost perfectly.
When asked if a Denisovan individual would stick out if they were to walk around in public today, Carmel wrote, “This is a question that I ask myself too ????! But I think they would.”
To create the portrait of the Denisovan teenager, Carmel hired scientific illustrator Maayan Harel. Working with the researchers, Harel helped them to build a 3D skull, which in turn allowed her to create the final image, which is a bit goosebump-inducing.
Stringer said these results suggest that Denisovans should have features such as a low braincase, a wide pelvis, large joint surfaces, and a big ribcage. That said, “our knowledge of real Denisovan anatomy is very limited,” he said.
Indeed, the new reconstruction, while undoubtedly mind-blowing, contains several important limitations and caveats.
In addition to the 85 per cent accuracy level (which is admittedly not too shabby), Carmel said his team wasn’t able to pinpoint the direction of change, that is, to predict whether or not the distinguishing traits were retained from a common ancestor or newly acquired.
In addition, and as Stringer explained, the research relies on a “complex chain of extrapolations, the validity of which others will have to judge,” he told Gizmodo. That said, a nice part of this research is that the results are “fully falsifiable by future discoveries,” he added.
“One more caveat is that genetic data from fossil and modern genomes suggest that Denisovans had a deep evolutionary history, with the development of considerable genetic variation across their reconstructed range in eastern and south eastern Asia,” said Stringer. “In reality, their anatomy is likely to have shown substantial variation through space and time.”
Which is an excellent point.
Take the Denisovan pinky finger bone and mandible, for example, which are separated by a whopping 80,000 years of evolution, not to mention nearly 1,800 kilometres, which is the distance between Denisova Cave and the Tibetan Plateau, where the jawbone was found. Complicating the picture even further is the realisation that some Denisovans interbred with Neanderthals, as evidenced by a 90,000-year-old fossil found in Denisova cave belonging to a female with a Neanderthal mother and a Denisovan father.
It’s conceivable that some Denisovans did not interbreed with Neanderthals, contributing to considerable diversity among these hominins. And just to complicate the picture even further, genetic evidence suggests Denisovans interbred with both modern humans and a yet-to-be-identified hominin species.
Still, the new reconstruction can be taken as a single snapshot of the Denisovans, and how they — or at least this one girl — may have appeared some 80,000 years ago. The mind boggles at what scientists are now capable of doing with DNA.