Ancient DNA reveals the first glimpse of what a Denisovan may have looked like

Scientists have painted a portrait of a young female who belonged to a mysterious, humanlike population known as Denisovans around 50,000 years ago.

Here’s the kicker: Only a handful of Denisovan fossils have been found, including the youngster’s pinky finger. So a team led by evolutionary geneticists David Gokhman and Liran Carmel of the Hebrew University of Jerusalem reconstructed the Denisovan teen’s skeleton using only a palette of ancient DNA patterns. A description of how the researchers transformed DNA into a physical appearance appears September 19 in Cell.

“This is the first reconstruction of the skeletal anatomy of Denisovans,” Carmel says.

A drawing based on that skeleton shows the Denisovan gazing ahead coolly with wide, dark eyes framing the bridge of a broad nose. That profile, and the rest of the girl’s appearance, was gleaned from key changes to parts of her DNA that regulate the activity of genes involved in skeletal development, the team says.  

Scientific reactions to the Denisovan girl’s genetically informed appearance range from cautious curiosity to outright skepticism. This is “a pioneering piece of research, which at first glance seems almost like science fiction,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. A final verdict on the accuracy of the ancient girl’s portrait awaits discoveries of more Denisovan skeletal parts, he adds.

Denisovans have posed an evolutionary enigma since the Siberian discovery of part of the ancient girl’s little finger in 2008 (SN: 8/30/12). Only a few other Denisovan fossils have been found — several teeth, a limb bone and a lower jaw (SN: 5/1/19). Ancient DNA analyses indicate that Denisovans, who inhabited parts of Asia from around 300,000 to 50,000 years ago, were more closely related to Neandertals than to Homo sapiens. Some present-day human populations carry small amounts of Denisovan ancestry.

Gokhman and Carmel’s group examined molecular markers of DNA methylation, a process that changes the activity of a segment of DNA without altering its chemical sequence (SN: 12/9/16). The researchers analyzed methylation patterns in DNA from the Denisovan girl, two Neandertals who lived around 50,000 years ago and five H. sapiens from between 45,000 and 7,500 years ago. Together with methylation data from 55 present-day humans and five chimpanzees, the team identified places in the genetic material where these species display methylation differences.

Previous studies of human skeletal disorders in which specific methylation genes lose their function helped the scientists estimate how methylation differences between species would affect particular bone shapes, such as making an upper leg longer or shorter. And, as a test of the technique, the researchers used the methylation patterns to identify known anatomical differences between Neandertal and chimp skeletons with at least 85 percent accuracy.

Methylation comparisons indicated that Denisovans likely shared many skeletal traits with their close Neandertal relatives, such as wide hips and a low forehead, the team found. Denisovan traits that likely evolved independently include wide dental arches and a broad braincase.  

Methylation-based predictions correctly identified many traits observed on the previously discovered Denisovan jaw, the researchers say. Two partial unidentified Homo braincases previously found in China, which date to between 130,000 and 100,000 years ago, also appear to display Denisovan features reported in the new study.

The team’s approach to reconstructing skeletons from methylation data shows promise, but much remains unknown about how DNA contributes to species differences, says evolutionary geneticist Pontus Skoglund of the Francis Crick Institute in London. “We don’t know exactly what it is in the genome that makes a chimpanzee a chimpanzee and a human a human.”

What’s more, the researchers didn’t account for complex ways in which skeletons of, say, Neandertals and H. sapiens differ, says paleoanthropologist John Hawks of the University of Wisconsin–Madison.

For instance, Gokhman and Carmel’s team assumes that Neandertals’ hip bones were larger in all ways than those of H. sapiens. Neandertal hip fossils tend to be especially wide, but include thinner pubic bones at the front of the pelvis than those observed in most people today, Hawks says. Complicated mixes of traits in the pelvis and other body parts raise doubts about the accuracy of the new methylation predictions, he contends.

So does a study posted February 19 at bioRxiv.org. DNA methylation patterns specific to five nonhuman primate species, including chimps and baboons, display generally weak links to differences in upper-leg bone shapes, reported a team led by evolutionary biologist Genevieve Housman, now at the University of Chicago.

Researchers have yet to evaluate whether methylation differences predict bone shapes in living people, Hawks says.