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.

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