Meet the Denisovans: High-tech gene analysis finally gives ancient humans a face
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ArchaeologyKin from 100,000 years ago

Meet the Denisovans: High-tech gene analysis finally gives ancient humans a face

Breakthrough Hebrew University methodology studies ancient DNA’s expression to determine physical characteristics of our extinct prehistoric relatives

Amanda Borschel-Dan is The Times of Israel's Jewish World and Archaeology editor.

  • Liran Carmel of the Hebrew University reveals a 3D printed model of the face of prehistoric human species Denisovan during a press conference at the Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
    Liran Carmel of the Hebrew University reveals a 3D printed model of the face of prehistoric human species Denisovan during a press conference at the Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
  • 3-D printed reconstruction of a female Denisovan. (Maayan Harel)
    3-D printed reconstruction of a female Denisovan. (Maayan Harel)
  • Liran Carmel of the Hebrew University speaks to the press before revealing a 3D printed model of the face of prehistoric human species Denisovan at Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
    Liran Carmel of the Hebrew University speaks to the press before revealing a 3D printed model of the face of prehistoric human species Denisovan at Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
  • Comparison of Modern Human Neanderthal and Denisovan Skulls (Maayan Harel)
    Comparison of Modern Human Neanderthal and Denisovan Skulls (Maayan Harel)
  • Liran Carmel of the Hebrew University reveals a 3D printed model of the face of prehistoric human species Denisovan during a press conference at the Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
    Liran Carmel of the Hebrew University reveals a 3D printed model of the face of prehistoric human species Denisovan during a press conference at the Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)
  • Anatomical Comparison of Modern Humans, Neanderthals, and Denisovan Skeletons (Maayan Harel)
    Anatomical Comparison of Modern Humans, Neanderthals, and Denisovan Skeletons (Maayan Harel)

A breakthrough Israeli method of genetic analysis finally gives a face to humanity’s “newest” ancient relative, the Denisovans.

Discovered in a Siberian cave in 2008, the Denisovans coexisted with Neanderthals and modern Homo sapiens some 100,000 years ago. However, unlike their Neanderthal relatives, the paucity of verified Denisovan remains — and their highly fragmented state — has until now made it impossible to create an anatomical picture of this early man.

A groundbreaking Israeli technique, published in the prestigious Cell journal this week, claims to finally lift the veil.

Using open-source sequencing of ancient Denisovan DNA taken from a single bone fragment, a team of researchers headed by Hebrew University’s Prof. Liran Carmel and Dr. David Gokhman says it has discovered a method of reconstructing what our long-ago relatives may have looked like. Professors Eran Meshorer from the Hebrew University, Yoel Rak from Tel Aviv University, and Tomas Marques-Bonet from Barcelona’s Institute of Evolutionary Biology (UPF-CSIC) also contributed to the study.

Liran Carmel of the Hebrew University reveals a 3D printed model of the face of prehistoric human species Denisovan during a press conference at the Hebrew University in Jerusalem on September 19, 2019. (MENAHEM KAHANA / AFP)

As unveiled at a Hebrew University of Jerusalem press conference on Thursday, the Denisovans looked a lot like us.

An early sketch done by artist Maayan Harel of the 13-year-old Denisovan girl. (Hebrew University)

Speaking over a soundtrack of a dozen cameras clicking, Carmel “introduced” the guest of honor: “This is a 13-year-old Denisovan girl who died in the cave, roughly 70,000 years ago, and left us her very tiny pinkie bone,” said Carmel, pointing to artist Maayan Harel’s colorful rendering.

After some 40 years of excavation in Siberia’s Anui River Valley, a cave located in the region’s Altai Mountains offered up its unexpected discovery in 2008: remains of a previously unknown form of ancient man. The cave, named after a hermit who once inhabited it named Denis, is located at a relatively low elevation of 700 meters, but within two minutes inside, you’d freeze, said Prof. Erella Hovers, a paleo-anthropologist at the Hebrew University Institute of Archaeology, who made the trip there in July 2018.

Hovers explained that until 55,000 years ago (when the Denisovans went extinct), the 270-square meter cave was inhabited on and off for some 250,000 years by several forms of humans, including Homo sapiens, Neanderthals and Denisovans — as well as hyenas and bears who clearly relished their bones.

Professor Erella Hovers, Paleo-Anthropologist at Hebrew University’s Institute of Archaeology at a press conference at the Hebrew University on September 19, 2019. (Amanda Borschel-Dan/Times of Israel)

After several of the cave’s human bone fragments underwent DNA analysis in Germany, it was discovered that one microscopic piece of bone was of a human who was neither Neanderthal nor Homo sapiens, but rather a new kind of human.

“It was the first time in the history of research that a taxon” — a taxonomic group — “was identified by DNA analysis,” said Hovers.

After that first tiny fragment of a pinkie finger, scant other clearly determined Denisovan bone fragments were discovered, including a few teeth and recently a jawbone in Tibet.

“There are very few remains, but we are very lucky because we live in the middle of a major revolution in genetics — the ancient DNA revolution,” said Carmel.

After isolation of the Denisovan DNA, it was found that traces are still found in some modern humans, including some six percent of aboriginal Australians, Malaysians and some other Southeast Asian populations. Likewise, Carmel said that Denisovan DNA may aid Inuits to adapt to extreme cold, and Tibetans to live in high altitudes.

Anatomical Comparison of Modern Humans, Neanderthals, and Denisovan Skeletons (Maayan Harel)

However, DNA analysis alone does not allow scientists to reconstruct physical characteristics, said Carmel, quipping that were DNA analysis alone able paint a person’s picture, police forensics units all over the world would have a much easier time apprehending suspects. Purely based on Denisovan DNA, scientists merely know that the people likely had moderate to dark hair, eyes, and skin, he said.

But then the stumped team of scientists kissed a proverbial frog.

When a frog becomes a Denisovan princess

As Carmel explained, a tadpole that evolves into a frog has identical DNA to that of the more evolved version of itself, but they appear to be two different organisms. One has gills and a tail; the other has four legs and can exist outside of water.

While the two creatures’ DNA is identical, the way it is expressed is different, explained Carmel. The expression is based on methylation or chemical changes that can activate or deactivate DNA.

Prof. Liran Carmel at a press conference at the Hebrew University on September 19, 2019. (Amanda Borschel-Dan/Times of Israel)

Essentially, the activation or deactivation of single genes can affect observable physical, phenotypic characteristics. To arrive at how a skeleton is influenced by the on-off methylation switch of certain genes, the team of scientists cross-checked physical characteristics with a database of single-gene diseases, said Carmel. Some monogenic disorders can point to changes in bone structure such as a small pelvis, he explained.

“We did this trick for all genes relevant to skeletal morphology and came up with a detailed anatomical prediction for how Denisovans look like,” said Carmel.

“We got 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 bone,” said Gokhman in a Hebrew University press release.

Comparison of Modern Human Neanderthal and Denisovan Skulls (Maayan Harel)

Over a three-year study, the team tested its methylation-based theory by drawing up physical characteristics of Neanderthals, Homo sapiens and chimpanzees based on their DNA’s methylation patterns. Based on the charted on-off switch of certain physical genetic characteristics, Carmel said the team’s predictions had an 85 percent accuracy.

The team then applied the methylation methodology to the Denisovans and found 56 anatomical traits which were different from modern humans and Neanderthals, 34 of which were in the skull, and probably included a longer dental arch and no chin.

The most striking characteristic, the Denisovans’ very wide skulls, made Carmel reexamine a mysterious recent find in China.

Portrait of a female Denisovan teen. (Maayan Harel)

In 2017, the archaeological world took notice when unusual 100,000-year old skulls were discovered in Xuchang, China. Carmel said that based on the methylation of the DNA, the projected Denisovan skulls would be a match for seven out of eight unique traits on those Chinese skulls.

“Our work suggests the Chinese skulls are Denisovans,” said Carmel.

“Denisovans and Neanderthals are our closest evolutionary relatives — they are humans,” said Carmel. “For people who study human evolution, we can make comparisons and see in what ways we are similar and in what ways we are different.”

The Hebrew University scientists can now use their DNA methylation maps to reconstruct an 85% accurate portrait of early man, said Carmel. But the police are still out of luck: Carmel said his methodology is not (yet) applicable to modern man.

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