Israeli reconstruction of ancient human face finalist for ‘Breakthrough of Year’

Israeli reconstruction of ancient human face finalist for ‘Breakthrough of Year’

Hebrew University researchers’ genetic analysis of Denisovans, cousins to Neanderthals, one of four ‘people’s choice’ finalists for recognition by prestigious Science magazine

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)

The prestigious scientific journal Science has announced Israeli scientists’ reconstruction of the face of an ancient Denisovan girl, cousin to modern humans and Neanderthals, as one of four finalists in the “people’s choice” category of its Breakthrough of the Year contest.

Twenty-three thousand voters picked the four finalists — new Ebola drugs, a technique that made a black hole “visible,” a new cystic fibrosis drug, and the Israeli genetic analysis technique that allowed us to “see” an ancient face from a different human subspecies.

“Denisovans, extinct cousins of Neanderthals, have been known only by scraps of fossils from a Russian cave in Siberia, yet their genetic traces are found in modern humans, especially in Melanesia and Australia,” the magazine’s contest web page says. “This year, scientists used a new protein method to identify a jaw bone from the Tibetan Plateau as Denisovan — the first physical trace outside Siberia — and another group used genetic data to reconstruct the face of a Denisovan girl.”

Voting closes at midnight Eastern time on Monday. On December 19 the journal will publicize its own breakthrough picks, as well as which of the four “people’s choice” finalists made the cut.

First 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.

Portrait of a female Denisovan teen. (Maayan Harel)

The groundbreaking Israeli technique mentioned by Science, which was first published in the prestigious journal Cell in mid-September, helped to finally lift the veil.

A team of researchers headed by Hebrew University’s Prof. Liran Carmel and Dr. David Gokhman discovered a method of reconstructing what our long-ago relatives may have looked like by using open-source sequencing of ancient Denisovan DNA taken from a single bone fragment. 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.

After some 40 years of excavation in Siberia’s Anui River Valley, scientists in 2008 discovered the remains of a previously unknown form of ancient human. At the time, only a microscopic bone fragment, which underwent DNA analysis in Germany together with the rest of the findings from the cave, turned out to be from a human who was neither Neanderthal nor Homo sapiens.

“It was the first time in the history of research that a taxon” — a taxonomic group — “was identified by DNA analysis,” according to Prof. Erella Hovers, a paleo-anthropologist at the Hebrew University Institute of Archaeology.

After that first tiny fragment, which was part of a pinkie finger, scant other clearly determined Denisovan bone fragments were discovered, including a few teeth and recently a jawbone in Tibet. But the DNA of the Denisovans is still around in modern humans, including some six percent of aboriginal Australians, Malaysians and some other Southeast Asian populations. It may be part of the remarkable genetic differences seen in Inuits and Tibetans that allows their bodies to better handle extreme cold and high altitudes, the Israeli researchers have said.

3-D printed reconstruction of a female Denisovan. (Maayan Harel)

According to Prof. Carmel, speaking at a September announcement of the findings, DNA analysis alone would not have allowed scientists to reconstruct physical characteristics of ancient humans, beyond vague information on their features, which included medium to dark hair, eyes, and skin.

Instead, the Israeli researchers had to reconstruct the ways those genes would express themselves in the living organism. As Carmel explained, a tadpole that grows into a frog has identical DNA to that of the adult 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 DNA is identical, the way it is expressed is different because of methylation, or chemical changes that can activate or deactivate DNA.

To arrive at how a skeleton is influenced by the methylation switch of certain genes, the team of scientists cross-checked physical characteristics with a database of single-gene diseases, as some “monogenic” disorders can point to changes in bone structure such as a small pelvis.

This undated photo provided by Bence Viola of the University of Toronto in August 2018 shows the valley above a cave where Denisovan fossils were found in the Altai Krai area of Russia. (Bence Viola/Department of Anthropology – University of Toronto/Max Planck Institute for Evolutionary Anthropology via AP)

Over a three-year study, the team tested its theory by drawing up physical characteristics of Neanderthals, Homo sapiens and chimpanzees based on their methylation patterns. Their predictions had an 85% 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, no chin and very wide skulls.

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

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