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Scientists use DNA methylation to determine what Denisovans looked like

By
Brooks Hays
A close-up of the 3D printed reconstruction of a female Denisovan, unveiled by Professor Liran Carmel, researcher at the Hebrew University in Jerusalem, at a press event on Thursday, Sept. 19, 2019. It is the first reconstruction of the Denisovan anatomy. Photo by Debbie Hill/UPI
A close-up of the 3D printed reconstruction of a female Denisovan, unveiled by Professor Liran Carmel, researcher at the Hebrew University in Jerusalem, at a press event on Thursday, Sept. 19, 2019. It is the first reconstruction of the Denisovan anatomy. Photo by Debbie Hill/UPI | License Photo

Sept. 19 (UPI) -- Scientists have, for the first time, determined what the archaic humans Denisovans looked like.

Research suggests Denisovans and Neanderthals evolved from a common ancestor. Both Neanderthals and Denisovans lived among and interbred with some groups of modern humans.

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Previous surveys suggest Denisovan DNA accounts for between three and five percent of the genome of Melanesians and Aboriginal Australians. The people of Papua New Guinea derive as much as six percent of their DNA from Denisovans. Research suggests Denisovan DNA helps Tibetans survive in high altitudes.

Despite their influence on the human genome, the appearance of Denisovans has remained a mystery, as very few complete Denisovan skulls have been found.

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To find out what the archaic humans looked like, scientists in Israel and the United States analyzed DNA methylation maps, comparing methylation patterns among humans, Neanderthals and Denisovans.

By first comparing the DNA methylation patterns among the three groups of humans, scientists were able to pinpoint the regions of genome that were differentially methylated.

When DNA experiences chemical modifications that affect the gene's expression, or activity, but not the base DNA coding, it is said to be methylated.

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After identifying differences in methylation in the human genome, researchers used what they know about genetic disorders to determine how the chemical modifications altered the functions of different genes -- specifically how methylated genes influenced anatomical features.

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"In doing so, 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," David Gokhman, currently a postdoctoral student at Stanford University, said in a news release.

Researchers tested the accuracy of their new methodology using modern humans and chimpanzees as their test models. The scientists found roughly 85 percent of their trait reconstructions were accurate.

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With the accuracy of their methods confirmed, scientists used the inferences from their DNA methylation analysis to reconstruct the anatomical profile of the Denisovan hominin. The results -- published Thursday in the journal Cell -- showed Denisovans shared anatomical traits with both Neanderthals and humans.

"One of the most exciting moments happened a few weeks after we sent our paper to peer-review," said Liran Carmel, a research professor at the Hebrew University of Jerusalem. "Scientists had discovered a Denisovan jawbone! We quickly compared this bone to our predictions and found that it matched perfectly. Without even planning on it, we received independent confirmation of our ability to reconstruct whole anatomical profiles using DNA that we extracted from a single fingertip."

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Like Neanderthals, Denisovans featured a sloping forehead, long face and large pelvis, and like humans, the mysterious hominins had a large dental arch and extra wide skull.

Scientists hope their anatomical reconstruction will help researchers determine whether the Denisovan's genetic and anatomical differences helped the archaic humans survive in cold climes and at high altitudes.

"There is still a long way to go to answer these questions but our study sheds light on how Denisovans adapted to their environment and highlights traits that are unique to modern humans and which separate us from these other, now extinct, human groups," Carmel said.

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