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15 Oct 2019 11:38
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  •   Home > News > International

    Genetic data allows scientists to reconstruct what a Denisovan may have looked like for the first time

    Scientists have used genetic data to reconstruct what an extinct group of ancient humans may have looked like.


    Part of a pinky finger bone, a lower jawbone and a few teeth.

    That's the entirety of the confirmed fossil record we have so far for the Denisovans, a group of ancient humans who were closely related to the Neanderthals.

    It's hardly enough to give us a picture of what these extinct hominids may have looked like, so instead scientists have turned to their genetic data for clues about their appearance.

    As they report in a paper published in Cell today, an Israeli-led team has produced a reconstruction of Denisovan skeletal anatomy based on information they've extracted from their DNA.

    The aim of the research was to gain insights into Denisovan traits that are currently not present in the fossil record – which is most of them, said study co-author Liran Carmel of the Hebrew University of Jerusalem, a computational biologist who studies human evolution.

    "We wanted to get a better idea of what these very elusive and mysterious humans looked like," Professor Carmel said.

    Who were the Denisovans?

    We first came across the Denisovans in 2008, when the aforementioned pinky bone, dated as being between 74,000 and 82,000 years old, was found in Denisova Cave in southern Siberia.

    Ancient DNA extracted from the tip of the bone showed it belonged to a previously undescribed group of hominids, more closely related to Neanderthals than modern humans.

    The ancestors of Neanderthals and Denisovans are thought to have split from our lineage between 520,000 and 630,000 years ago. The two groups are then thought to have diverged between 390,000 and 440,000 years ago.

    The DNA extracted from the finger bone allowed scientists to map the complete genome of the Denisovan in 2012.

    As further finds of Denisovan remains have proved elusive, Professor Carmel and his colleagues decided to use this genetic data to find out more about this mysterious human's anatomy.

    A glimpse back in time

    The research team wasn't looking at DNA sequences in the Denisovan genome, but rather analysing it to reconstruct epigenetic patterns in the ancient DNA, also known as DNA methylation data.

    You can think of methylation as basically like a post-it note on the DNA, said Bastien Llamas, a paleogeneticist from the University of Adelaide who was not involved in the study.

    "This is a signal for the cell to say '[At] this place, I can read the neighbouring gene, or not read the gene'."

    Or in other words, these chemical post-it notes tell the cell whether to turn the gene on (express it) or off (repress it), without making any changes to the underlying DNA sequence.

    While DNA sequences themselves will usually not change, your DNA methylation data is different for different cells in your body.

    "If you take like a bone cell and a blood cell and a brain cell, they have basically the same DNA," Dr Llamas said. "The information is exactly the same but those post-its are going to be different."

    Which is what makes those cells a bone cell, a blood cell and a brain cell respectively.

    Being able to reconstruct these epigenetic patterns in ancient DNA has provided us with a totally new layer of information about these ancient genomes, Professor Carmel said.

    "DNA methylation holds a lot of information about anatomical features," he said. "Probably now more than the DNA sequence itself."

    By comparing DNA methylation data of the three human groups – modern humans, Neanderthals and Denisovans – the researchers were able to identify regions in their genomes where there were differences.

    They then looked at what genes might be affected by these differences, and then cross-referenced this information with a database which links specific human genes with observable traits.

    So, what did the Denisovans look like?

    From their modelling, the researchers were able to make predictions about how the anatomy of the Denisovans was different from either modern humans or Neanderthals, and in what direction it differed.

    Unsurprisingly, Denisovans shared many similarities with their closest relations, the Neanderthals, including an elongated face and a wide pelvis.

    "But of course, the most exciting stuff is what ways they are unique or different from both modern humans and Neanderthals," Professor Carmel said.

    The Denisovans had a longer dental arch, and a much wider skull than both modern humans and Neanderthals.

    Their jaw was also more protruding that modern humans, Professor Carmel said.

    In total, the research team was able to predict 56 anatomical features that were different between Denisovans and either modern humans, Neanderthals or both.

    Differences between the craniums accounted for 34 of these features.

    Testing their predictions against other discoveries

    Professor Carmel and his team have been able to test their model against other fossil finds.

    A cranium of an unknown species discovered in Xuchang, China also had a very wide skull, prompting researchers to speculate if it was Denisovan.

    "We went to the paper and looked at the unique characteristics of these crania," Professor Carmel said.

    "There were eight such traits and we compared these traits to our predictions, and in seven of them we were correct."

    Another team recently reported the discovery of the first confirmed Denisovan jawbone, and Professor Carmel was able to test it against their model.

    Again, the model got the shape of the jawbone right in seven out of eight predictions.

    "It was exciting for us to test our predictions in real time," he said.

    Going from a completely unknown hominid to being able to predict what they looked like based on what genes were expressed or repressed in their genome was incredible work, said Dr Llamas.

    As well as satisfying our curiosity, it could help us better understand how Denisovans adapted to their environment, and how they evolved, he said.

    Professor Carmel agreed that extending the list of known differences between modern humans and Denisovans will not only help us answer more questions about them, but also in what ways we are different from them.

    However, he acknowledged it was not currently possible to fully test the accuracy of their Denisovan model.

    "This is a very unique situation in science because we offer a prediction that cannot be fully tested," Professor Carmel said.

    That is ... until more Denisovan remains are found.

    © 2019 ABC Australian Broadcasting Corporation. All rights reserved


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