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Ancient human DNA found in Ice Age caves — even when bones were missing

The undated photo provided by the Max Planck Institute for Evolutionary Anthropology shows the entrance to the archaeological site of Vindija Cave, Croatia. Scientists say they have succeeded in extracting DNA of ancient humans from sediment in caves where no bones were found in what could provide vast amounts of genetic material for future research.
Johannes Krause, Max Planck Institute for Evolutionary Anthropology | AP
The undated photo provided by the Max Planck Institute for Evolutionary Anthropology shows the entrance to the archaeological site of Vindija Cave, Croatia. Scientists say they have succeeded in extracting DNA of ancient humans from sediment in caves where no bones were found in what could provide vast amounts of genetic material for future research.

Scientists found DNA from ancient humans in the soil of caves — even when there were no bones uncovered at the site. The research shows that, even when no fossils are around, sediments inside caves can tell us which early humans were present where and when. This information is key for understanding the evolution of our human ancestors.

The study, published today in Science, describes a highly sensitive technique for analyzing ancient DNA. The technique was used to study sediment from seven caves in Europe and Russia, dating between about 14,000 and 550,000 years ago. Among countless genetic fragments, the researchers were able to detect the DNA of Neanderthals and Denisovans, even when no bones were around.

"This approach is really the first to look specifically for human and hominin DNA directly in sediments. I think this is the novelty," says Beth Shapiro, a professor of ecology and evolutionary biology at UCSC, who did not take part in the study. "It opens up new possibilities for research in archaeology."

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To date, our understanding of how early humans, collectively called hominins, evolved is mostly based on the few fossils we have found scattered around the world. The skeletal remains are rare — sometimes there are just teeth or a pinky toe fragment — and so they provide a very limited picture of where and when our human ancestors lived. Our extinct kin include Neanderthals, who lived between about 400,000 to 40,000 years ago in Europe and parts of Asia; and Denisovans, who split off from Neanderthals some 380,000 years ago. Both were eventually replaced by Homo sapiens.

Scientists have long known that soil in caves is filled with valuable DNA. But ancient DNA is very fragmented, and until recently, the technology didn't really allow us to analyze this damaged genetic material and get very accurate results. The group that worked on today's study — including author Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology — have been at the forefront of recovering ancient DNA from poorly preserved specimens, Shapiro tells The Verge. Meyer is "one of the most creative people when it comes to thinking about methods for recovering ancient DNA," she says.

The technique described in the study was able to identify genetic material that belonged to hominins as well as a variety of animals such as the woolly mammoth and woolly rhino, both of which are extinct. "This is really a great study that kind of returns to this earlier question that was out of reach for so long, applying all these new methods," says Christina Warinner, an assistant professor of anthropology at the University of Oklahoma, who did not take part in the study. "It's really exciting."

The undated photo provided by the Max Planck Institute for Evolutionary Anthropology shows Becky Miller sampling sediment for genetic analyses at the archaeological site of Trou Al'Wesse, Belgium.
Monika V. Knul | Max Planck Institute for Evolutionary Anthropology | AP
The undated photo provided by the Max Planck Institute for Evolutionary Anthropology shows Becky Miller sampling sediment for genetic analyses at the archaeological site of Trou Al'Wesse, Belgium.

The researchers collected 85 sediment samples from seven caves in Europe and Russia dated to the Pleistocene. The caves were known to have housed early humans and other animals at some point; they either contained bones or stone tools. First, the researchers isolated DNA from the soil — and found that most of it belonged to bacteria, as expected. Only between 0.05 percent and 10 percent belonged to mammals — either animals or humans. They then used a method that allowed them to basically create custom baits to identify the exact DNA they were looking for. "It's kind of like creating very specific fishing lures," Shapiro says. The DNA you're looking for latches onto your bait and the rest washes out.

That's how the researchers were able to identify the DNA of several animals, as well as DNA belonging to Neanderthals and Denisovans. The Neanderthal DNA was found in four caves, including one in Belgium and one in Russia were no hominin bones were found at the site or in the sediment layers. "The beauty of this method is that it allows us to confirm who occupied a site with much less ambiguity than we had before, especially when you don't have any human bone remains," says study co-author John Stewart, an evolutionary paleoecologist at Bournemouth University in the UK.

The technique, obviously, isn't perfect. It doesn't allow us to directly date the DNA, for instance. One way around this is to date the soil where the DNA was found — by dating a fossil found in the same layer or by observing evidence of a volcanic eruption. That can give researchers a sense of when the hominins lived. However, DNA can move within sediments — although we don't really know how. "It's not something that's been studied very well," Warinner says.

Though the analysis lets scientists figure out whether the DNA came from one individual or several, it's not precise enough to let researchers figure out how many hominins are in the sample. And it doesn't really let researchers determine relationships, either, at least for now, says Johannes Krause, the director of the Max Planck Institute for the Science of Human History, who did not take part in the study.

Still, the technique opens up incredible opportunities for researchers. It creates a new way to determine whether an early human was present at a site even if we have no bones. That's important because it means that, say, a Neanderthal didn't have to necessarily die in a cave to leave a genetic footprint, Stewart says. It could have just peed or pooped there, leaving a genetic mark behind for paleontologists to pick up thousands of years later. "It takes us beyond the fossils, which is fantastic," says Keith Dobney, the head of department and chair of human paleoecology at the University of Liverpool, who was not involved in the research.

There are still a lot of questions about when Neanderthals went extinct and where exactly Denisovans lived, says Krause. Finding more remains — whether fossil or biochemical — is the only way we can answer those questions. And now we have a new method for doing just that.