Long After Their Bones Were Gone, Neanderthals' DNA Survived in a Cave
Scientists found DNA related to the extinct human lineage called Denisovans in Denisova Cave in Siberia. Here, Richard (Bert) Roberts, Vladimir Ulianov and Maxim Kozlikin (clockwise from top) plan the sampling of sediments in the cave's east chamber.
Credit: IAET SB RAS/Sergei Zelensky

DNA from two extinct human relatives — the Neanderthals, and a mysterious branch of humanity called the Denisovans — has been detected in the ancient mud of caves, even though those caves hold no fossils of those individuals, new research shows.

The finding suggests that scientists could detect such extinct lineages in places devoid of skeletal remains, the researchers said. This technique, if verified, could fill blank spots in scientists' understanding of how and where humans evolved, according to the authors of the new study describing the finding. [Denisovan Gallery: Tracing the Genetics of Human Ancestors]

The ancestors of modern humans once shared the world with archaic human lineages such as the Neanderthals — the closest extinct relatives of modern humans — as well as the Denisovans. Little is known about the Denisovans, but scientists think this ancient human relative might have roamed a vast range stretching from Siberia to Southeast Asia. DNA extracted from fossilized bones and teeth of Neanderthals and Denisovans has revealed many secrets about human evolution, such as how modern humans interbred with both lineages.

But although there are numerous prehistoric sites that hold tools and other artifacts from ancient humans — such as the ancestors of modern humans, or members of extinct human lineages — their skeletal remains are scarce, thus limiting research into human evolution. Moreover, the ancient human fossils that archaeologists do unearth do not always have enough suitable DNA for genetic analysis.

"Humans are a very small proportion of the fauna found in caves," said study senior author Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "In most excavation sites, if you find thousands of bones from animals, you're very lucky if you find one human tooth or a long-bone fragment."

Scientists took samples from different layers of this sediment profile in Trou Al'Wesse cave in Belgium. They ran genetic analyses on the samples.
Scientists took samples from different layers of this sediment profile in Trou Al'Wesse cave in Belgium. They ran genetic analyses on the samples.
Credit: Monika V. Knul

Instead, Meyer and his colleagues investigated whether ancient sediments found in caves might latch on to DNA. "We know that with DNA preserved in bones, the DNA binds to the mineral component of bone, so the same can, in principle, happen in sediments full of minerals," Meyer said.

The scientists collected 85 samples of sediment covering a time span from 14,000 to more than 550,000 years ago, from seven sites in Belgium, France, Spain, Croatia and Russia, where previous research suggested ancient humans once lived. These sites included Denisova Cave in Siberia, which is where Denisovan fossils were first discovered.

The researchers identified DNA from a variety of mammals, including woolly mammoths, woolly rhinoceroses, cave bears and cave hyenas. Mixed in with this animal DNA were small traces of human DNA: The researchers found Neanderthal DNA in four caves, and Denisovan DNA in Denisova Cave.

"The fact that sediment can indeed preserve DNA from extinct humans that lived there thousands of years ago is a pretty amazing finding," Meyer said.

In addition, at each of the two sites where the researchers did not discover DNA from ancient humans, they had only a few samples to analyze, Meyer noted. "Maybe if we looked at more samples from each site, we'd find Neanderthal or Denisovan DNA as well," he said.

The scientists aren't sure what part of the bodies of the extinct human lineages this DNA came from — for instance, skin flakes, hairs or bodily fluids such as sweat or blood. "Another possibility stems from how, in many sites, we find a lot of hyena DNA," Meyer said. "Maybe the hyenas were eating human corpses outside the caves, and went into the caves and left feces there, and maybe entrapped in the hyena feces was human DNA."

Most of the DNA from extinct humans that was recovered came from layers of sediment where no human fossils had been found previously. This suggests that, in the future, DNA could help researchers detect the presence of humans even in the absence of their skeletal remains, the study authors said.

For instance, "there are some very interesting open questions regarding the Denisovans — we only have fossils of them from a single site in Russia, but we know they must have been much more widespread due to the pattern of interbreeding we see with modern humans," Meyer said. "By looking for DNA, there's the chance we can find many more Denisovan sites than we would by just looking for bones or teeth."

One concern, however, is that DNA could seep across layers of sediment, thus making it difficult to figure out when, specifically, extinct humans or others lived at a site. (The deeper a layer of sediment is, the older it usually is.)

Still, the research team "didn't find any obvious evidence of DNA movement," Meyer said, "but it's certainly a possibility that needs to be investigated for every site."

Depending on how well DNA is preserved in any given cave, scientists "could learn much more information," Meyer added. "There's big potential here," he said, "and we need to do more work to understand just how big that potential is."

The scientists detailed their findings online today (April 27) in the journal Science.

Originally published on Live Science.