Neanderthal and Denisovan DNA has been extracted from sediments in caves they once inhabited, even where we've found no bones. The discovery could transform our knowledge of early human evolution and the branches of humanity that have gone extinct. Given the extreme shortage of Denisovan fossils, the technique could multiply our knowledge of these mysterious peoples many times over.

The capture of DNA from objects where blood or hair was shed has become a staple of TV detective shows, but it's harder than TV makes it look. We've only been collecting Neanderthal DNA from bones for 20 years, resolving the old question of whether Homo sapiens and Neanderthals interbred, and raising a new one of whether Neanderthals were a separate species from us at all.

In this light, extracting DNA that has spent hundreds of thousands of years unprotected by bones, teeth, or amber is an astonishing step forward. Yet this is exactly what has been announced in Science. Using 85 samples from seven suspected Ice Age homes for early humans, a team from a dozen scientific institutions collected DNA from 14,000- to 550,000-year-old sedimentary layers.

Despite the astonishing preservation, most of the DNA extracted from these sediments could not be matched to a specific species. Unsurprisingly, most of what could be identified belonged to microorganisms or animals that were probably prey to the cave's inhabitants. Nevertheless, four of the seven caves studied were confirmed to hold Neanderthal mitochondrial DNA.

Mitochondrial DNA is easier than nuclear DNA to find in these circumstances because it has more copies in most animal cells. Although it can tell us less than nuclear DNA about the people from which it came, mitochondrial DNA is still capable of being distinguished by organism. Study co-author Professor Richard Roberts of the University of Wollongong told IFLScience the chances of finding nuclear DNA depend on the form in which it has been preserved.

"Is it bits of hair or fecal matter or is it loose strands of DNA attached to grains of sand?" he said. Other authors are investigating this at the moment. In some sediments, the mitochondrial human DNA is so rich, they think there may be prospects for getting nuclear DNA as well – providing a much more complete picture of the people who lived there and their relationship to us.

^{Excavations at El Sidrón, Spain. Credit: El Sidrón research team}

The sediments in the Denisova cave, where Denisovan bones were first discovered, produced genetic material from these people, as well as Neanderthal DNA. Neanderthals in the region are known to have interbred with the Denisovans, but the DNA from the two populations came from different sedimentary layers. Roberts told IFLScience the error bars on the dating of these layers are sufficiently wide that we don't as yet know whether the two branches of humanity occupied the cave tens of thousands of years apart or almost co-existed. 

Hominid bones have not been found in one of the caves that yielded DNA, although their presence was suspected from cut marks on animal bones. Moreover, some layers yielded DNA from more than one individual, suggesting the technique has the capacity to greatly expand our knowledge of prehistoric humans compared to the limited supply of fossils available.

Prior to this work, a tooth, finger, toe bone, and two unconfirmed skulls provided our entire body of knowledge about Denisovans. Yet these were sufficient to establish that Melanesians and Indigenous Australians source 3-5 percent of their genetic material from these mysterious people, with a particular influence on the modern immune system. DNA from sediments might give us a chance to learn a lot more about these people and the legacy they have left in our genes.

It's not just the DNA from early humans that makes sedimentary extraction so valuable. The other animals identified in the same paper offer us unprecedented insight into what early humans were eating at sites across Eurasia. Fans of the Earth's Children series will be pleased to hear that the Vindija Cave, Croatia, known to be home to both Neanderthals and modern humans, hosted plenty of DNA from Ursus ingressus, an Eastern European cave bear.

^{A sediment sample. Credit: MPI f. Evolutionary Anthropology/ S. Tüpke}