Humans, modern and otherwise, have lived in Denisova Cave in Siberia for tens of thousands of years, where they left behind a treasury of archaeological artifacts. The cave is famous for giving its name to Denisovans, a species of human closely related to Neanderthals. But Neanderthals have lived there, too.

In the cave’s Main Gallery, stone tools had been left behind by people who lived thousands of years ago. Those people were probably Neanderthals, according to a paper in Science this week: The soil says so. Even though no Neanderthal bones have been found with the tools, the paper’s authors are the first to be able to detect the presence of humans based on DNA found in the soil. This allows them to paint a much more detailed picture of the past, in Denisova Cave and elsewhere.

“This is a game changer for researchers studying our hominin past,” says Christian Hoggard, an archaeologist at Aarhus University who wasn’t involved with the story. His words are echoed by myriad researchers excitedly tweeting the paper: “This is pretty damn incredible,” says Rob Scott, an evolutionary anthropologist at Rutgers. Tom Higham, an Oxford professor who specializes in dating bones, called the discovery a “new era in Paleolithic archaeology.”

Fishing for DNA

The rarity of ancient bones has always been a big obstacle for archaeologists. Ancient tools are slightly less rare, but without bones, figuring out which group of human was responsible for making them can be very difficult. That’s why detecting the presence of humans without any bones is such a huge deal for the field.

Viviane Slon, a researcher at the Max Planck Institute for Evolutionary Anthropology, worked with a large team of colleagues to extract genetic material from sediment samples across four caves in Europe. They focused on mitochondrial DNA, which is genetic material that is separate from the main DNA of a cell. “Mitochondrial DNA evolves faster... and is present in more copies per cell,” Slon told Ars. “So that would allow us more chances to retrieve it from the sediment and also a better way to distinguish between different [species].”

How do you find out if there’s Neanderthal mitochondrial DNA in soil from an ancient cave? You take the soil—just a tiny bit, says Slon, only half a teaspoon or so—and use chemical reagents to release the genetic material into solution. Once it’s in this form, you can extract DNA that can be read by a sequencing machine.

Slon and her colleagues were the first to capture mitochondrial DNA using a particularly clever extraction method. DNA works a bit like a zipper combined with a jigsaw puzzle, where each tooth on the zipper can only fit together with another tooth of a particular kind. Because we already have data on a number of different ancient species, it’s possible to make a kind of genetic bait for DNA sequences by synthesizing one half of the zip. Once the bait is put in the solution, the other half of the zip attaches to it and can be extracted.

Neanderthals and mammoths and rhinos, oh my

Using this technique, Slon and her colleagues found the DNA of ancient mammals like woolly mammoths and woolly rhinos, as well as DNA from Neanderthals and Denisovans. They checked for contamination from modern genetic material by looking for the damage that occurs in ancient DNA. They also made sure to identify exactly which mammal species were being identified by the DNA. They wanted to be sure that the DNA belonged, in fact, to ancient species.

The researchers also checked that their results lined up with the existing archaeological record. In three different caves, they found Neanderthal DNA in places where Neanderthal bones had previously been found, exactly where you would expect it to be.

These signs that the method was working reliably meant that the researchers could move on to sites whose previous occupants were unknown. That included the discovery of Neanderthal DNA with the tools in Denisova Cave. Neanderthal DNA also showed up in Trou Al’Wesse in Belgium, where tools and animal bones have suggested Neanderthal presence, but no Neanderthal bones have ever been found.

“It’s a really well-conducted study,” says Mikkel Winther Pedersen, a researcher who specializes in ancient DNA and wasn’t involved in the paper. They’re building on a solid body of existing research on these methods, he says, and the results are important for archaeology—not just because of the findings, but because it means that it’s possible to actually use “what the archaeologists usually just throw away: the dirt. Save the dirt!”

Hoggard agrees, saying that the research will be likely to change how researchers approach archaeological sites. Researchers might be more inclined to choose sites with good sediments rather than just good artifacts, he told Ars, and “We will be more inclined to analyze the sediments and preserve them in a different way than before.” There will probably also be increasing awareness of contamination.

The new method described in Science doesn’t mean that the past is an open book now—the oldest sequence that has been analyzed so far is around 700,000 years old, says Slon, and that was preserved particularly well because of low temperatures. Older sequences could still be recovered, but, right now, it isn’t feasible that DNA evidence could be used to solve questions about early Homo species. Also, DNA could leach from one layer in a cave to another, which could make results difficult to interpret.

The next step, says Slon, will be to look at the archaeological sites that have stone tools but no clear evidence of who made them. “We could get DNA from the sediments to weigh in on which groups of hominins were present,” she says. Hoggard thinks a fascinating avenue would be to see “whether we could detect Neanderthal DNA at sites known to feature modern humans.” Or, he adds, this method could answer questions about another story in the news this week, the hints of humans in America 130,000 years ago.

Science, 2016. DOI: 10.1126/science.aam9695 (About DOIs).