Dirty Secrets: Sediment DNA Reveals a 300,000-Year Timeline of Ancient and Modern Humans Living in Siberia

Science Magazine reports that analysis of more than 700 soil samples from Siberia’s Denisova Cave has detected traces of modern human DNA, which suggests that modern humans may have occupied the cave alongside Denisovans and Neanderthals.

The group was named “Denisovans” in its honour. Now, an extensive analysis of DNA in the cave’s soils reveals it also hosted modern humans—who arrived early enough that they may have once lived there alongside Denisovans and Neanderthals.

The new study “gives [researchers] unprecedented insight into the past,” says Mikkel Winther Pedersen, a molecular paleoecologist at the University of Copenhagen who was not involved with the work. “It literally shows what [before] they have only been able to hypothesize.”

Humans—including Neanderthals and Denisovans—are known to have occupied Denisova Cave for at least 300,000 years.

Among the eight human fossils unearthed, there are the pinkie, three bones from Neanderthals, and even one from a child with one Neanderthal and one Denisovan parent.

The cave also contains sophisticated stone tools and jewellery at higher, later levels. But no modern human fossils have been found there.

Those artefacts, extensive studies of DNA from these bones, and even one early study of DNA from soils have cemented the cave’s importance for piecing together human evolution.

But eight fossils are not much to go on, so Elena Zavala, a graduate student at the Max Planck Institute for Evolutionary Anthropology, and colleagues teamed up with Russian researchers to see what kind of DNA was present in the soils of the three-chamber cave (see the video, below).

Researchers have been studying DNA isolated from soils for more than 40 years, including sequencing DNA from permafrost, but only in the past 4 years has anyone found DNA from extinct humans in ancient soils.

Working with another team of experts who had previously dated the layers of the cave, the researchers dug out 728 soil samples. After 2 years of analysis, in which they isolated and sequenced the samples, the researchers found human DNA in 175 of them. That makes the study “the largest and most systematic of its kind,” says Katerina Douka, an archaeological scientist at the Max Planck Institute for the Science of Human History who was not involved in the work.

The data reveal a complex history of human and animal habitation, with different groups moving in and out of the cave over time, Zavala and her colleagues report today in Nature. Their work confirms that Denisovans were the cave’s first human inhabitants, about 300,000 years ago.

They disappeared 130,000 years ago, only to be followed by a different group of Denisovans, who likely made many of the stone tools, some 30,000 years later. Neanderthals appeared on the scene about 170,000 years ago, with different groups using the cave at various points in time, some overlapping with the Denisovans.

The last to arrive were modern humans, who showed up about 45,000 years ago. The soil layer that corresponds with that period contained DNA from all three human groups, the researchers report.

“The time periods [of each layer] are quite large, so we can’t concretely say if they overlapped or not,” Zavala says. But, Douka adds, “I cannot think of another site where three human species lived through time.”

Given the jewellery and sophisticated artefacts in later layers, some researchers suspected moderns had been there. But no one knew they had arrived as early as 45,000 years ago—and overlapped with both of our archaic cousins.

“It suggests a more complicated interplay between archaic and modern humans,” says Ron Pinhasi, an evolutionary anthropologist at the University of Vienna who was not involved with the work.

The soil samples also yielded DNA from many species of animals. About 170,000 years ago, the climate went from warmer to colder, and Neanderthals moved in, so did different species of hyenas and bears.

It’s the combination of genomic data from both the fossils and the soil samples that really makes the new work stand out, Pinhasi says. “It’s a super promising direction [for future work].” Douka agrees, and says the new study should help ancient soil DNA become “a mainstream archaeological tool.”

She is already amazed at the progress that it, combined with other studies, has made possible. “Let’s not forget that as recently as in 2010 we had absolutely no evidence that Denisovans existed and that these various hominins ever met, let alone that they interbred repeatedly and co-existed for millennia,” she wrote in an email.

Ancient Structures in The Arabian Desert Reveal Fragments of Mysterious Rituals

We might be getting closer to understanding why hundreds of large stone structures were built across the deserts of northwest Saudi Arabia thousands of years ago.

According to an in-depth new analysis, the mysterious, rectangular enclosures were used by Neolithic people for unknown rituals, depositing animal offerings, perhaps as votives to an unknown deity or deities. Excavations have revealed hundreds of fragments of animal remains, clustered around an upright slab of stone interpreted as sacred.

The roughly 7,000-year-old monuments known as mustatils (an Arabic word meaning rectangles) have baffled archaeologists since attracting scientific attention in the 1970s.

It wasn’t until 2017, however, that the full extent of their spread across the Arabian Peninsula was revealed in the first scientific paper documenting their discovery. Aerial surveys have aided in the identification of over 1,600 mustatils, sometimes in groups, scattered throughout the desert.

Nicknamed ‘gates’ because of their appearance from the air, mustatils were described in that paper as “two short, thick lines of heaped stones, roughly parallel, linked by two or more much longer and thinner walls.”

They consist of two short, thick platforms, linked by low walls of much greater length, measuring up to 600 meters (2,000 feet), but never more than half a meter (1.64 feet) high.

Though often collapsed, one of the two short ends forms an entrance, while the other contains chambers that range in size. What these chambers were used for is unknown, but there’s a curious absence of tools in and around them.

Archaeologists believe this set of characteristics suggests their use was not a utile one; the low walls and lack of roofs would make them unsuitable as livestock pens or storage facilities, for instance.

What they can contain in some cases are standing and decorated stone slabs, as well as a scattering of animal bones. A number of mustatils also feature a long courtyard, suggestive of a processional element.

In 2019, an international team of scientists led by archaeologist Melissa Kennedy of the University of Western Australia excavated a 140-meter-long sandstone mustatil near Al-‘Ula, named IDIHA-F-0011081, collecting fragments of material and cataloging the various features of the monument.

At the head of the mustatil – the short end featuring chambers – they found a space with standing stone slabs. They also collected 260 fragments of animal bone, teeth, and horns, mostly clustered around the stone slab.

They identified 246 of these fragments; and, even more intriguing, the pieces of bone were exclusively pieces of the animals’ skulls, taken from goats, gazelles, small ruminants, and domestic cattle.

This, the team says, suggests that the stone slab is what is known as a betyl – a sacred stone representing the god or gods of the people who lived in the region thousands of years ago, with animal heads deposited as ritual offerings.

“We hypothesize that the standing stones (betyls) from mustatil IDIHA-F-0011081 … may have functioned as a mediator between humankind and the divine, acting as a proxy or a manifestation of an unknown Neolithic deity/deities or religious idea, to which the faunal elements were deposited as votive offerings,” they write in their paper.

“Due to the number and age of the animals slaughtered and the presence of fragile cranial elements, suggestive of fresh skulls, and anthropic marks indicating specific processing practices, we hypothesize that ritual feasting also played a role at mustatil IDIHA-F-0011081.”

And there’s one more curious clue pointing to the monument’s use in ancient society: a small, rectangular stone chamber, in which the researchers found human remains, next to the head of the mustatil, where the betyl chamber lay. This is a cist; a small, ancient burial chamber, constructed of slabs of unworked sandstone. It had collapsed in on itself over time but still contained broken and partially articulated human remains.

Time had done its work on those bones, too, but Kennedy and her team were able to ascertain that the deceased was an adult male who probably suffered from osteoarthritis. Who he was, and why he was buried at the mustatil, remains unknown; but there’s something a little peculiar about the burial.

The mustatil itself was relatively hidden in sandstone canyons, but the human remains were deposited several hundred years after the animal remains. This suggests that the site remained important long after it was no longer in use, and was possibly a site of pilgrimage, or at least shrine revisiting.

“The evidence from [the site] suggests that the mustatil tradition was characterized by the intersection of belief and economic life-ways,” the researchers write.

“The incorporation of these two facets suggests a deeply rooted ideological entanglement, one which was shared over a vast geographic distance, indicating a far more interconnected landscape and culture than had previously been supposed for the Neolithic period in north-west Arabia.”

The research was funded by the Royal Commission for AlUla and has been published in PLOS ONE.