Researchers sampled these Denisova Cave artifacts — bone points and pierced teeth — and fossils to determine a more precise timeline for hominins using the site. The Siberian cave has been home to Neanderthals as well as Denisovans, our enigmatic evolutionary cousins. (Credit: Katerina Douka)

Nestled in the foothills of southern Siberia’s Altai Mountains, Denisova Cave has yielded numerous artifacts, as well as fossils of many animals and at least two hominins: Neanderthals and Denisovans. The cave is the only place in the world known to have remains of the Denisovans, who, like Neanderthals, were our close evolutionary cousins.

The site is one of the most significant for understanding human evolution, but study of it has been hampered by difficulty dating the finds. Today, a pair of papers reveal new Denisovan fossils, scores of new dates and a refined timeline for a hominin presence at the cave: important steps in untangling the complicated role it has played in the human story.

Known for decades as an important paleoanthropological site, Denisova Cave revealed its greatest treasure little more than a decade ago: fragmentary remains of a previously unknown close evolutionary relative, the Denisovans. Despite the limited remains found, researchers were able to extract ancient DNA (aDNA) and establish that the Denisovans were most closely related to Neanderthals.

The aDNA studies from cave’s hominins, both Denisovan and Neanderthal, helped confirm that both populations have, at various times, interbred with Homo sapiensand each other. In 2018, additional partial remains from the cave turned out to be from the first known Neanderthal-Denisovan hybrid individual.

(Sidenote: Most researchers consider all three groups — modern humans, Denisovans and Neanderthals — as separate species of human, though the definition of species has itself evolved from what you may have learned in school. Harvard University anthropologist and frequent Discover contributor Bridget Alex recently wrote an excellent primer on what makes a species. It’s worth reading, especially before commenting on this latest research.)

Unfortunately, full analysis of the fossils and artifacts found at the site has been problematic because precise dating is difficult to establish. The ages of many of the finds are beyond the limits of radiocarbon dating (which only goes back about 50,000 years).

While other methods of dating have longer ranges, they generally date the sediments in which items are found, not the items themselves. This is a problem at Denisova because sediment layers have been disturbed in several areas thanks to activities such as animals trampling and digging and generally making a mess of things. The area is also prone to freeze-thaw cycles that can thrust layers up or down, irregularly, as the ground and air temperatures fluctuate dramatically.

It’s easy for fragmentary fossil finds and small artifacts to get shoved from one layer to another in such chaos.

Natalia Belousova (Russian Academy of Sciences) and Tom Higham taking samples from Denisova Cave’s Main Chamber. The researchers were part of a team that created a new and more refined timeline of both Neanderthals and Denisovans at the site. (Credit: Sergey Zelinski, Russian Academy of Sciences)

Order from Chaos

In the studies published today, two teams took different approaches to untangling the cave’s complicated setting and establishing a more precise timeline for Denisovans and Neanderthals at the site.

(Right about now, you may be wondering whether Homo sapiens were also present during these periods. The answer is we don’t know for sure — yet. No definitive H. sapiens fossils have been found at Denisova Cave from the same time periods as Neanderthal and Denisovan remains, though hominin remains at the site are generally fragmentary and many remain unstudied. Some researchers have attributed a few of the artifacts from the site to modern humans based on style. In 2014, a team sequenced aDNA from a femur found at another site in southern Siberia and determined that it belonged to a modern human who lived about 45,000 years ago, establishing that our species was in the region by that time, if not earlier.)

One team obtained 50 radiocarbon dates from material collected from areas that were not previously disturbed. The material included charcoal and artifacts, such as deer and elk teeth that had been modified by hominins. Some of the items, including tooth pendants and bone points, turned out to be the earliest such artifacts from northern Eurasia, produced between 43,000 and 49,000 years ago. It was not possible to determine which hominin made the items, however.

The researchers also tested more than 2,000 bone fragments and found three with chemical signatures suggesting they were from hominins. Additional analysis found one of the fragments contained mitochondrial DNA consistent with Neanderthals; of the other two fragments, one yielded no aDNA evidence and the other is still being tested.

The team focused on dating most of the new fossil fragments and those previously unearthed by comparing aDNA sequences, identifying subtle changes and determining how much time it took for those changes to appear. This dating-by-genetic-analysis method is new and based on the fact that the DNA of every species, every population, evolves over time at its own, knowable rate.

The method, while promising, has not yet been perfected, which the authors acknowledge. Their study is, however, the first time it has been attempted on the Denisova Cave hominins.

Combining the new information with previously reported data, the team determined that the oldest Denisovan fossil from the cave could be as much as 195,000 years old. The youngest Denisovan fossil is 52,000-76,000 years old. Meanwhile, all of the Neanderthal fossils, as well as the Denisovan-Neanderthal hybrid described last year, were between 80,000 and 140,000 years old.

The entrance to Denisova Cave. (Credit: Richard Roberts)

Cave Chronology

The second team conducted a careful stratigraphic analysis of all three chambers in the cave, determining more than 100 new dating references for layers deposited over millennia. This work allowed the researchers to build a new and more precise timeline for the fossils, artifacts and other material found at Denisova. The team used a dating method called optically stimulated luminescence, which can determine when certain minerals within the layers were last exposed to sunlight.

Because they focused on dating the layers of the cave itself, rather than direct-dating the fossils and artifacts like the other team, the researchers’ conclusions are different than that of their colleagues — but not contradictory.

The stratigraphic analysis suggests that Denisovans were present in the cave beginning at least 287,000 years ago and continuing until about 55,000 years ago. They determined a Neanderthal presence starting about 193,000 years ago until 97,000 years ago. This timeline matches loosely with the fossil dates, suggesting a previously undocumented long period of Denisovan presence at the site punctuated with a shorter Neanderthal presence.

Differences in the results may be the result of the genetic dating method used for the fossils; modeling age based on aDNA is a new and bold approach that is still being refined. The inconsistencies may also be down to disturbances in the sediment after the fossils were deposited, either due to animal activity or freeze-thaw cycles.

So, for folks who like absolutes, the new research may be a disappointment. The studies are, however, a giant step forward in understanding the cave’s complex past, including its ancient residents.

The two papers, describing the new fossils and dating samples and establishing a more precise timeline, appear today in Nature along with a News & Views commentary.