Evidence of three human species and dangerous animals in one ancient Siberian cave

As technology advances, the archaeological field is utilizing new tools to make discoveries that otherwise would have been missed. And thanks to new microscope technology, scientists are getting an even better look at the prehistoric Denisova Cave in Siberia where three species of humans and an assortment of ancient beasts took refuge.

For tens of thousands of years, the Denisova Cave in Siberia has been a complex system of intense interest by researchers.

Ancient needles dating back 50,000 years ago have been found, as have the remains of a 32,000-year-old horse species. In addition, remains from Homo sapiens, Neanderthals and the Denisovans for which the cave is named, have also been uncovered.


Denisova Cave artifacts found by researchers include beads and pendants. Image via Wikimedia.

The cave system is a rich treasure trove that gives us a huge window through which to look into the past. But because most of what could be found by the naked eye has already been unearthed, archaeologists are looking to find more by looking under a microscope.

Luckily enough, microscopy has advanced over the years enough to allow for scientists to employ the technology after first sifting through the sediment in an effort to find microscopic evidence to further tell the story of what happened in these caves.

Flinders University ARC Future Fellow and lead study author Dr. Mike Morley said in a statement:

“These hominin groups and large carnivores such as hyenas and wolves left a wealth of microscopic traces that illuminate the use of the cave over the last three glacial-interglacial cycles,” stated Morley.

Denisova Cave Siberia
Image of the cave via Wikimedia Commons

In the study as published by Nature, the team points out how new this program is and its purpose:

A new program of geoarchaeological investigation was initiated in 2014, aimed at documenting the microstratigraphic aspects of the depositional and post-depositional environments represented in the deposits. This work employs micromorphology and contextually-specific elemental mapping of the sediments to seek trace-evidence of processes that formed the site and obtain insights into the behaviours and activities of the site’s occupants—both hominins and other animals—and contextualise at high resolution the artefacts, fossils and genetic material.

A Denisovan tooth found in the Denisova Cave in 2000. Image via Wikimedia.

As a result of the microscopic research, the team not only found new fossils and stone artifacts, but also DNA.

Hominin fossils and aDNA have been recovered from the sediments preserved at Denisova Cave as well as significant numbers of stone artefacts and faunal remains, specimens of which show signs of human modification…Unequivocal signs of hominin activity in the sediments at the field scale are limited, including evidence for fire-use in the Middle Palaeolithic deposits that form the majority of the sequence.

“Our results complement previous work by some of our colleagues at the site that has identified ancient DNA in the same dirt, belonging to Neanderthals and a previously unknown human group, the Denisovans, as well as a wide range of other animals,” Morley says.

The limited fire-use is interesting, especially since we’re talking about a site in Siberia. However, it’s possible the team just hasn’t found the right spot yet or the ancient humans preferred to limit fire within such a space.

The team speculates that the cave served as a periodic refuge for all three species of humans and that they may have interacted with each other at some point.

Overall, the microstratigraphic record for Denisova Cave indicates that human activity was intermittent over the past three glacial–interglacial cycles represented by the Pleistocene sedimentary infill (>300 ka to ~20 ka). The stone artefact assemblages indicate long-term hominin occupation of the site during both warm climates and cold conditions, when the foothills of the Altai Mountains likely served as a refugium.

When humans were not using the caves, animals sought refuge there as well, as evidenced by the presence of ancient animal feces.

The University of Wollongong Distinguished Professor Richard Roberts noted:

“Using microscopic analyses, our latest study shows sporadic hominin visits, illustrated by traces of the use of fire such as miniscule fragments, but with continuous use of the site by cave-dwelling carnivores such as hyenas and wolves,” said Roberts.

“Fossil droppings (coprolites) indicate the persistent presence of non-human cave dwellers, which are very unlikely to have co-habited with humans using the cave for shelter.”

Indeed, can you imagine trying to sleep in the same cave with an animal that could attack and eat you?

That’s a pretty scary scenario.


The Cave Hyena, also known as the Ice Age Spotted Hyena, made use of the Denisova Cave. Image via YouTube.

And the human species who frequented the cave were well aware of these dangerous predators because they drew them on cave walls.


Depiction of Cave Hyena on a cave wall circa 20,000 years ago. Image via Wikimedia.

As for evidence that the separate human species interacted, a bone fragment found in the sediments by a different team revealed the existence of a teenage girl who was the product of a Neanderthal and a Denisovan around 90,000 years ago.

According to Nature:

In the latest study, the team sought to get a clearer understanding of the specimen’s ancestry by sequencing its genome and comparing the variation in its DNA to that of three other hominins — a Neanderthal and a Denisovan, both found in Denisova Cave, and a modern-day human from Africa. Around 40% of DNA fragments from the specimen matched Neanderthal DNA — but another 40% matched the Denisovan. By sequencing the sex chromosomes, the researchers also determined that the fragment came from a female, and the thickness of the bone suggested she was at least 13 years old.

Related: Researchers Find First Ever Human Hybrid—Result of Two Extinct Human Species

Francis Crick Institute population geneticist Pontus Skoglund noted:

“To find a first-generation person of mixed ancestry from these groups is absolutely extraordinary,” said Skoglund. “It’s really great science coupled with a little bit of luck.”

That being said, there may be a reason why there aren’t more specimens with intermixed DNA being found on a more common scale. It’s likely that while Neanderthals and Denisovans could reproduce, their offspring were infertile themselves. That would certainly explain why we don’t find many examples of it.

Both teams have used microscopy to make some fascinating finds that would not have been possible without the use of advanced technology, thus opening up an entirely new field of study that could shed further light on human history like never before as well as confirm or contradict previous research.

Micromorphological analysis of the Denisova Cave sequence has provided micro-contextualised insights into the use of the site by hominins and other animals. These new data largely support previous interpretations based on field observations and other proxy datasets (e.g., faunal and pollen records, thus increasing confidence in environmental reconstructions for the cave and surrounding region….Ongoing work at Denisova Cave aims to more fully integrate micromorphology and sedimentary aDNA analyses to develop a predictive tool for organic material preservation in the deposits at this unique hominin locality.

Scientists would be wise to adopt and use new technology whenever they can to improve the study of various sites. After all, you never know what information a new technique can yield. In this case, it paved the way to find an ancient pairing between two human species that resulted in offspring. That’s an incredibly rare find that would not have been possible decades ago.

Related: Researchers use ‘game-changer’ method to easily analyze ancient bones without risking damage

More about these fascinating finds from Let Me Know below:

Featured Image: Screenshot via YouTube

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