Ancient DNA Found On Cave Walls

Human DNA can survive on cave walls for thousands of years – shedding light on prehistoric human activity even where bones, sediments or artifacts are absent

To the Point

• First evidence of ancient human DNA on cave walls: As part of a multidisciplinary study of Palaeolithic rock art in Spain and Portugal, researchers have successfully recovered ancient mitochondrial and nuclear human DNA from both pigmented and unpigmented cave wall surfaces.
• Possible direct human contact preserved: Cave wall samples from Escoural Cave in Portugal, including a pigmented calcite crust, revealed the presence of human DNA but no faunal DNA, suggesting that the DNA was deposited directly through human interaction with the cave walls.
• DNA on cave walls can survive millennia: The ancient human DNA recovered from the cave walls is at least 2,000 years old, likely much older, showing that these surfaces can preserve biological traces for considerable periods of time.
• New window into prehistoric life: This breakthrough opens up a new frontier in archaeogenetics. Future studies might be able to gain insights into the occupation, movement and behaviour of humans in caves by analysing DNA on cave walls, even when skeletal remains are absent.

For the first time, scientists have shown that ancient human DNA can survive for thousands of years on cave walls, opening new ways to study prehistoric human activity. This interdisciplinary study was conducted within the framework of the First Art project, which is led by researchers from Spain and Portugal in collaboration with institutions across Spain, Portugal, the UK, China and Germany.

The First Art project aims to date the earliest cave art and to characterise its chemical composition. In collaboration with researchers from the Max Planck Institute for Evolutionary Anthropology, the team has now extended their analyses to include DNA analysis.

The findings explore the possibility of recovering ancient DNA directly from cave art, going beyond bones, sediments or, more recently, bone artefacts. The research focused on 24 rock art panels from eleven caves, including simple marks, hand stencils, as well as pigment naturally falling from some figurative paintings from the famous Cave of Altamira. Using cutting-edge DNA extraction and sequencing methods, the team analysed pigmented and unpigmented cave wall fragments, sediments, bones and a rare ancient airbrush tool used for applying paint.

Although the researchers found traces of ancient human DNA in one pigmented calcite crust sampled in Escoural Cave (Portugal), to their surprise they also found ancient human DNA in several non-pigmented parts of the cave wall in Escoural as well as in Covarón Cave (northern Spain), which had initially been sampled as negative controls.

The study shows that human DNA can be preserved on cave walls long after the populations that visited the cave have disappeared.

A hidden legacy in the stone

Of the 54 samples collected, only five yielded authentic ancient human mitochondrial DNA: a calcite crust with pigment underneath from Panel 11 at Escoural Cave, two unpigmented cave wall samples from a deeper gallery also from the same site, and two unpigmented samples adjacent to rock art in Covarón. Importantly, two of these samples showed no detectable faunal mitochondrial DNA, a rare finding which strongly suggests that the DNA was deposited directly by humans through saliva or other bodily fluids. By contrast, three other unpigmented wall samples contained both human and faunal DNA, suggesting indirect deposition, likely via sediment transfer or water movement, rather than direct contact.

“We know that some of the art was applied to cave walls by blowing or rubbing pigment onto the surface. Given the enormous sensitivity of current ancient DNA analysis techniques, we were eager to see if this type of contact could leave traces of DNA in the rock art, potentially allowing us to obtain genetic profiles from the makers of the art”, says Hipólito Collado Giraldo, an archaeologist and rock art specialist from the Extremadura Government in Spain, who brought together the First Art team.

“Although we cannot directly connect the traces of ancient human DNA we have found to the creation of rock art, this is the first evidence for human DNA preservation on cave walls for thousands of years”, says first author Alba Bossoms Mesa, a doctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig. “It is exciting to think that we may have uncovered a new way to study prehistoric human presence”.

The human DNA of three of these samples comes mostly from females, one mostly from males, and one remains undetermined. Further analysis of the two unpigmented cave wall samples from Covarón revealed that their DNA belonged to modern humans, with nuclear DNA placing them within the Western hunter-gatherer genetic cluster. This is consistent with the findings for other ancient Iberian populations.

The team also tested a prehistoric bird bone airbrush from Altamira Cave that was used to blow red ochre onto the walls. Despite expectations of finding saliva-derived DNA, no ancient human DNA was recovered, most likely due to the extremely high contamination by present-day human DNA, combined with only minimal sampling. This highlights the fragility of DNA preservation, especially in material that has been heavily handled over decades of study.

A new chapter in prehistory research

“This study fundamentally changes how we think about where ancient DNA can be found”, says senior author Matthias Meyer, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology who co-led the work with Hipólito Collado Giraldo. “We were surprised to see that ancient DNA can be recovered not only from pigmented samples, but also from cave walls that show no visible evidence of past human activity. We can now ask new questions: Who touched this wall? Was it a man or a woman? Which population did they belong to? How far did ancient humans venture into deep cave systems?”

This discovery opens up new possibilities for studying prehistoric human behaviour without disturbing archaeological deposits. By analysing DNA found on cave walls, researchers can potentially now learn more about the occupants of the caves, determining for example their biological sex and genetic ancestry. “This is not just about rock art”, says Hipólito Collado Giraldo. “It’s about understanding how people used caves and where they left their marks”.

Not all art yields DNA

Despite favourable conditions for ancient DNA preservation at many sites, ancient DNA was detected in only one of the 24 rock art panels examined, and two additional locations adjacent to other rock art panels. This rarity suggests that pigment surfaces rarely retain enough DNA to survive for thousands of years, particularly if they are not protected by mineral crusts or sealed environments. “The preservation of human DNA on cave walls is highly variable”, says Bossoms Mesa. “But when it does survive, it tells a powerful story. And while these first results are promising, I think our priority now should be to refine the methods and to understand under what conditions we can expect a higher success rate”.

“This is just the beginning”, adds Meyer. “We now know that cave walls are archives of past human presence. The next step is to test more sites, art styles and techniques, especially hand stencils and figurative art in caves with good molecular preservation, as far as minimally invasive sampling allows”. With further work, it may become possible to reveal the makers of at least some pieces of cave art – and to put faces, or at least genetic identities, to the artists who created them.