Ancient DNA found on cave walls

 

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.

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Journal

Nature Communications

DOI

10.1038/s41467-026-74234-2 

Ancient tooth protein reveals 'all-female' fossil site of extinct human relation

 Scientists have extracted and analysed the first-ever ancient proteins from the fossils of Homo naledi, revealing a potential all female burial site.

The study, published in the journal Cell, raises the possibility that South Africa’s famous Rising Star Cave system could represent the first known example of a sex-specific burial site by a non-Homo sapiens.

Homo naledi, an extinct cousin of modern humans that lived between 335,000 and 241,000 years ago, has puzzled researchers since its initial discovery in 2013. The species possessed an unusual mixture of primitive, ape-like traits alongside human-like features.

But for over a decade, scientists have wondered why the adult fossils recovered from the cave’s Dinaledi Chamber looked so remarkably identical. The remains showed almost none of the physical variations that would be expected between males and females.

To solve this puzzle, researchers from the University of York, the University of Copenhagen, and more than 10 other international institutions, investigated proteins from the skeletal remains. 

Using a minimally destructive acid etching technique, the team extracted microscopic protein fragments, called peptides, from 23 teeth representing at least 20 different individuals.

Researchers analysed the tooth enamel for Amelogenin-Y, a protein uniquely coded by the male Y chromosome.  

The results revealed that the male marker was absent.  To ensure the validity of the results, a team at the University of York’s specialized chemistry facility analysed the amino acids to prove the proteins were genuinely ancient and not the result of modern contamination.

Dr Marc Dickinson, from the University of York’s Department of Chemistry, said: “The lack of male markers with the group is truly fascinating. It is incredibly exciting to gain a window not only into the biology of our ancestors, but also into how they lived. 

“These findings offer rare insights into a culture that has, until now, been difficult to access directly. Advances in ancient protein analysis are opening the door to a far richer and more nuanced understanding of ancient hominins.” 

The findings open up new questions about the culture and social structure of these ancient hominins. If the chamber was reserved exclusively for females, it may imply a level of complex, symbolic mortuary practice previously thought unique to Homo sapiens - modern humans.

The team noted, however, that there could be a biological explanation as well as a cultural one.  It is possible that the Homo naledi population was highly isolated, causing the male-specific Amelogenin-Y gene to mutate or be deleted. 

This would mean males were present, but their teeth simply lacked the typical genetic signature.

Palesa Madupe, who completed the work as part of her postdoctoral research at the University of Copenhagen, said: “Unlike those found in other remains like bone fragments, proteins in tooth enamel are preserved because dental enamel – the hardest tissue in the human body – shields proteins from environmental contamination even for millions of years. 

“This makes them ideal carriers of genetic information from deep time. Our study helps in the long-standing mystery of why Homo naledi lacked significant variation; it’s probably because they could have all belonged to one sex.”

As the largest extinct hominin population ever to undergo protein analysis, these ancient females - or genetically unique males - have prompted a rewrite of what scientists thought they knew about the dawn of human society.

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Journal

Cell

Neanderthals in Western Europe were doing well right before they went extinct

 Key takeaways

• Neanderthals died out around 40,000 years ago, possibly due to climate change and competition and interbreeding with modern humans, but no one knows for sure.
• New research on one Neanderthal population in Belgium right before extinction shows that it had healthy levels of genetic diversity and no signs of stress from interbreeding with modern humans.
•  The findings suggest that extinction played out differently across the vast range that Neanderthals occupied across Europe and Central Asia.

Neanderthals thrived across Europe and the Middle East for hundreds of thousands of years. They occupied vast distances, ranging from Europe through the Altai Mountains in Central Asia. They survived large variations in climate and the arrival of modern humans until around 40,000 years ago, when they died out. The exact factors that resulted in their disappearance remain unknown, with possible explanations including climate change, resource competition and interbreeding with anatomically modern humans.

A new study published in Nature reveals that a Neanderthal population around 45,000 years ago in Belgium and France was doing well, with no signs of inbreeding or pressure from or genetic mixture with modern humans, who lived in the area at that time. The finding suggests that localized Neanderthal groups in this area were large and well-connected enough that individuals could have children with partners who were not closely related. Nonetheless, around 2,000 years later, even this population vanished.

“In other, earlier Neanderthal populations, close relatives were interbreeding, leading to unhealthy levels of genetic diversity similar to what we see today in some endangered species. But this population in Belgium and France does not seem to be dying out, even though we know that they will die out in the end,” said UCLA computational geneticist Benjamin Peter, who is one of the paper’s corresponding authors.

The research examined DNA extracted from the bones of 27 individuals who lived between 49-40,000 years ago in the Meuse Basin, which spans Belgium and France, using established computational techniques for studying ancient DNA and a new technique the researchers developed for these particular samples. They found no close relatives among any of the individuals up to third-degree relatedness, in which individuals share about 12.5% of their DNA and was the limit of what their methods could detect. This is comparable to the amount of DNA shared between first cousins.

The mitochondrial DNA, which is inherited only from the mother, showed that most individuals belonged to a large lineage common to late Neanderthals in Southern and Southwestern Europe. This means that all these individuals shared female ancestors. One individual, however, belonged to a different maternal lineage found in a handful of other Neanderthals, suggesting that more than one of these mitochondrial lineages coexisted. On the other hand, data from the Y-chromosome of three male individuals, which is passed on from father to son, showed that they did not belong to a single lineage, meaning that they each had different male ancestors.

To study the amount of genetic diversity, the researchers looked for stretches of DNA that contained identical base pairs. This happens when a person inherits copies of the same genes from both parents, which is much more likely when the parents are related. When close relatives reproduce over time, a situation likely when a population is small and isolated, eventually most of the population will end up having similar genes, which will show up as long stretches of identical pairs on the DNA strands.

This reduction in genetic diversity, which population geneticists call “inbreeding depression,” means that harmful genes are more likely to be passed on, which reduces the potential to adapt to changing environments or respond to new diseases and may cause lower fertility. All of these factors make it harder for a population to survive and reproduce and, without an influx of new genes, can lead to the population’s extinction.

“I think the most interesting finding we made is that these Neanderthals are genetically relatively healthy, with no strong signs that there was inbreeding depression,” said Peter, who conducted the research as a group leader at the Max Planck Institute for Evolutionary Anthropology and is now a UCLA assistant professor of ecology and evolutionary biology and the Institute for Quantitative and Computational Biology. “It’s also interesting that we didn’t find evidence that they have ancestry from anatomically modern humans, even though we know that at least they must have overlapped in time.”  

A final point of interest was the finding that all of the remains from one site, Goyet, were of unrelated females, juvenile males and one newborn baby.

Taken together, the genetic analysis shows that although this Belgian population was more closely related to one another than to other Neanderthal groups, the difference wasn’t substantial, suggesting there may have been considerable movement among these Western Neanderthal groups.

“Over the very long time scale that Neanderthals existed in Eurasia, their entire range was not inhabited consistently. There were probably some areas where Neanderthals could survive through climatic events like ice ages, and they expanded into other areas when conditions were suitable for human habitation,” said Peter. “It seems that Western Europe at this time was a good place to be a Neanderthal. I think a climate shift later on, and maybe competition from modern humans, or a combination, led to the extinction very soon after the individuals that we studied.”

Ancient DNA reveals genetic history of medieval Sicily

 

A study has revealed that despite centuries of violent regime changes, medieval Sicily was a genetic ‘melting pot’, where Christians and Muslims thrived together.

The research, led by Dr Aurore Monnereau from the University of York and published in the journal PLOS One, analysed ancient DNA from 111 individuals excavated from 19 different archaeological sites across Sicily, spanning from the Roman Age to the Late Middle Ages.

The study shows that Sicily's genetic diversity landscape has persisted through conquests, challenging the idea of large-scale population change and instead suggests a certain continuity.

Between the 5th and 15th centuries CE, Sicily was a central Mediterranean hub of trade and conflict, ruled by a succession of major powers, from the Roman and Byzantine Empires, to the Islamic Dynasties, and the Normans and Swabians.

Dr Aurore Monnereau, who completed the work as part of her PhD at the University of York’s Department of Archaeology, said: “While historical records are important to our understanding of the past, they often leave the experiences of ‘everyday’ people in the shadows, capturing major events of the Middle Ages through the lens of their authors. 

“Through the analysis of ancient DNA, our study seeks to restore some of those missing voices. By integrating aDNA with written and archaeological evidence, we show that Sicily served as a central crossroads in the highly interconnected medieval world.”

The data also demonstrated that individuals of sub-Saharan African descent were living on the island throughout the medieval period, suggesting ancient, ongoing migrations across the Mediterranean. 

Dr Nathan Wales, from the University of York’s Department of Archaeology, said: “Contrary to some past ideas, we can see this period shouldn’t be considered to be the “Dark Ages”, but rather a dynamic period with interactions and distant connections. 

“From the individuals’ DNA, we see people buried in Christian and Muslim cemeteries had similar ancestries stemming from North Africa and the European and Mediterranean area.”

The researchers highlight that future data from additional Mediterranean archaeological sites will be needed to provide an even more refined understanding of how these ancient populations lived and shifted over time.

Professor Martin Carver, from the University of York's Department of Archaeology, said: “The study has shed a new light on people who traditionally don’t appear in the historical record, showing Christians and Muslims to have largely lived in prosperous multi-faith societies until the early thirteenth century, when Sicily became part of the Holy Roman Empire.”

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Scientists help verify Yucatan origin of cotton’s domestication

 Cotton is the world’s leading source of natural textile fiber, but much of its genetic history remains a mystery. Mississippi State scientists are part of an international team investigating when and where cotton was first domesticated. Their findings, recently published in the Proceedings of the National Academy of Sciences, weave together a clearer picture of cotton’s genomic past while offering insight to help improve the crop’s future.

Researchers sequenced nearly 400 wild and domestic cotton plants across Florida, the Caribbean and Mexico. They traced modern cotton’s roots to Mexico’s Yucatán Peninsula more than five millennia ago, uncovering genetic diversity that could help today’s breeders develop more resilient cotton.

Professor Dan Peterson, head of MSU’s Department of Biochemistry, Nutrition and Health Promotion and a Mississippi Agricultural and Forestry Experiment Station scientist, said the team confirmed a longstanding hypothesis that the Northwestern Yucatán Peninsula was the center of domestication of Gossypium hirsutum, known as upland cotton. Peterson noted wild specimens of the species hold valuable reservoirs of traits that could improve the crop today.

“When breeders select plants for desirable traits, they create highly specialized cotton varieties but also reduce genetic diversity,” he said. “As diversity declines, so does the plant’s ability to withstand new threats. Protective genes can be lost during breeding, leaving modern cotton vulnerable to emerging diseases. That’s why wild cotton populations are vital. Their rich genetic diversity continues to evolve under natural environmental pressures, providing valuable traits for future breeding efforts.”

Peterson said researchers have studied the origin of cotton’s domestication for more than 75 years. Early scientists noticed much of cotton’s diversity appeared to originate in the Yucatán, supported by closely related plant types and archaeological evidence of ancient people in the area using cotton.

“We’re confirming and building upon what earlier researchers discovered through years of painstaking work,” Peterson said.

Sequencing a genome, he said, is like solving a jigsaw puzzle.

“We can’t read a chromosome from end to end. We must sequence then reassemble many DNA pieces. In the past, those pieces were very short, making the process incredibly complex. Recent advances allow us to sequence much longer DNA stretches,” Peterson said. “It’s the difference between solving a 100-piece puzzle compared to one with a million pieces.”

Tony Arick, interim director of the MSU Institute for Genomics, Biocomputing and Biotechnology, said the modern process is easier and less expensive.

“The longer the DNA string, the better and easier it is to map. Using the jigsaw puzzle analogy, it’s much easier to see the big picture when there are fewer missing pieces,” he said.

Bigger bodies were a late addition for humans

 

The biggest jump in body size among our ancestors happened around 2 to 2.5 million years ago, with the appearance of Homo rudolfensis or Homo erectus/ergaster, rather than gradually across the whole human family tree. 

New research published today (Monday, 22 June 2026) in the journal PNAS, found that some species bucked the trend completely. Homo floresiensis and Homo naledi stayed small, with the early hominin Australopithecus weighing 40kg, on average, and reaching the height of a child. Other branches of Homo grew larger. Homo erectus/ergaster were the first hominins to weigh around 60 kg or more, on average, achieving weights similar to many modern humans.    

The University of Reading and University of Oxford findings challenge the idea that bodies simply got bigger and bigger over time in a steady line, eventually leading to modern humans. 

Dr Jacob Gardner, lead author at the University of Reading, said: "For years, different studies have come to different conclusions about whether our ancestors steadily grew bigger over time or jumped in size at some key point in our Homo ancestors. We think that's because everyone was looking at slightly different pieces of a much bigger puzzle. When you put all the fossils together, examine multiple competing ideas, and account for how species are related to each other, a clearer picture emerges. The answer is most likely a combination of these ideas. 

“The human story is not simply one of constant growth, but also of a major change that happened later, within our own genus, while other branches of the family, including some surprisingly small relatives, went their own way entirely." 

Piecing together the human puzzle 

Researchers reached these conclusions by looking at body weight from 386 fossils across 21 different species of hominins, the group that includes humans and our extinct relatives. They used statistical models to track how body size changed over millions of years. 

Previous studies disagreed because some focused on early relatives such as Australopithecus, others on later members of Homo, and some used different methods to estimate body weight from fossil bones. These studies also did not account for how hominin species were related to one another or the various uncertainties that come with an incomplete fossil record, such as which fossils belong to which species. Bringing all of this together in one model shows that these studies weren't actually disagreeing with each other, they were just looking at different parts of a more complicated story. Body weight steadily increased over time in our earlier hominin relatives, like Australopithecus, but then jumped in size at a key point later in Homo.  

The timing of this growth spurt lines up with other changes in later Homo. These ancestors were walking on two legs more efficiently than earlier hominins, eating more meat, and roaming over much larger areas in search of food and suitable habitat. A bigger body may have helped with all of these things, making it easier to travel long distances and survive on a varied diet. The findings suggest that growing larger was closely tied to a wider shift in how these early humans lived. 

Dr Thomas Puschel, co-author from the School of Anthropology and Museum Ethnography, University of Oxford, said: “Our results suggest that human body size evolution was not simply a story of steady growth over time. Although body mass generally increased throughout our evolutionary history, the most significant shift occurred later within the genus Homo. This change coincided with broader developments in how our ancestors moved across landscapes and exploited their environments, pointing to a close relationship between body size and major ecological and behavioural transitions."

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2521732123 

See the world of Stonehenge from your sofa

 

A new free online experience allowing anyone in the world to step inside the world of Stonehenge exhibition and explore thousands of years of history launches today (Sunday, 21 June). 

The Virtual World of Stonehenge, developed by researchers at the University of Reading and the British Museum, gives users an immersive digital tour of one of the most celebrated museum exhibitions in recent years. The original World of Stonehenge exhibition ran at the British Museum in 2022, attracting more than 190,000 visitors and bringing together over 400 objects from 36 institutions across Europe. 

Timed to release alongside the summer solstice, the new virtual version goes well beyond a simple recreation of the gallery. Users can go inside Stonehenge itself and watch it change through time, explore Neolithic flint mines at Grimes Graves, and discover rarely seen prehistoric objects through animation, soundscapes and interactive content. The experience is free to access via the British Museum website and works on desktop computers, tablets and phones. 

Professor Duncan Garrow, Professor of Archaeology at the University of Reading, said: "The original exhibition brought together an extraordinary collection of prehistoric objects, many of which had never been displayed together before. Now anyone, anywhere they are, can not only see those objects but understand the world of Stonehenge and experience how it looked and felt thousands of years ago. We hope it brings prehistoric Britain to life in a completely new way." 

Dr Neil Wilkin, at the British Museum, said: “This has been an amazing opportunity to think about the future of virtual museum exhibitions, not just at the British Museum but everywhere across the world”.  

Laser-scanning leaves, bracelets and crumbs 

The project was funded by UK Research and Innovation and builds on AHRC-funded research led by British Museum curator Dr Neil Wilkin, in partnership with Professor Duncan Garrow at the University of Reading. The team worked with the University of Southampton and digital heritage specialists ArtasMedia to transform a 3D laser scan of the original gallery, captured during the final weeks of the exhibition in 2022, into a fully interactive online experience. 

A particular focus of the project was making the stories behind lesser-known prehistoric objects more accessible. These include a 6,000-year-old elm leaf, a woven cow-hair bracelet, and the remains of a prehistoric feast, all of which are brought to life through new digital content developed specifically for the virtual exhibition. 

The launch coincides with the summer solstice, the moment when Stonehenge's alignment with the rising sun has drawn people to the site for thousands of years. 

The Virtual World of Stonehenge is free to access from Sunday 21 June: The World of Stonehenge: University of Reading and British Museum