Scientists Find 60,000-Year-Old Antelope Proteins in Ancient Pigment, Revealing New Clues to Early Human Life

An extraordinary discovery in a South African rock shelter suggests that early Homo sapiens combined red ochre with animal-derived materials tens of thousands of years ago. The findings open a new window into prehistoric technology, symbolic behaviour and the invisible traces left behind by our ancestors.

By Open Chronicle History Desk

ARCHAEOLOGY | HUMAN EVOLUTION | PREHISTORIC TECHNOLOGY | SOUTH AFRICA

An invisible discovery from the Stone Age

Approximately 60,000 years ago, people living along the southern coast of Africa used a rocky shelter overlooking a landscape very different from the modern world.

They gathered materials, worked with mineral pigments and carried out activities whose physical traces would survive for tens of thousands of years.

Some of those traces were visible to archaeologists.

Others remained hidden until modern laboratory techniques made it possible to identify molecules preserved within ancient sediments.

A scientific investigation published on 21 October 2026 in Proceedings of the Royal Society B has revealed evidence of proteins associated with the common eland, a large African antelope, within an ochre-rich archaeological surface at Klipdrift Shelter in South Africa.

The discovery provides new insight into the ways early humans may have combined mineral and animal materials.

Researchers identified type I collagen, a structural protein found in animal connective tissues, in two sediment samples associated with the ancient pigment deposit.

The proteins were confidently attributed to the common eland, scientifically known as Taurotragus oryx.

The findings suggest that animal-derived material was present alongside the ochre, possibly because people deliberately mixed the substances or worked with animal hides treated using the pigment.

The discovery does not reveal the exact activity that produced the deposit.

Nevertheless, it offers rare molecular evidence of a relationship between mineral pigments and animal materials during the Middle Stone Age.

It also demonstrates that ancient proteins can survive in archaeological sediments even when the original objects or tissues have disappeared.

A rock shelter on the southern African coast

Klipdrift Shelter forms part of the Klipdrift Complex, situated within the coastal cliffs of the De Hoop Nature Reserve in South Africa’s Western Cape.

The site has become important for understanding the behaviour of early Homo sapiens.

Its archaeological deposits preserve evidence of human activity during the Middle Stone Age, a period associated with important developments in technology, material culture and behaviour.

The particular sediments examined in the new study belong to the Howiesons Poort archaeological tradition.

This period is known for distinctive stone tool technologies and evidence of complex human activities.

The ochre-rich feature investigated by the researchers was remarkable in its physical form.

It extended laterally across the archaeological deposits, possibly reaching more than one metre in length and approximately 40 centimetres in width.

The preserved material was relatively thin, reaching a maximum thickness of about one centimetre.

Rather than appearing as a single isolated lump of pigment, the ochre formed a broad surface within the sediment.

This raised questions about how it had accumulated.

Was the material deliberately spread across the ground?

Had people used the area for preparing pigments?

Could the deposit represent the remains of an activity involving animal skins or other organic materials?

The archaeological evidence alone could not provide a definitive answer.

To investigate further, researchers turned to the microscopic remains of ancient proteins.

Why ochre mattered to early humans

Ochre is a natural mineral pigment containing iron-rich compounds.

Its colours can range from yellow and brown to deep red, depending on its mineral composition and treatment.

Red ochre has a particularly long history in human societies.

Archaeologists have recovered ochre from numerous prehistoric sites, sometimes alongside grinding stones, containers or objects bearing traces of pigment.

Its uses were diverse.

Ochre could serve practical functions, including colouring materials and participating in technological processes.

It could also be used for bodily decoration, marking objects or activities carrying symbolic meaning.

However, the discovery of ochre at an archaeological site does not automatically demonstrate artistic or religious behaviour.

The same mineral could be used for several purposes.

A pigment deposit might represent the preparation of colouring material, the treatment of animal skins or an activity that left little other archaeological evidence.

Understanding the original function requires information about the surrounding objects, the structure of the deposit and any surviving chemical traces.

At Klipdrift Shelter, the presence of animal proteins offers an additional source of evidence.

The pigment was not simply associated with an unidentified organic residue.

The researchers were able to connect the detected protein to a particular animal species.

That identification provides a new way to investigate the activities that may have taken place at the site.

The unexpected presence of an antelope

The common eland is one of Africa’s largest antelope species.

It belongs to the family Bovidae and inhabits parts of eastern and southern Africa.

The animal has long been important in the ecology and cultural history of the region.

For prehistoric communities, a large antelope could provide meat, hides and other materials.

Its tissues could enter the archaeological record through many different activities, including food preparation and the processing of animal skins.

The new study identified type I collagen matching the common eland in two samples from the ochre-rich surface.

Collagen is a structural protein found in skin, bone, tendons and other connective tissues.

Its identification is significant because the original animal material was no longer visible.

The researchers were not examining an intact hide or a recognisable fragment of bone.

Instead, they recovered molecular traces from sediments that had remained buried for approximately 60 millennia.

The finding suggests that material derived from an eland was associated with the ochre deposit.

But the chemical evidence cannot identify which specific tissue produced the protein.

It also cannot determine precisely how that material came into contact with the pigment.

Those questions require interpretation of the archaeological context.

A prehistoric pigment mixture?

One possibility considered by the researchers is that people deliberately combined ochre powder with animal-derived materials.

Such a mixture could have been used to produce a substance with particular physical properties.

Adding organic material to mineral pigment can alter its texture, adhesion or behaviour when applied to a surface.

The researchers therefore consider whether the deposit may preserve traces of a prepared material.

Another explanation involves animal hides.

People may have treated an eland skin with ochre, perhaps during hide processing or for another practical purpose.

If the treated hide was left at the site and subsequently decomposed, its collagen could have become incorporated into the surrounding pigment-rich sediments.

Both interpretations are consistent with a relationship between human activity, animal material and ochre.

Neither has been conclusively demonstrated.

The researchers cannot reconstruct the original mixture or determine whether the material was applied to a human body, an object, an animal skin or another surface.

They also cannot establish whether the pigment was used primarily for practical or symbolic purposes.

The importance of the discovery lies in the molecular association itself.

It provides direct evidence that animal proteins were present in a prehistoric ochre deposit, allowing researchers to investigate possibilities that previously depended largely on indirect archaeological comparisons.

How scientists identified proteins after 60,000 years

The research used palaeoproteomics, a field that investigates ancient proteins preserved in archaeological and palaeontological materials.

Proteins are biological molecules composed of chains of amino acids.

Different organisms possess proteins with characteristic sequences, allowing scientists to identify biological sources when sufficiently informative fragments survive.

The team examined archived sediment samples from the ochre-rich feature.

They extracted protein residues and analysed them using liquid chromatography coupled with tandem mass spectrometry.

The method separates molecular components and measures fragments produced from protein-derived peptides.

Researchers then compare the resulting information with reference databases.

This allows them to identify proteins and, in favourable circumstances, distinguish between animal groups or species.

In the Klipdrift samples, the team detected peptide sequences associated with type I collagen.

Particular amino acid substitutions supported the identification of the common eland.

The researchers used a customised collagen reference database to strengthen the analysis.

This was especially important because collagen is found across many animal species.

A general collagen signal would not have been sufficient to identify the animal.

The informative peptide sequences provided a more specific result.

The discovery demonstrates the potential of studying archaeological sediments rather than relying exclusively on preserved bones, teeth or other recognisable remains.

Why proteins can survive when DNA disappears

Ancient DNA has transformed archaeology by allowing researchers to investigate ancestry, population movement and relationships between organisms.

However, DNA does not survive equally well in every environment.

Heat, moisture and other environmental processes can damage genetic material over time.

This presents particular challenges in parts of Africa, where climatic conditions often limit the preservation of ancient DNA.

Some proteins can remain detectable under conditions in which DNA is no longer recoverable.

Their molecular structures and interactions with surrounding materials may contribute to their long-term preservation.

This does not mean proteins survive indefinitely or that every ancient deposit contains usable biological evidence.

Preservation depends on environmental conditions, the original material and subsequent chemical changes.

Nevertheless, palaeoproteomics can provide valuable information when conventional genetic methods are unsuccessful.

The Klipdrift discovery illustrates this potential.

Scientists recovered species-informative protein fragments from sediments associated with human activity tens of thousands of years ago.

Such techniques may eventually reveal the biological origins of materials used in prehistoric technologies.

They could also help researchers identify activities that left no recognisable organic artefacts.

A connection with symbolic behaviour?

One of the most intriguing aspects of the discovery concerns the possible symbolic importance of the eland.

In the traditions of some San communities of southern Africa, eland have held important ceremonial and symbolic significance.

The animal appears in cultural traditions and interpretations of rock art.

This historical and ethnographic context makes the association between eland proteins and ochre particularly interesting.

Ochre itself has frequently been connected with symbolic activities in prehistoric societies.

The presence of both materials in a Middle Stone Age deposit therefore raises questions about the depth of human symbolic traditions.

Could the use of eland-derived materials with ochre reflect practices whose cultural significance extended beyond practical technology?

The possibility deserves investigation.

However, the researchers explicitly caution against drawing conclusions that exceed the evidence.

A single prehistoric deposit cannot demonstrate that the symbolic meaning of eland documented in much later traditions already existed 60,000 years ago.

The study does not establish that the ochre was used in a ritual.

Nor does it demonstrate a continuous religious tradition connecting Middle Stone Age communities with historically documented San practices.

Such conclusions would require additional archaeological evidence.

The discovery is significant because it opens a question, not because it resolves the history of prehistoric belief.

The technological abilities of early Homo sapiens

The findings contribute to a wider understanding of early human technological behaviour.

For much of the history of archaeological research, stone tools provided the most visible evidence of prehistoric technology.

Stone survives well in the ground, making it easier to recover and study.

Organic materials are more fragile.

Wood, plant fibres, animal skins and other substances can disappear, leaving little trace of how they were used.

As a result, the technological abilities of early humans may be underrepresented in the surviving archaeological record.

The identification of animal proteins in an ochre-rich deposit suggests that some activities involved combinations of materials that are difficult to recognise through conventional excavation.

If people deliberately mixed mineral pigment with animal-derived substances, this would represent knowledge of how different materials behaved together.

If the deposit resulted from the treatment of hides, it would provide evidence of another important technical activity.

Both possibilities fit within a broader picture of early Homo sapiens as a species capable of sophisticated material practices.

However, the study does not establish the precise technical process used at Klipdrift.

The evidence supports the association between ochre and eland-derived material, while the nature of the activity remains open to interpretation.

A discovery made possible by archived samples

Another important aspect of the investigation is that the researchers examined sediment samples already collected during earlier archaeological work.

The discovery did not require the excavation of an entirely new site.

Instead, the team applied advanced laboratory techniques to material preserved for scientific study.

This demonstrates the continuing value of archaeological archives.

Samples collected for one research purpose may later provide answers to questions that could not be investigated when they were first recovered.

Improvements in laboratory instruments, reference databases and analytical methods can transform the scientific value of existing collections.

At Klipdrift, sediments that appeared to preserve only mineral and archaeological information also contained biological evidence.

The discovery suggests that other archived samples from prehistoric sites may contain comparable traces.

Researchers could potentially identify proteins associated with animal skins, food preparation or other activities involving organic materials.

However, the technique must be applied carefully.

Ancient proteins can occur in very small quantities, and contamination from modern sources must be considered.

Reliable identification depends on appropriate laboratory procedures, reference comparisons and interpretation of the archaeological context.

The study provides a methodological example for future investigations.

What the discovery does not prove

The identification of eland collagen is the central scientific finding.

Several broader interpretations remain uncertain.

The research does not establish whether the protein originated from skin, bone, tendon or another animal tissue.

It does not identify a complete pigment recipe.

It does not demonstrate that the ochre was applied to human bodies.

It does not prove that the deposit represents prehistoric art, ceremonial activity or religious practice.

Nor can the researchers determine whether the material was deliberately mixed with ochre or became associated with the pigment through the use and decomposition of an animal hide.

These uncertainties do not diminish the discovery.

They define the boundary between measurable evidence and archaeological interpretation.

The study provides an important molecular observation that can now be tested against findings from other sites.

Repeated identification of similar associations could help establish whether combining animal-derived materials with ochre was a widespread practice.

Further experiments could also investigate how proteins behave when mixed with pigments or incorporated into treated hides.

Such research may eventually make it possible to distinguish between different prehistoric activities.

A new way to investigate humanity’s distant past

The importance of the Klipdrift discovery extends beyond the identification of one animal.

It demonstrates that archaeological sediments can preserve biological information about activities that took place tens of thousands of years ago.

The discovery also shows how interdisciplinary research can expand the questions archaeologists are able to ask.

Excavation reveals the physical structure of a site.

Geology and sediment analysis help reconstruct how deposits formed.

Chemistry and molecular biology can identify substances invisible to the human eye.

Historical and ethnographic research may then provide possible contexts for interpreting the evidence.

Each approach contributes something different.

None can independently reconstruct the complete lives of prehistoric people.

Together, however, they can produce a more detailed understanding of early human behaviour.

The researchers suggest that palaeoproteomics could become an increasingly valuable tool for investigating organic materials that have disappeared from the archaeological record.

This may be especially important in regions where ancient DNA preservation is limited.

The invisible traces of human ingenuity

Sixty thousand years ago, the people who used Klipdrift Shelter could not have imagined that fragments of animal proteins would remain detectable in the ground long after their activities had ended.

Their tools, materials and practices belonged to a world that left no written records.

Much of that world has disappeared.

Yet the ochre-rich sediments preserved a molecular connection between a mineral pigment and one of Africa’s largest antelope species.

Scientists can now identify that connection with remarkable precision.

What they cannot yet determine is exactly what the people at Klipdrift were doing.

Perhaps they were preparing a pigment mixture.

Perhaps they were working with an animal hide.

Perhaps the activity carried meanings that extended beyond its practical purpose.

The available evidence does not permit a definitive choice between those possibilities.

But the discovery changes what researchers can investigate.

It reveals that some of the most informative traces of early human life may not be visible as objects, structures or artworks.

They may survive as molecules hidden within the soil.

And with each improvement in scientific technology, those invisible traces offer new opportunities to understand the ingenuity, experiences and cultural complexity of our distant ancestors.