'Biological time capsules': How DNA from cave dirt is revealing clues about early humans and Neanderthals

The last two decades have seen a revolution in scientists' ability to reconstruct the past. This has been made possible through technological advances in the way DNA is extracted from ancient bones and analyzed.

These advances have revealed that Neanderthals and modern humans interbred — something that wasn't previously thought to have happened. It has allowed researchers to disentangle the various migrations that shaped modern people. It has also allowed teams to sequence the genomes of extinct animals, such as the mammoth, and extinct agents of disease, such as defunct strains of plague.

While much of this work has been carried out by analyzing the physical remains of humans or animals, there is another way to obtain ancient DNA from the environment. Researchers can now extract and sequence DNA (determine the order of "letters" in the molecule) directly from cave sediments rather than relying on bones. This is transforming the field, known as paleogenetics.

Caves can preserve tens of thousands of years of genetic history, providing ideal archives for studying long-term human–ecosystem interactions. The deposits beneath our feet become biological time capsules.

It is something we are exploring here at the Geogenomic Archaeology Campus Tübingen (GACT) in Germany. Analyzing DNA from cave sediments allows us to reconstruct who lived in ice age Europe, how ecosystems changed and what role humans played. For example, did modern humans and Neanderthals overlap in the same caves? It's also possible to obtain genetic material from faeces left in caves. At the moment we are analyzing DNA from the droppings of a cave hyena that lived in Europe around 40,000 years ago.

The oldest sediment DNA discovered so far comes from Greenland and is 2 million years old.

Paleogenetics has come a long way since the first genome of an extinct animal, the quagga, a close relative of modern zebras, was sequenced in 1984. Over the past two decades, next-generation genetic sequencing machines, laboratory robotics and bioinformatics (the ability to analyze large, complex biological datasets) have turned ancient DNA from a fragile curiosity into a high-throughput scientific tool.

Today, sequencing machines can decode up to a hundred million times more DNA than their early predecessors. Where the first human genome took over a decade to complete, modern laboratories can now sequence hundreds of full human genomes in a single day.

In 2022, the Nobel prize in physiology or medicine was awarded to Svante Pääbo, a leading light in this field. It highlighted the global significance of this research. Ancient DNA now regularly makes headlines, from attempts to recreate mammoth-like elephants, to tracing hundreds of thousands of years of human presence in parts of the world. Crucially, advances in robotics and computing have allowed us to recover DNA from sediments as well as bones.

GACT is a growing research network based in Tübingen, Germany, where three institutions collaborate across disciplines to establish new methods for finding DNA in sediments. Archaeologists, geoscientists, bioinformaticians, microbiologists and ancient-DNA specialists combine their expertise to uncover insights that no single field could achieve alone —- a collaboration in which the whole genuinely becomes greater than the sum of its parts.

The network extends well beyond Germany. International partners enable fieldwork in archaeological cave sites and natural caves all over the world. This summer, for example, the team investigated cave sites in Serbia, collecting several hundred sediment samples for ancient DNA and related ecological analyses. Future work is planned in South Africa and the western United States to test the limits of ancient DNA preservation in sediments from different environments and time periods.

A needle in a haystack

Recovering DNA from sediments sounds simple: take a scoop, extract, sequence. In reality, it is far more complex. The molecules are scarce, degraded and fragmented, and mixed with modern contamination from cave visitors and wildlife. Detecting authentic ice age molecules relies on subtle chemical damage patterns to the DNA itself, ultra-clean laboratories, robotic extraction, and specialized bioinformatics. Every positive identification is a small triumph, revealing patterns invisible to conventional archaeology.

Much of GACT's work takes place in the caves of the Swabian Jura within Unesco World Heritage sites such as Hohle Fels, home to the world's oldest musical instruments and figurative art. Neanderthals and Homo sapiens left behind stone artifacts, bones, ivory and sediments that accumulated over tens of millennia. Caves are natural DNA archives, where stable conditions preserve fragile biomolecules, enabling researchers to build up a genetic history of ice age Europe.

One of the most exciting aspects of sediment DNA research is its ability to detect species long gone, even when no bones or artifacts remain. A particular focus lies on humans: who lived in the cave, and when? How modern humans and Neanderthals use the caves and, as mentioned, were they there at the same times? Did cave bears and humans compete for shelter and resources? And what might the microbes that lived alongside them reveal about the impact humans had on past ecosystems?

Sediment DNA also traces life outside the cave. Predators dragged prey into sheltered chambers, humans left waste behind. By following changes in human, animal and microbial DNA over time, researchers can examine ancient extinctions and ecosystem shifts, offering insights relevant to today's biodiversity crisis.

The work is ambitious: using sedimentary DNA to reconstruct ice age ecosystems and to understand the ecological consequences of human presence. Only two years into GACT, every dataset generates new questions. Every cave layer adds another twist to the story.

With hundreds of samples now being processed, major discoveries lie ahead. Researchers expect soon to detect the first cave bear genomes, the earliest human traces, and complex microbial communities that once thrived in darkness. Will the sediments reveal all their secrets? Time will tell — but the prospects are exhilarating.

This edited article is republished from The Conversation under a Creative Commons license. Read the original article.