The last two decades have seen a revolution in scientists' ability to reconstruct the past. This was made possible thanks to technological advances in the field DNA extracted from ancient bones and analyzed.
These achievements showed that Neanderthals and modern humans interbred — something happened that we had not thought about before. This has allowed researchers to untangle the various migrations that shaped modern humans. It also allowed teams to sequence the genomes of extinct animals, such as mammoths, and extinct pathogens, such as defunct strains of plague.
Caves can store tens of thousands of years of genetic history, providing ideal archives for studying long-term human-ecosystem interactions. The sediments under our feet become biological time capsules.
This is what we study here at the Geogenomic Archeology Campus Tübingen (GACT) in Germany. DNA analysis of cave deposits allows us to reconstruct who lived in Europe during the Ice Age, how ecosystems changed and what role people played. For example, did modern humans and Neanderthals live in the same caves? It is also possible to obtain genetic material from feces left in caves. We are currently analyzing DNA from the scat of a cave hyena that lived in Europe about 40,000 years ago.
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 sets of biological data) have transformed ancient DNA from a fragile curiosity into a high-performance scientific tool.
Today's sequencing machines can decode a hundred million times more DNA than their early predecessors. While it took more than a decade to create the first human genome, modern laboratories can now sequence hundreds of complete human genomes in a single day.
In 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, a leading specialist in this field. He emphasized the global significance of this research. Ancient DNA is now regularly making headlines, from attempts to recreate mammoth-like elephants to tracing hundreds of thousands of years of human presence in some parts of the world. Importantly, advances in robotics and computing have allowed us to recover DNA from both sediment and bone.
GACT is a growing research network based in Tübingen, Germany, where three institutions are collaborating across disciplines to develop new methods for searching for DNA in sediments. Archaeologists, geologists, bioinformaticians, microbiologists, and ancient DNA experts combine their expertise to uncover insights that no single field of science could achieve alone—a collaboration in which the whole truly becomes greater than the sum of its parts.
The network extends far beyond Germany. International partners enable field research to be carried out in archaeological caves and natural caves around the world. This summer, for example, the team explored caves in Serbia, collecting several hundred sediment samples for ancient DNA and conducting related environmental 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.
Needle in a haystack
Recovering DNA from sediment sounds simple: grab a scoop, extract it, sequence it. In reality, everything is much more complicated. The molecules are rare, degraded and fragmented, and mixed with modern contamination from cave visitors and wildlife. Finding genuine Ice Age molecules relies on subtle models of chemical damage to the DNA itself, ultrapure laboratories, robotic extraction and specialized bioinformatics. Each positive identification is a small triumph, revealing patterns invisible to traditional archaeology.
Much of GACT's work takes place in the caves of the Swabian Jura at UNESCO World Heritage Sites such as Hohle Fels, which houses the world's oldest musical instruments and works of fine 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 fragile biomolecules are preserved in stable conditions, allowing researchers to reconstruct the genetic history of Ice Age Europe.
One of the most interesting aspects of sediment DNA research is its ability to reveal long-extinct species even when no bones or artifacts remain. Particular attention is paid to people: who lived in the cave and when? Like modern people and Neanderthals used the caves and, as mentioned, were they there at the same time? Did cave bears and humans compete for shelter and resources? And what can the microbes that lived next to them tell us about human influence on past ecosystems?
The DNA of the sediments also provides traces of life outside the cave. Predators dragged their prey into sheltered spaces, and people left waste behind. By monitoring changes in the DNA of humans, animals and microbes over time, researchers can study ancient extinctions and shifts in ecosystems, offering insight into today's biodiversity crisis.
The work is ambitious: using sedimentary DNA to reconstruct Ice Age ecosystems and understand the ecological consequences of human presence. Just two years after GACT began, each set of data raises new questions. Each layer of the cave adds another twist to the story.
Hundreds of samples are currently being processed, and important discoveries lie ahead. Researchers expect to soon discover the first genomes of cave bears, the earliest traces of humans and complex microbial communities that once thrived in the dark. Will the sediments reveal all their secrets? Time will tell, but the outlook is encouraging.
This edited article is republished from Talk under Creative Commons license. Read original article.
