DNA evidence reveals a Stone Age population collapse in France

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By analyzing DNA of ancient skeletons at a Neolithic burial site near Paris, an international team of researchers has uncovered evidence of a dramatic population replacement 5,000 years ago. The findings indicate that the population collapse known as the "Neolithic decline" was a far-reaching phenomenon.

"By joining forces of experts from a wide variety of disciplines, we can now begin to understand what happened during one of the most dramatic transitions in European prehistory," says Kristian Kristiansen, Professor of Archaeology at the University of Gothenburg and one of the researchers behind the study.

The large-scale genetic study shows that the people buried at the site belonged to two completely different populations, separated by a dramatic collapse around 5,000 years ago. The study was led by researchers from the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen and is based on DNA analysis of 132 individuals buried at the Bury site, about 50 kilometers north of Paris.

"We can see a clear genetic break between the two burial phases. The people who used the tomb before and after the collapse appear to be two completely different populations," says Frederik Seersholm, researcher at the University of Copenhagen. "This tells us that something significant happened, like a major disruption that led to the decline of one population and the arrival of another."

The article "Population discontinuity in the Paris Basin linked to evidence of the Neolithic decline" is published in Nature Ecology & Evolution.

A collapse in Stone Age society

The Bury burial site was used in two distinct phases: one before and one after what archaeologists call the "Neolithic decline," a period when populations across northwestern Europe sharply decreased.

The first phase, around 3200–3100 BC, shows signs of unusually high mortality, particularly among younger individuals.

"This kind of mortality pattern is not what we expect in a normal, healthy population," says Laure Salanova, Directrice de recherche at CNRS and responsible for the Bury project. "It suggests that some catastrophic event may have occurred, such as disease, famine or conflict."

After this period, the site was abandoned for several centuries. When it was reused, the people buried there were genetically different.

"This second group had strong genetic ties to Southern France and Iberia, suggesting that it represents people who migrated northwards into the Paris Basin after the population collapse," says Salanova.

Disease detected in the dead

The researchers also identified DNA from several pathogens in the ancient remains—including Yersinia pestis, the bacterium that causes plague, and Borrelia recurrentis, the causative agent of louse-borne relapsing fever. Plague was detected in individuals from both phases, though it was more common in the earlier population.

"The presence of pathogenic DNA shows that infectious diseases were affecting human populations at this time," says Martin Sikora, Associate Professor at the University of Copenhagen.

"While there is no strong case to say that plague alone caused the population collapse, the total disease load could have been one of several contributing factors."

Family structures revealed

Using advanced DNA techniques, the researchers were also able to reconstruct relationships within the burial site. In the earlier phase, the tomb was dominated by large, closely related families spanning multiple generations.

"This suggests a tightly knit community where biological family ties were central," says Sikora. In the later phase, there are fewer close relatives, most of whom are related through a single paternal line. "This tells us that not only the population changed, but also how society itself was structured, at least in the funerary sphere."

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A Europe-Wide phenomenon

The study strengthens the picture that the Neolithic decline affected large parts of Europe.

"In demographic terms, the later phase is characterized by burials spread out over time, which may correspond to a highly reduced population or to a selected part of the population," says Philippe Chambon at CNRS, who was responsible for the analysis of the skeletal remains.

Environmental data from the same period shows forest regrowth, suggesting that farmland was abandoned and human activity decreased significantly.

The study also shows that new populations moved into previously inhabited areas following the collapse.

"These results suggest that the decline created space for new groups to expand into the region," says Salanova.

"The research is the result of strong interdisciplinary collaboration, combining genetics and archaeology with strontium analyses, radiocarbon dating and palynology [the study of ancient pollen]," says Kristiansen at the University of Gothenburg.

Publication details

Frederik V. Seersholm et al, Population discontinuity in the Paris Basin linked to evidence of the Neolithic decline, Nature Ecology & Evolution (2026). DOI: 10.1038/s41559-026-03027-z. www.nature.com/articles/s41559-026-03027-z

Journal information: Nature Ecology & Evolution

Provided by University of Gothenburg