132 Stone Age genomes near Paris link plague to Europe’s Neolithic collapse

A single Stone Age tomb 50 kilometres north of Paris now anchors one of Europe’s most stubborn archaeological puzzles. Researchers sequenced full genomes from 132 individuals buried inside the megalithic gallery at Bury and found two genetically distinct populations stacked in the same chamber, separated by an apparent abandonment. The community that returned to bury its dead there centuries later was not descended from the one that left.

The burials fall into two phases. The first runs roughly from 3200 to 3100 BC. The second resumes around 2900 BC and continues until about 2450 BC. The gap between them lines up with a broader signal that archaeologists have flagged for years: empty cemeteries, forest regrowth on once-farmed land, and shrinking settlement counts across France, Germany, Scandinavia and the British Isles around 3000 BC. Genomic continuity across that boundary is what nobody had been able to test directly. At Bury, there is no continuity.

The earlier group looks like the late descendants of Europe’s first farmers, whose ancestors had walked in from Anatolia thousands of years earlier. The later group carries a different ancestry profile, with input from communities further south. Inside the older phase, several individuals’ teeth still hold genetic traces of two infectious diseases: Yersinia pestis, the plague bacterium, and the spirochete that causes relapsing fever. Child and adolescent skeletons are over-represented in that phase, a demographic signature that fits an epidemic rather than ordinary attrition.

For reference, the previous best evidence for a Neolithic die-off was indirect — pollen cores showing forests reclaiming abandoned fields, archaeological counts of dwellings dropping by more than half in some regions. Those data could be read as people moving, not people dying. A 132-genome sample from one site, with plague DNA in the older layer and a genetic break across the gap, narrows the alternatives.

The social architecture also shifts between the two phases. The earlier burials look like multi-generational families laid down together. The later ones cluster around a single male lineage, with women and children attached to that line. That is a pattern recognised across much of Late Neolithic and Early Bronze Age Europe and usually associated with the Corded Ware and Bell Beaker expansions.

A single tomb is still a single tomb. Whether the same break shows up at other Paris Basin sites, and whether plague was the cause of the collapse or only a symptom of populations already in trouble, remains open. The team sequenced teeth from one cemetery, and recovered pathogen DNA from a subset of them. Pathogen survival in ancient teeth is uneven, so absence elsewhere will not be straightforward to interpret.

The Copenhagen-led group, working with French archaeologists, now wants to extend the same approach to other gallery graves in northern France and to compare the genomic signature against contemporaneous sites in Germany. The paper appeared in Nature Ecology & Evolution on 3 April 2026.