Repeated plague infections across six generations of Neolithic Farmers

In the period between 5,300 and 4,900 calibrated years before present (cal. BP), populations across large parts of Europe underwent a period of demographic decline. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline; others for the spread of an early form of plague. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detectable in at least 17% of the sampled population across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics show that these prehistoric plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis. Using reference genomes from ancient ancestors Yersinia pestis and colleagues over the last 50,000 years and has been infecting humans since prehistoric times. The vast majority of prehistoric plague genomes are from Late Neolithic and Bronze Age (LNBA) individuals dating to 4700–2400 cal. BP. These genomes fall within two distinct lineages that can be distinguished by the absence (LNBA) or presence (LNBA') of the y gene. The y gene is crucial for the bacterium’s survival in the plague digestive tract when the source is an infected mouse, black rat or human, and hence for the development of bubonic plague.