Abstract
<jats:title>Abstract</jats:title><jats:p>In the period between 5,300 and 4,900 calibrated years before present (cal.<jats:sc>bp</jats:sc>), populations across large parts of Europe underwent a period of demographic decline<jats:sup>1,2</jats:sup>. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline<jats:sup>3</jats:sup>, others for the spread of an early form of plague<jats:sup>4</jats:sup>. 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, detected in at least 17% of the sampled population and 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 shows that the Neolithic plague genomes retained ancestral genomic variation present in<jats:italic>Yersinia pseudotuberculosis</jats:italic>, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.</jats:p>