Repeated plague infections across six generations of Neolithic Farmers

Frederik Valeur Seersholm (), Karl-Göran Sjögren, Julia Koelman, Malou Blank, Emma M. Svensson, Jacqueline Staring, Magdalena Fraser, Thomaz Pinotti, Hugh McColl, Charleen Gaunitz, Tatiana Ruiz-Bedoya, Lena Granehäll, Berenice Villegas-Ramirez, Anders Fischer, T. Douglas Price, Morten E. Allentoft, Astrid K. N. Iversen, Tony Axelsson, Torbjörn Ahlström, Anders Götherström, Jan Storå, Kristian Kristiansen, Eske Willerslev, Mattias Jakobsson, Helena Malmström and Martin Sikora ()
Additional contact information
Frederik Valeur Seersholm: University of Copenhagen
Karl-Göran Sjögren: University of Gothenburg
Julia Koelman: Uppsala University
Malou Blank: University of Gothenburg
Emma M. Svensson: Uppsala University
Jacqueline Staring: Lygature
Magdalena Fraser: Uppsala University
Thomaz Pinotti: University of Copenhagen
Hugh McColl: University of Copenhagen
Charleen Gaunitz: University of Copenhagen
Tatiana Ruiz-Bedoya: Uppsala University
Lena Granehäll: Uppsala University
Berenice Villegas-Ramirez: Uppsala University
Anders Fischer: Sealand Archaeology
T. Douglas Price: University of Gothenburg
Morten E. Allentoft: University of Copenhagen
Astrid K. N. Iversen: University of Oxford
Tony Axelsson: University of Gothenburg
Torbjörn Ahlström: Lund University
Anders Götherström: Stockholm University and the Swedish Museum of Natural History
Jan Storå: Stockholm University
Kristian Kristiansen: University of Copenhagen
Eske Willerslev: University of Copenhagen
Mattias Jakobsson: Uppsala University
Helena Malmström: Uppsala University
Martin Sikora: University of Copenhagen

Nature, 2024, vol. 632, issue 8023, 114-121

Abstract: Abstract 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 decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. 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 Yersinia pseudotuberculosis, 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.

Date: 2024
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DOI: 10.1038/s41586-024-07651-2

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