A refined phylochronology of the second plague pandemic in Western Eurasia
The origin and spread of consecutive outbreaks of the second plague pandemic in Europe (14th to 18th c.) are still poorly understood, although over one hundred ancient Yersinia pestis genomes and a vast corpus of documentary data have been collected. For most ancient genomes, radiocarbon (RC) dates regularly spanning more than 100 y are the only temporal information. This hampers an association with historically recorded outbreaks and limits our understanding of the microevolution and phylogeography of Y. pestis in the four centuries following the European Black Death (1347–1353). Here, we present new genomic evidence of the Second Pandemic from 11 sites in Europe, yielding 11 full and 15 lower-coverage genomes of Y. pestis dating to 1349–1710. To improve the dating information of our newly sequenced and previously published Y. pestis genomes, we present “Phylogenetically Informed Radiocarbon Modeling”, an approach that integrates chronological information retrieved from phylogenetic analysis with respective RC dates, leading to more accurate and precise dating intervals. Together with a fine-grained analysis of recorded plague outbreaks, this allows us to tentatively associate 75 genomes of the Second Pandemic with historically documented plague outbreaks.
Authors
- Lehti Saag (ORCID: https://orcid.org/0000-0002-2274-8138)
- Martin Malve
- Craig Cessford (ORCID: https://orcid.org/0000-0001-7291-7828)
- Mait Metspalu (ORCID: https://orcid.org/0000-0003-3099-9161)
- Philip Slavin (ORCID: https://orcid.org/0000-0002-6460-145X)
- John Robb (ORCID: https://orcid.org/0000-0002-7987-4549)
- W. A. Baetsen
- Айвар Крийска (ORCID: https://orcid.org/0000-0002-0900-7626)
- Thomas Reitmaier (ORCID: https://orcid.org/0000-0003-3810-5839)
- Anu Solnik (ORCID: https://orcid.org/0009-0009-5615-5726)
- Sandra Lösch (ORCID: https://orcid.org/0000-0003-3442-9764)
- Marcel Keller (ORCID: https://orcid.org/0000-0001-9668-6817)
- Heiki Valk (ORCID: https://orcid.org/0000-0003-4059-896X)
- Sönke Szidat (ORCID: https://orcid.org/0000-0002-1824-6207)
- Kadri Irdt
- Mathias Seifert (ORCID: https://orcid.org/0000-0002-6361-9295)
- C. von Planta
- Meriam Guellil (ORCID: https://orcid.org/0000-0002-7235-4604)
- Don D. Walker (ORCID: https://orcid.org/0000-0003-1230-6069)
- Sarah A. Inskip (ORCID: https://orcid.org/0000-0001-7424-2094)
- Kristiina Tambets (ORCID: https://orcid.org/0000-0002-8173-6380)
- Toomas Kivisild (ORCID: https://orcid.org/0000-0002-6297-7808)
- Helja Kabral (ORCID: https://orcid.org/0009-0003-6068-0650)
- Christine Cooper (ORCID: https://orcid.org/0000-0001-7904-808X)
- Christiana L. Scheib
Institutions
- University of Bern (CH)
- University of Stirling (GB)
- Museum of London Archaeology (GB)
- University of Vienna (AT)
- Oeschger Centre for Climate Change Research (CH)
- Ministry of Culture (IN)
- University of Leicester (GB)
- St. John's College of Nursing (US)
- University of Cambridge (GB)
- Arthur B. McDonald-Canadian Astroparticle Physics Research Institute (CA)
- Institut für Kulturforschung Graubünden (CH)
- Cantonal Archives of the Grisons (CH)
- Genomics England (GB)
- Swiss Archaeology (CH)
- Department of Archaeology (LK)
- Institute of History and Archaeology (RU)
- Estonian Biocentre (EE)
- University of Tartu (EE)
- KU Leuven (BE)
Publication Details
- Journal
- Proceedings of the National Academy of Sciences
- Published
- 2026-09-10
- DOI
- https://doi.org/10.1073/pnas.2534899123
- Primary Topic
- Yersinia bacterium, plague, ectoparasites research
- Type
- article
- Field-Weighted Citation Impact
- 0.00