Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

Maria A. Spyrou (), Marcel Keller, Rezeda I. Tukhbatova, Christiana L. Scheib, Elizabeth A. Nelson, Aida Andrades Valtueña, Gunnar U. Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A. Inskip, Sacha Kacki, Felix M. Key, Elizabeth L. Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E. Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I. Bos () and Johannes Krause ()
Additional contact information
Maria A. Spyrou: Max Planck Institute for the Science of Human History
Marcel Keller: Max Planck Institute for the Science of Human History
Rezeda I. Tukhbatova: Max Planck Institute for the Science of Human History
Christiana L. Scheib: University of Tartu, Riia 23b
Elizabeth A. Nelson: Max Planck Institute for the Science of Human History
Aida Andrades Valtueña: Max Planck Institute for the Science of Human History
Gunnar U. Neumann: Max Planck Institute for the Science of Human History
Don Walker: MOLA (Museum of London Archaeology)
Amelie Alterauge: University of Bern
Niamh Carty: MOLA (Museum of London Archaeology)
Craig Cessford: University of Cambridge
Hermann Fetz: State Archive Nidwalden
Michaël Gourvennec: Agency Toulouse, 8 allée Michel de Montaigne
Robert Hartle: MOLA (Museum of London Archaeology)
Michael Henderson: MOLA (Museum of London Archaeology)
Kristin von Heyking: SNSB, State Collection for Anthropology and Palaeoanatomy Munich
Sarah A. Inskip: University of Cambridge
Sacha Kacki: PACEA, CNRS Institute, Université de Bordeaux
Felix M. Key: Massachusetts Institute of Technology
Elizabeth L. Knox: MOLA (Museum of London Archaeology)
Christian Later: Bavarian State Department of Monuments and Sites
Prishita Maheshwari-Aplin: University of Cambridge
Joris Peters: SNSB, State Collection for Anthropology and Palaeoanatomy Munich
John E. Robb: University of Cambridge
Jürgen Schreiber: Dig it! Company GbR
Toomas Kivisild: University of Tartu, Riia 23b
Dominique Castex: PACEA, CNRS Institute, Université de Bordeaux
Sandra Lösch: University of Bern
Michaela Harbeck: SNSB, State Collection for Anthropology and Palaeoanatomy Munich
Alexander Herbig: Max Planck Institute for the Science of Human History
Kirsten I. Bos: Max Planck Institute for the Science of Human History
Johannes Krause: Max Planck Institute for the Science of Human History

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.

Date: 2019
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DOI: 10.1038/s41467-019-12154-0

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