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

Maria A. Spyrou(Max Planck Institute for the Science of Human History), Marcel Keller(Bavarian State Collection of Zoology), Rezeda I. Tukhbatova(Kazan Federal University), Christiana L. Scheib(University of Tartu), 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 D. Walker(Museum of London Archaeology), Amelie Alterauge(University of Bern), Niamh Carty(Museum of London Archaeology), Craig Cessford(University of Cambridge), Hermann Fetz, Michaël Gourvennec, Robert Hartle(Museum of London Archaeology), Michael Henderson(Museum of London Archaeology), Kristin von Heyking(Bavarian State Collection of Zoology), Sarah A. Inskip(University of Cambridge), Sacha Kacki(Centre National de la Recherche Scientifique), Felix M. Key(Massachusetts Institute of Technology), Elizabeth L. Knox(Museum of London Archaeology), Christian Later, Prishita Maheshwari-Aplin(University of Cambridge), Joris Peters(Bavarian State Collection of Zoology), John Robb(University of Cambridge), Jürgen Schreiber, Toomas Kivisild(University of Tartu), Dominique Castex(Centre National de la Recherche Scientifique), Sandra Lösch(University of Bern), Michaela Harbeck(Bavarian State Collection of Zoology), 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
October 2, 2019
10.1038/s41467-019-12154-0
Cited by 174Open Access
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Abstract

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.

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