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

  • Spyrou MA Max Planck Institute for the Science of Human History, 07745, Jena, Germany. spyrou@shh.mpg.de.
  • Keller M Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Tukhbatova RI Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Scheib CL Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
  • Nelson EA Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Andrades Valtueña A Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Neumann GU Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Walker D MOLA (Museum of London Archaeology), London, N1 7ED, UK.
  • Alterauge A Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland.
  • Carty N MOLA (Museum of London Archaeology), London, N1 7ED, UK.
  • Cessford C Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK.
  • Fetz H Archaeological Service, State Archive Nidwalden, 6371, Nidwalden, Switzerland.
  • Gourvennec M Archeodunum SAS, Agency Toulouse, 8 allée Michel de Montaigne, 31770, Colomiers, France.
  • Hartle R MOLA (Museum of London Archaeology), London, N1 7ED, UK.
  • Henderson M MOLA (Museum of London Archaeology), London, N1 7ED, UK.
  • von Heyking K SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany.
  • Inskip SA McDonald Institute for Archaeological Research, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK.
  • Kacki S PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France.
  • Key FM Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
  • Knox EL MOLA (Museum of London Archaeology), London, N1 7ED, UK.
  • Later C Bavarian State Department of Monuments and Sites, 80539, Munich, Germany.
  • Maheshwari-Aplin P Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK.
  • Peters J SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany.
  • Robb JE Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK.
  • Schreiber J Dig it! Company GbR, 86971, Peiting, Germany.
  • Kivisild T Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
  • Castex D PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France.
  • Lösch S Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland.
  • Harbeck M SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany.
  • Herbig A Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
  • Bos KI Max Planck Institute for the Science of Human History, 07745, Jena, Germany. bos@shh.mpg.de.
  • Krause J Max Planck Institute for the Science of Human History, 07745, Jena, Germany. krause@shh.mpg.de.
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  • 2019-10-04
Published in:
  • Nature communications. - 2019
Archaeology
DNA, Bacterial
Europe, Eastern
Fossils
Genome, Bacterial
High-Throughput Nucleotide Sequencing
Humans
Pandemics
Phylogeny
Phylogeography
Plague
Polymorphism, Single Nucleotide
Time Factors
Virulence
Yersinia pestis
English 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.
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://sonar.ch/global/documents/228036
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