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

Author

Listed:
  • Maria A. Spyrou

    (Max Planck Institute for the Science of Human History
    University of Tübingen)

  • Marcel Keller

    (Max Planck Institute for the Science of Human History
    SNSB, State Collection for Anthropology and Palaeoanatomy Munich)

  • Rezeda I. Tukhbatova

    (Max Planck Institute for the Science of Human History
    Kazan Federal University)

  • Christiana L. Scheib

    (University of Tartu, Riia 23b)

  • Elizabeth A. Nelson

    (Max Planck Institute for the Science of Human History
    University of Tübingen)

  • 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
    Durham University)

  • 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
    Ludwig Maximilian University Munich)

  • John E. Robb

    (University of Cambridge)

  • Jürgen Schreiber

    (Dig it! Company GbR)

  • Toomas Kivisild

    (University of Tartu, Riia 23b
    Katholieke Universiteit Leuven)

  • 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
    University of Tübingen)

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.

Suggested Citation

  • 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 C, 2019. "Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12154-0
    DOI: 10.1038/s41467-019-12154-0
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    Cited by:

    1. Madsen, Jakob B. & Robertson, Peter E. & Ye, Longfeng, 2024. "Lives versus livelihoods in the middle ages: The impact of the plague on trade over 400 years," European Economic Review, Elsevier, vol. 162(C).
    2. Paul Slack, 2022. "Perceptions of plague in eighteenth‐century Europe," Economic History Review, Economic History Society, vol. 75(1), pages 138-156, February.

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