Microevolution and history of the plague bacillus, Yersinia pestis

Mark Achtman, Giovanna Morelli, Peixuan Zhu, Thierry Wirth, Ines Diehl, Barica Kusecek, Amy J. Vogler, David M. Wagner, Christopher J. Allender, W. Ryan Easterday, Viviane Chenal-Francisque, Patricia Worsham, Nicholas R. Thomson, Julian Parkhill, Luther E. Lindler, Elisabeth Carniel, Paul Keim

Research output: Contribution to journalArticlepeer-review

404 Scopus citations


The association of historical plague pandemics with Yersinia pestis remains controversial, partly because the evolutionary history of this largely monomorphic bacterium was unknown. The microevolution of Y. pestis was therefore investigated by three different multilocus molecular methods, targeting genomewide synonymous SNPs, variation in number of tandem repeats, and insertion of IS100 insertion elements. Eight populations were recognized by the three methods, and we propose an evolutionary tree for these populations, rooted on Yersinia pseudotuberculosis. The tree invokes microevolution over millennia, during which enzootic pestoides isolates evolved. This initial phase was followed by a binary split 6,500 years ago, which led to populations that are more frequently associated with human disease. These populations do not correspond directly to classical biovars that are based on phenotypic properties. Thus, we recommend that henceforth groupings should be based on molecular signatures. The age of Y. pestis inferred here is compatible with the dates of historical pandemic plague. However, it is premature to infer an association between any modern molecular grouping and a particular pandemic wave that occurred before the 20th century.

Original languageEnglish (US)
Pages (from-to)17837-17842
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number51
StatePublished - Dec 21 2004


  • Insertion element
  • Molecular clock
  • Pandemic
  • SNP
  • Variable number tandem repeats

ASJC Scopus subject areas

  • General


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