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Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12363-12372. doi: 10.1073/pnas.1820447116. Epub 2019 Jun 4.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

Author information

1
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de.
2
State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany.
3
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.
4
Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom.
5
Institute of Genomics, University of Tartu, 51010 Tartu, Estonia.
6
Friedrich Schiller University Jena, 07743 Jena, Germany.
7
Archaeological Collection of the Bavarian State, 80538 Munich, Germany.
8
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799 Munich, Germany.
9
Bavarian State Department of Monuments and Sites, 80539 Munich, Germany.
10
Department for Municipal Archaeology, Valencia City Council, 46014 Valencia, Spain.
11
CNRS, UMR5140, Archéologie des Sociétés Méditerranéennes, 34199 Montpellier, France.
12
Service d'Archéologie Préventive de l'Agglomération de Bourges Plus, 18023 Bourges Cedex, France.
13
Department of Pre- and Protohistory, University of Vienna, 1190 Vienna, Austria.
14
McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom.
15
ArchaeoBioCenter, Ludwig Maximilian University Munich, 80539 Munich, Germany.
16
Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, 80539 Munich, Germany.
17
Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
18
UMR 5199, PACEA, CNRS Institute, 33615 Pessac Cedex, France.
19
Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, MA 02138.
20
Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany.
21
State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany; marcel.keller@ut.ee harbeck@snsb.de herbig@shh.mpg.de krause@shh.mpg.de.

Abstract

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

KEYWORDS:

Anglo-Saxons; Justinianic Plague; Merovingians; ancient DNA; bacterial evolution

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