Giuseppe
Emeritus
[Source: PLoS ONE, full page: (LINK). Abstract, edited.]
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Yersinia pestis: New Evidence for an Old Infection
Kirsten I. Bos<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>*</SUP>, Philip Stevens<SUP>3</SUP>, Kay Nieselt<SUP>3</SUP>, Hendrik N. Poinar<SUP>4</SUP><SUP>,</SUP><SUP>5</SUP>, Sharon N. DeWitte<SUP>6</SUP>, Johannes Krause<SUP>1</SUP><SUP>*</SUP>
<SUP></SUP>
1 Institute for Archeological Sciences, University of T?bingen, T?bingen, Germany, 2 Laboratoire de Pal?oanthropologie, ?cole Pratique des Hautes ?tudes, Universit? de Bordeaux, Bordeaux, France, 3 Center for Bioinformatics, University of T?bingen, T?bingen, Germany, 4 McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada, 5 Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada, 6 University of South Carolina, Departments of Anthropology and Biological Sciences, Columbia, South Carolina, United States of America
Abstract
The successful reconstruction of an ancient bacterial genome from archaeological material presents an important methodological advancement for infectious disease research. The reliability of evolutionary histories inferred by the incorporation of ancient data, however, are highly contingent upon the level of genetic diversity represented in modern genomic sequences that are publicly accessible, and the paucity of available complete genomes restricts the level of phylogenetic resolution that can be obtained. Here we add to our original analysis of the Yersinia pestis strain implicated in the Black Death by consolidating our dataset for 18 modern genomes with single nucleotide polymorphism (SNP) data for an additional 289 strains at over 600 positions. The inclusion of this additional data reveals a cluster of Y. pestis strains that diverge at a time significantly in advance of the Black Death, with divergence dates roughly coincident with the Plague of Justinian (6<SUP>th</SUP> to 8<SUP>th</SUP> century AD). In addition, the analysis reveals further clues regarding potential radiation events that occurred immediately preceding the Black Death, and the legacy it may have left in modern Y. pestis populations. This work reiterates the need for more publicly available complete genomes, both modern and ancient, to achieve an accurate understanding of the history of this bacterium.
Citation: Bos KI, Stevens P, Nieselt K, Poinar HN, DeWitte SN, et al. (2012) Yersinia pestis: New Evidence for an Old Infection. PLoS ONE 7(11): e49803. doi:10.1371/journal.pone.0049803
Editor: M. Thomas P. Gilbert, Natural History Museum of Denmark, Denmark
Received: June 22, 2012; Accepted: October 16, 2012; Published: November 28, 2012
Copyright: ? 2012 Bos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding was provided by the Social Sciences and Humanities Research Council of Canada postdoctoral fellowship 756-2011-501. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: kirsten.bos@ifu.uni-tuebingen.de (KB); johannes.krause@uni-tuebingen.de (JK)
-Kirsten I. Bos<SUP>1</SUP><SUP>,</SUP><SUP>2</SUP><SUP>*</SUP>, Philip Stevens<SUP>3</SUP>, Kay Nieselt<SUP>3</SUP>, Hendrik N. Poinar<SUP>4</SUP><SUP>,</SUP><SUP>5</SUP>, Sharon N. DeWitte<SUP>6</SUP>, Johannes Krause<SUP>1</SUP><SUP>*</SUP>
<SUP></SUP>
1 Institute for Archeological Sciences, University of T?bingen, T?bingen, Germany, 2 Laboratoire de Pal?oanthropologie, ?cole Pratique des Hautes ?tudes, Universit? de Bordeaux, Bordeaux, France, 3 Center for Bioinformatics, University of T?bingen, T?bingen, Germany, 4 McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada, 5 Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada, 6 University of South Carolina, Departments of Anthropology and Biological Sciences, Columbia, South Carolina, United States of America
Abstract
The successful reconstruction of an ancient bacterial genome from archaeological material presents an important methodological advancement for infectious disease research. The reliability of evolutionary histories inferred by the incorporation of ancient data, however, are highly contingent upon the level of genetic diversity represented in modern genomic sequences that are publicly accessible, and the paucity of available complete genomes restricts the level of phylogenetic resolution that can be obtained. Here we add to our original analysis of the Yersinia pestis strain implicated in the Black Death by consolidating our dataset for 18 modern genomes with single nucleotide polymorphism (SNP) data for an additional 289 strains at over 600 positions. The inclusion of this additional data reveals a cluster of Y. pestis strains that diverge at a time significantly in advance of the Black Death, with divergence dates roughly coincident with the Plague of Justinian (6<SUP>th</SUP> to 8<SUP>th</SUP> century AD). In addition, the analysis reveals further clues regarding potential radiation events that occurred immediately preceding the Black Death, and the legacy it may have left in modern Y. pestis populations. This work reiterates the need for more publicly available complete genomes, both modern and ancient, to achieve an accurate understanding of the history of this bacterium.
Citation: Bos KI, Stevens P, Nieselt K, Poinar HN, DeWitte SN, et al. (2012) Yersinia pestis: New Evidence for an Old Infection. PLoS ONE 7(11): e49803. doi:10.1371/journal.pone.0049803
Editor: M. Thomas P. Gilbert, Natural History Museum of Denmark, Denmark
Received: June 22, 2012; Accepted: October 16, 2012; Published: November 28, 2012
Copyright: ? 2012 Bos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding was provided by the Social Sciences and Humanities Research Council of Canada postdoctoral fellowship 756-2011-501. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: kirsten.bos@ifu.uni-tuebingen.de (KB); johannes.krause@uni-tuebingen.de (JK)
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