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Cited by 192

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Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague

Harbeck, Michaela, Seifert, Lisa, Hänsch, Stephanie, Wagner, David M., Birdsell, Dawn, Parise, Katy L., Wiechmann, Ingrid, Grupe, Gisela, Thomas, Astrid, Keim, Paul, Zöller, Lothar, Bramanti, Barbara, Riehm, Julia M., Scholz, Holger C.·2013·PLoS Pathogens
DOI 10.1371/journal.ppat.1003349PMC PMC3642051
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Figure 1 Global phylogeny for Y. pestis. This global phylogeny for Y. pestis is based upon figures 1A and S3B in Cui et al. [11]. It includes four major branches (0–4) and is rooted with Y. pseudotuberculosis, the ancestor of Y. pestis [28]. The identities of many of the major nodes defined by Cui et al. [11] are presented in blue text. Circles represent specific populations; populations highlighted in gray have, to date, only been found in Asia [10], [11]. Note that the location where strain Angola was isolated, which is the sole representative of population 0.PE3, is unknown. The phylogenetic position of Mongolian strain MNG 2972 is indicated with the blue box (see text). Five previously identified [10], [11] key SNPs were utilized in the current study: s545, which occurs along the branch between nodes N06 and N07 (not shown); s87 and s89; which occur along the branch between N04 and N05; s82, which occurs along the branch between the branching point of strain MNG 2972 and N04; and s463, which occurs along the branch between the branching point of strain MNG 2972 and N03. It is known that these SNPs occur along these specific branches but the exact position and order of these SNPs along each branch is unknown. Sample A120 possesses ancestral states for SNPs s87, s89, and s545; and derived states for SNPs s82 and s463. Thus, the position of sample A120 in this phylogeny is along the branch between the branching point of strain MNG 2972 and N04, along branch N04-N05, along the branch from N04 to 0.ANT1 (red branches), or along one of the sub-branches within 0.ANT.1 (not shown). The phylogenetic positions of strains from the second pandemic [3], [12] are indicated with the yellow boxes according to Cui et al. [11]. The basal node for the 1.ORI group, which caused the third pandemic, is N14 [11].
Figure 1 Global phylogeny for Y. pestis. This global phylogeny for Y. pestis is based upon figures 1A and S3B in Cui et al. [11]. It includes four major branches (0–4) and is rooted with Y. pseudotuberculosis, the ancestor of Y. pestis [28]. The identities of many of the major nodes defined by Cui et al. [11] are presented in blue text. Circles represent specific populations; populations highlighted in gray have, to date, only been found in Asia [10], [11]. Note that the location where strain Angola was isolated, which is the sole representative of population 0.PE3, is unknown. The phylogenetic position of Mongolian strain MNG 2972 is indicated with the blue box (see text). Five previously identified [10], [11] key SNPs were utilized in the current study: s545, which occurs along the branch between nodes N06 and N07 (not shown); s87 and s89; which occur along the branch between N04 and N05; s82, which occurs along the branch between the branching point of strain MNG 2972 and N04; and s463, which occurs along the branch between the branching point of strain MNG 2972 and N03. It is known that these SNPs occur along these specific branches but the exact position and order of these SNPs along each branch is unknown. Sample A120 possesses ancestral states for SNPs s87, s89, and s545; and derived states for SNPs s82 and s463. Thus, the position of sample A120 in this phylogeny is along the branch between the branching point of strain MNG 2972 and N04, along branch N04-N05, along the branch from N04 to 0.ANT1 (red branches), or along one of the sub-branches within 0.ANT.1 (not shown). The phylogenetic positions of strains from the second pandemic [3], [12] are indicated with the yellow boxes according to Cui et al. [11]. The basal node for the 1.ORI group, which caused the third pandemic, is N14 [11].CC BY · PubMed Central

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Citations

Cites

Research works printed but not linked: 25

  1. Little LK (2007) Life and afterlife of the first plague pandemic. In: Little LK, editor. Plague and the end of Antiquity The pandemic of 541–750. Cambridge: Cambridge University Press. pp. 3–32.
  2. Sallares R (2007) Ecology, evolution and epidemiology of plague. In: Little LK, editor. Plague and the end of Antiquity The pandemic of 541–750. Cambridge: Cambridge University Press. pp. 231–290.
  3. KI Bos, 2011, A draft genome of Yersinia pestis from victims of the Black Death, Nature, 478, 506, 10.1038/nature10549 · DOI · Paper page
  4. EC Holmes, 2011, Genomics: Plague's progress, Nature, 478, 465, 10.1038/478465a · DOI
  5. R Devignat, 1951, Variétés de l'espèce Pasteurella pestis. Nouvelle hypothèse, Bull World Health Organ, 4, 247
  6. AP Anisimov, 2004, Intraspecific diversity of Yersinia pestis, Clin Microbiol Rev, 17, 434, 10.1128/CMR.17.2.434-464.2004 · DOI
  7. Y Li, 2009, Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci, PLoS One, 4, e6000, 10.1371/journal.pone.0006000 · DOI
  8. JM Riehm, 2012, Yersinia pestis lineages in Mongolia, PLoS ONE, 7, e30624, 10.1371/journal.pone.0030624 · DOI · Paper page
  9. M Achtman, 2004, Microevolution and history of the plague bacillus, Yersinia pestis, Proc Natl Acad Sci U S A, 101, 17837, 10.1073/pnas.0408026101 · DOI · Paper page
  10. G Morelli, 2010, Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity, Nat Genet, 42, 1140, 10.1038/ng.705 · DOI · Paper page
  11. Y Cui, 2013, Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis, Proc Natl Acad Sci U S A, 110, 577, 10.1073/pnas.1205750110 · DOI
  12. S Haensch, 2010, Distinct clones of Yersinia pestis caused the black death, PLoS Pathog, 6, e1001134, 10.1371/journal.ppat.1001134 · DOI
  13. M Drancourt, 2004, Genotyping, Orientalis-like Yersinia pestis, and plague pandemics, Emerg Infect Dis, 10, 1585, 10.3201/eid1009.030933 · DOI
  14. M Drancourt, 2007, Yersinia pestis Orientalis in remains of ancient plague patients, Emerg Infect Dis, 13, 332, 10.3201/eid1302.060197 · DOI
  15. I Wiechmann, 2005, Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.), Am J Phys Anthropol, 126, 48, 10.1002/ajpa.10276 · DOI
  16. MB Prentice, 2004, Was the Black Death caused by Yersinia pestis?, Lancet Infect Dis, 4, 72, 10.1016/S1473-3099(04)00923-5 · DOI
  17. K Tsangaras, 2012, Museums and disease: using tissue archive and museums samples to study pathogens, Ann Anat, 194, 58, 10.1016/j.aanat.2011.04.003 · DOI
  18. G Vergnaud, 2005, Yersinia pestis genotyping, Emerg Infect Dis, 11, 1317, 10.3201/eid1108.040942 · DOI
  19. M Achtman, 2012, Insights from genomic comparisons of genetically monomorphic bacterial pathogens, Philos Trans R Soc Lond B Biol Sci, 367, 860, 10.1098/rstb.2011.0303 · DOI
  20. C Roberts, 2008, Using ancient DNA analysis in palaeopathology: a critical analysis of published papers, with recommendations for future work, Int J of Osteoarchaeol, 18, 600, 10.1002/oa.966 · DOI
  21. I Wiechmann, 2010, Yersinia pestis DNA sequences in late medieval skeletal finds, Bavaria, Emerg Infect Dis, 16, 1806, 10.3201/eid1611.100598 · DOI
  22. S Paabo, 2004, Genetic analyses from ancient DNA, Annu Rev Genet, 38, 645, 10.1146/annurev.genet.37.110801.143214 · DOI · Paper page
  23. Rosen W (2007) Justinian's Flea: Plague, empire, and the birth of Europe. London: Viking Penguin.
  24. T Schneider, 2008, Mehrfachbestattungen von Männern in der Merowingerzeit, Z Archaol Mittel, 36, 1
  25. McCormick M (2007) Towards a molecular history of the Justinianic Plague. In: Little LK, editor. Plague and the end of Antiquity The pandemic of 541–750. Cambridge: Cambridge University Press. pp. 290–312.

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Metadata

Authors
Harbeck, M., Seifert, L., Hänsch, S., Wagner, D. M., Birdsell, D., Parise, K. L., Wiechmann, I., Grupe, G., Thomas, A., Keim, P., Zöller, L., Bramanti, B., Riehm, J. M., & Scholz, H. C.
Venue
PLoS Pathogens
Publisher
Public Library of Science (PLoS)
Published
2013-05-02
Volume
9
Issue
5
Pages
e1003349
ISSN
1553-7374
DOI
10.1371/journal.ppat.1003349
PMC
PMC3642051
Cited by
192
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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