1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
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Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

  1. Kirsten I Bos  Is a corresponding author
  2. Alexander Herbig
  3. Jason Sahl
  4. Nicholas Waglechner
  5. Mathieu Fourment
  6. Stephen A Forrest
  7. Jennifer Klunk
  8. Verena J Schuenemann
  9. Debi Poinar
  10. Melanie Kuch
  11. G Brian Golding
  12. Olivier Dutour
  13. Paul Keim
  14. David M Wagner
  15. Edward C Holmes
  16. Johannes Krause  Is a corresponding author
  17. Hendrik N Poinar  Is a corresponding author
  1. University of Tübingen, Germany
  2. Max Planck Institute for the Science of Human History, Germany
  3. Northern Arizona University, United States
  4. McMaster University, Canada
  5. The University of Sydney, Australia
  6. Université Bordeaux, France
Research Article
Cite this article as: eLife 2016;5:e12994 doi: 10.7554/eLife.12994
3 figures, 2 tables and 2 additional files

Figures

Photograph of rescue excavations at l’Observance in Marseille, France.

LAPMO Université de Provence – URA 164 CNRS/AFAN.

https://doi.org/10.7554/eLife.12994.003
Coverage plots for all reconstructed Observance core genomes.

Inner ring: GC content from low (brown, <30%) to high (orange, >55%). Outer concentric rings: from inner to outer, coverage plots of OBS107, 110, 116, 124, and 137 on a logarithmic scale. Axes are at 30x and 100x. Dots: SNPs (black = non-synonymous, grey = synonymous, white = intergenic). Outer ring (larger dots) is SNPs shared by all five strains. Inner rings (smaller dots) are associated with the strain immediately outside and are SNPs that are not shared by all five strains (but may be shared by 2–4 strains). Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639–1645

https://doi.org/10.7554/eLife.12994.006
Phylogenetic tree for Yersinia pestis.

(A) Maximum likelihood phylogeny of Y. pestis genomic SNPs showing the position of the Observance (OBS) lineage (red) relative to those of 130 modern (black) and three ancient strains (Black Death in green and Justinian Plague in blue). Modern strains from the third pandemic are shown in purple to highlight their close genetic relatedness. Monophyletic groups of sequences have been collapsed to improve clarity and are shown as triangles. The tree is rooted using single strain of Y. pseudotuberculosis (IP32953), with all derived SNPs removed to assist scaling, with branch lengths reflecting the number of nucleotide substitutions/SNP site. The length of the branch leading to the 0.PE3_Angola (AFR) lineage was reduced because its excessive length adversely affected the scaling of the tree. Location abbreviations are as follows: CNH (China), GEO (Georgia), FSU (Former Soviet Union), MNG (Mongolia), NPL (Nepal), IRN (Iran), AFR (Africa), USA (United States of America), MDG (Madagascar), IND (India). (B) Expanded phylogeny schematic to show the relative positions of the Black Death and the Observance lineages. Numbers on branches correspond to SNPs.

https://doi.org/10.7554/eLife.12994.007

Tables

Table 1

Quantitative PCR data for the pla gene obtained for the 19 Observance teeth extracted. Values below std curve detection are highlighted in grey.

https://doi.org/10.7554/eLife.12994.004
PCR Blks:Copies per μl
PCR Blk 10
PCR Blk 20
PCR Blk 30
PCR Blk 40
Extraction Blks:Copies per μl
BLk 10
Blk 20
Blk 30
Blk 40
Extracts:
SampleCopies per μl
101a0
101b0
1020
1030
10739
1080
1090
11050
116105
117a0
117b1
1180
1230
124142
1250
1260
1300
1341
13730
1440
Table 2

Mapping statistics.

https://doi.org/10.7554/eLife.12994.005
Sample IDRaw read
pairs
Preprocessed
reads
Mapped
reads
% mappedDeduppedDuplication
factor
Fold
coverage
% covered
OBS10714,646,71015,395,2871,850,73412.02%851,0962.1712.2084.79
OBS1109,879,25710,458,5711,581,15815.12%855,9881.8514.6190.63
OBS11616,858,27317,876,8832,931,55416.40%1,363,4152.1520.0492.56
OBS12448,797,60252,345,8844,972,3479.50%973,7635.1113.3485.37
OBS137120,018,142129,095,43412,669,6259.81%1,583,5968.0024.4092.76

Additional files

Supplementary file 1

Combined SNP table from three SNP calling approaches.

https://doi.org/10.7554/eLife.12994.008
Supplementary file 2

List of genomes used in SNP calling and phylogeny.

https://doi.org/10.7554/eLife.12994.009

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