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
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 …

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 …

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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