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Peer-reviewedCC BYNature

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago

  • Ruairidh Macleod1,2,3,4,5,6
  • Frederik Valeur Seersholm7,8,6
  • Bianca De Sanctis9,10,11,8,12,13,6
  • Angela R. Lieverse14,15
  • Adrian Timpson16,17
  • Rick Schulting18,6
  • Jesper T. Stenderup7,8,6
  • Charleen Gaunitz8,6
  • Lasse Vinner7,8,19
  • Olga Ivanovna Goriunova20,21
  • Vladimir Ivanovich Bazaliiskii20,21
  • Sergei V. Vasilyev22,23
9 more authors
  • Erin Jessup24,25
  • Yucheng Wang7,10,26,8,5,27,6
  • Christopher Bronk Ramsey18,17
  • Mark Thomas16,12,13
  • Russell B Corbett-Detig9,11,6,28
  • Astrid K. N. Iversen8,28,25,21
  • Andrzej Witold Weber29,30,6
  • Martin Sikora31,32,7,5,6
  • Eske Willerslev33,34,35
35 affiliations
  1. 1All Souls College, University of Oxford, Oxford, UK. [email protected]
  2. 2Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
  3. 3Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
  4. 4Department of Archaeology, University of Cambridge, UK
  5. 5Department of Genetics, University of Cambridge, UK
  6. 6Lundbeck Foundation Centre for Geogenetics, University of Copenhagen, Denmark
  7. 7Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
  8. 8Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
  9. 9Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, USA
  10. 10Department of Genetics, University of Cambridge, Cambridge, UK
  11. 11Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
  12. 12Department of Biomolecular Engineering, UC Santa Cruz, USA
  13. 13Genomics Institute, UC Santa Cruz, USA
  14. 14Department of Anthropology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
  15. 15Department of Anthropology, University of Saskatchewan, Canada
  16. 16Research Department of Genetics, Evolution and Environment, University College London, London, UK
  17. 17Research Department of Genetics, Evolution and Environment, University College London, UK
  18. 18School of Archaeology, University of Oxford, Oxford, UK
  19. 19Department of Archaeology, University of Oxford, UK
  20. 20Scientific Research Centre "Baikalskii Region", Irkutsk State University, Irkutsk, Russia
  21. 21Scientific Research Centre "Baikalskii Region", Irkutsk State University, Russia
  22. 22Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
  23. 23Institute of Ethnography and Anthropology, Russian Academy of Sciences, Russia
  24. 24Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
  25. 25Department of Anthropology, University of Alberta, Canada
  26. 26Group of Alpine Paleoecology and Human Adaptation (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
  27. 27Group of Alpine Paleoecology and Human Adaptation (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, China
  28. 28Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
  29. 29Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. [email protected]
  30. 30Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia. [email protected]
  31. 31Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
  32. 32Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
  33. 33Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
  34. 34Department of Genetics, University of Cambridge, Cambridge, UK. [email protected]
  35. 35Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. [email protected]
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Abstract

Plague is among the most devastating diseases in human history 1 . However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago 2,3 . Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis . The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics.

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Cite

BibTeXRIS
BibTeX
@article{macleod2026lethal,
  title = {{Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago}},
  author = {Ruairidh Macleod and Frederik Valeur Seersholm and Bianca De Sanctis and Angela R. Lieverse and Adrian Timpson and Rick Schulting and Jesper T. Stenderup and Charleen Gaunitz and Lasse Vinner and Olga Ivanovna Goriunova and Vladimir Ivanovich Bazaliiskii and Sergei V. Vasilyev and Erin Jessup and Yucheng Wang and Christopher Bronk Ramsey and Mark Thomas and Russell B Corbett-Detig and Astrid K. N. Iversen and Andrzej Witold Weber and Martin Sikora and Eske Willerslev},
  journal = {Nature},
  year = {2026},
  month = jun,
  doi = {10.1038/s41586-026-10540-5},
  url = {https://doi.org/10.1038/s41586-026-10540-5},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago
AU  - Ruairidh Macleod
AU  - Frederik Valeur Seersholm
AU  - Bianca De Sanctis
AU  - Angela R. Lieverse
AU  - Adrian Timpson
AU  - Rick Schulting
AU  - Jesper T. Stenderup
AU  - Charleen Gaunitz
AU  - Lasse Vinner
AU  - Olga Ivanovna Goriunova
AU  - Vladimir Ivanovich Bazaliiskii
AU  - Sergei V. Vasilyev
AU  - Erin Jessup
AU  - Yucheng Wang
AU  - Christopher Bronk Ramsey
AU  - Mark Thomas
AU  - Russell B Corbett-Detig
AU  - Astrid K. N. Iversen
AU  - Andrzej Witold Weber
AU  - Martin Sikora
AU  - Eske Willerslev
PY  - 2026
DA  - 2026/06/17
JO  - Nature
DO  - 10.1038/s41586-026-10540-5
UR  - https://doi.org/10.1038/s41586-026-10540-5
AB  - Plague is among the most devastating diseases in human history 1 . However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago 2,3 . Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis . The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics.
SN  - 0028-0836
SN  - 1476-4687
ER  -