{ "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.", "abstract_shown": true, "affiliations": [ "All Souls College, University of Oxford, Oxford, UK. ruairidh.macleod@all-souls.ox.ac.uk", "Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ruairidh.macleod@all-souls.ox.ac.uk", "Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ruairidh.macleod@all-souls.ox.ac.uk", "Department of Archaeology, University of Cambridge, UK", "Department of Genetics, University of Cambridge, UK", "Lundbeck Foundation Centre for Geogenetics, University of Copenhagen, Denmark", "Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark", "Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark", "Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, USA", "Department of Genetics, University of Cambridge, Cambridge, UK", "Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA", "Department of Biomolecular Engineering, UC Santa Cruz, USA", "Genomics Institute, UC Santa Cruz, USA", "Department of Anthropology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada", "Department of Anthropology, University of Saskatchewan, Canada", "Research Department of Genetics, Evolution and Environment, University College London, London, UK", "Research Department of Genetics, Evolution and Environment, University College London, UK", "School of Archaeology, University of Oxford, Oxford, UK", "Department of Archaeology, University of Oxford, UK", "Scientific Research Centre \"Baikalskii Region\", Irkutsk State University, Irkutsk, Russia", "Scientific Research Centre \"Baikalskii Region\", Irkutsk State University, Russia", "Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia", "Institute of Ethnography and Anthropology, Russian Academy of Sciences, Russia", "Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada", "Department of Anthropology, University of Alberta, Canada", "Group 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", "Group 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", "Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK", "Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada. aweber@ualberta.ca", "Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia. aweber@ualberta.ca", "Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. martin.sikora@sund.ku.dk", "Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. martin.sikora@sund.ku.dk", "Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ewillerslev@sund.ku.dk", "Department of Genetics, University of Cambridge, Cambridge, UK. ewillerslev@sund.ku.dk", "Lundbeck Foundation Geogenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. ewillerslev@sund.ku.dk" ], "article_type": null, "arxiv": null, "author_total": 21, "authors": [ { "affs": [ 0, 1, 2, 3, 4, 5 ], "name": "Ruairidh Macleod", "orcid": "0000-0001-8086-4420" }, { "affs": [ 6, 7, 5 ], "name": "Frederik Valeur Seersholm", "orcid": "0000-0003-2217-3247" }, { "affs": [ 8, 9, 10, 7, 11, 12, 5 ], "name": "Bianca De Sanctis", "orcid": "0000-0002-0648-4224" }, { "affs": [ 13, 14 ], "name": "Angela R. Lieverse", "orcid": "0000-0003-0711-1793" }, { "affs": [ 15, 16 ], "name": "Adrian Timpson", "orcid": "0000-0003-0292-8729" }, { "affs": [ 17, 5 ], "name": "Rick Schulting", "orcid": "0000-0002-4444-766X" }, { "affs": [ 6, 7, 5 ], "name": "Jesper T. Stenderup", "orcid": "0000-0002-6916-106X" }, { "affs": [ 7, 5 ], "name": "Charleen Gaunitz", "orcid": "0000-0003-3681-528X" }, { "affs": [ 6, 7, 18 ], "name": "Lasse Vinner", "orcid": "0000-0002-3081-3702" }, { "affs": [ 19, 20 ], "name": "Olga Ivanovna Goriunova", "orcid": "0000-0002-5159-0894" }, { "affs": [ 19, 20 ], "name": "Vladimir Ivanovich Bazaliiskii", "orcid": "0000-0002-6940-7592" }, { "affs": [ 21, 22 ], "name": "Sergei V. Vasilyev", "orcid": "0000-0003-0128-6568" }, { "affs": [ 23, 24 ], "name": "Erin Jessup", "orcid": "0009-0006-0429-2030" }, { "affs": [ 6, 9, 25, 7, 4, 26, 5 ], "name": "Yucheng Wang", "orcid": "0000-0002-7838-226X" }, { "affs": [ 17, 16 ], "name": "Christopher Bronk Ramsey", "orcid": "0000-0002-8641-9309" }, { "affs": [ 15, 11, 12 ], "name": "Mark Thomas", "orcid": "0000-0002-2452-981X" }, { "affs": [ 8, 10, 5, 27 ], "name": "Russell B Corbett-Detig", "orcid": "0000-0001-6535-2478" }, { "affs": [ 7, 27, 24, 20 ], "name": "Astrid K. N. Iversen", "orcid": "0000-0002-3507-5956" }, { "affs": [ 28, 29, 5 ], "name": "Andrzej Witold Weber", "orcid": "0000-0003-3992-2160" }, { "affs": [ 30, 31, 6, 4, 5 ], "name": "Martin Sikora", "orcid": "0000-0003-2818-8319" }, { "affs": [ 32, 33, 34 ], "name": "Eske Willerslev", "orcid": "0000-0002-7081-6748" } ], "bibtex": "https://research.draconitic.com/paper/6nrp1km1rd0dr.bib", "cited_by": 12, "doi": "10.1038/s41586-026-10540-5", "fulltext_url": null, "id": "6nrp1km1rd0dr", "issns": [ "0028-0836", "1476-4687" ], "landing_url": "https://doi.org/10.1038/s41586-026-10540-5", "language": "en", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1311|Yersinia bacterium, plague, ectoparasites research" ], [ "openalex", "2725|Yersinia bacterium, plague, ectoparasites research" ] ], "openalex": "W4404366661", "pdf_url": "https://www.nature.com/articles/s41586-026-10540-5.pdf", "pmcid": "PMC13275307", "pmid": "42310115", "published": "2026-06-17", "publisher": "Nature Portfolio", "ris": "https://research.draconitic.com/paper/6nrp1km1rd0dr.ris", "sources": [ { "first_seen": "2026-10-30T13:26:46Z", "native_id": "W4404366661", "source": "openalex", "url": "https://doi.org/10.1038/s41586-026-10540-5" } ], "subjects": [ { "field": "biology", "origin": "openalex:1311|Yersinia bacterium, plague, ectoparasites research", "subfield": "genetics-genomics" }, { "field": "medicine", "origin": "openalex:2725|Yersinia bacterium, plague, ectoparasites research", "subfield": "infectious-disease" } ], "title": "Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago", "title_text": "Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago", "type": "peer-reviewed", "updated_at": "2026-11-08T13:20:51Z", "url": "https://research.draconitic.com/paper/6nrp1km1rd0dr", "venue": "Nature", "versions": [] }