Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Valtueña A.A. Neumann G.U. Spyrou M.A. Musralina L. Aron F. Beisenov A. Belinskiy A.B. Bos K.I. Buzhilova A. Conrad M. Djansugurova L.B. Dobes M. Ernee M. Fernandez-Eraso J. Frohlich B. Furmanek M. Hałuszko A. Hansen S. Harney E. Hiss A.N. Hubner A. Key F.M. Khussainova E. Kitov E. Kitova A.O. Knipper C. Kuhnert D. Lalueza-Fox C. Littleton J. Massy K. Mittnik A. Mujika-Alustiza J.A. Olalde I. Papac L. Penske S. Peska J. Pinhasi R. Reich D. Reinhold S. Stahl R. Stauble H. Tukhbatova R.I. Vasilyev S. Veselovskaya E. Warinner C. Stockhammer P.W. Haak W. Krause J. Herbig A.
26 April 2022 National Academy of Sciences

Proceedings of the National Academy of Sciences of the United States of America
2022 #119 Issue 17

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/ Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology. Copyright

ancient DNA , plague , Yersinia pestis

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Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
Institute for Archaeological Sciences, Eberhard Karls University of Tubingen, Tubingen, 72074, Germany
Biology and Biotechnology Faculty, l-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Institute of Genetics and Physiology, l-Farabi Kazakh National University, Almaty, 050060, Kazakhstan
Faculty of Mathematics and Computer Science, Friedrich-Schiller University, Jena, 07743, Germany
Begazy-Tasmola Research Center of History and Archeology, Almaty, 050008, Kazakhstan
Nasledie Cultural Heritage Unit, Stavropol, 355006, Russian Federation
Research Institute, Museum of Anthropology, Lomonosov Moscow State University, Moscow, 125009, Russian Federation
Department of Heritage Management, rchaeological Heritage Office Saxony, Dresden, 01108, Germany
Department of Prehistoric Archaeology, Institute of Archaeology, Czech Academy of Sciences, Prague, 11801, Czech Republic
Department of Geography, Prehistory, and Archaeology, University of the Basque Country, Vitoria-Gasteiz, 01006, Spain
Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, 20560, DC, United States
Institute of Archaeology, University of Wrocław, Wrocław, 50139, Poland
rcheolodzy.org Foundation, Wrocław, 50316, Poland
Eurasia-Department, German Archaeological Institute, Berlin, 14195, Germany
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, MA, United States
Department of Genetics, Harvard Medical School, Boston, 02115, MA, United States
Faculty of Biological Sciences, Friedrich-Schiller University, Jena, 07743, Germany
Evolutionary Pathogenomics, Max Planck Institute for Infection Biology, Berlin, 10117, Germany
Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, 119991, Russian Federation
Research Laboratory of Paleoanthropological Study, Institute of Archaeology named after A.Kh Margulan, Almaty, 50010, Kazakhstan
History Department, l-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Centre for Egyptological Studies, The Russian Academy of Sciences, Russian Academy of Sciences, Moscow, 119991, Russian Federation
Curt Engelhorn Center Archaeometry, Mannheim, 68159, Germany
Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
Institute of Evolutionary Biology, Consejo Superior de Investigaciones Cientificas-Universitat Pompeu Fabra, Barcelona, 08003, Spain
Department of Anthropology, University of Auckland, Auckland, 01010, New Zealand
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, 80539, Germany
Department of Human Evolutionary Biology, Harvard University, Cambridge, 02138, MA, United States
BIOMICs Research Group, University of the Basque Country Universidad del Pais Vasco, Euskal Herriko Unibertsitatea, Vitoria-Gasteiz, 01006, Spain
rchaeological Centre, Olomouc, 779 00, Czech Republic
Department of Evolutionary Anthropology, University of Vienna, Vienna, 1030, Austria
Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russian Federation
Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center “Kazan Scientific Center, The Russian Academy of Sciences”, Kazan, 420111, Russian Federation
Department of Anthropology, Harvard University, Cambridge, 02138, MA, United States

Department of Archaeogenetics
Department of Archaeogenetics
Institute for Archaeological Sciences
Biology and Biotechnology Faculty
Institute of Genetics and Physiology
Faculty of Mathematics and Computer Science
Begazy-Tasmola Research Center of History and Archeology
Nasledie Cultural Heritage Unit
Research Institute
Department of Heritage Management
Department of Prehistoric Archaeology
Department of Geography
Department of Anthropology
Institute of Archaeology
rcheolodzy.org Foundation
Eurasia-Department
Department of Organismic and Evolutionary Biology
Department of Genetics
Faculty of Biological Sciences
Evolutionary Pathogenomics
Institute of Ethnology and Anthropology
Research Laboratory of Paleoanthropological Study
History Department
Centre for Egyptological Studies
Curt Engelhorn Center Archaeometry
Transmission
Institute of Evolutionary Biology
Department of Anthropology
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces
Department of Human Evolutionary Biology
BIOMICs Research Group
rchaeological Centre
Department of Evolutionary Anthropology
Institute of Fundamental Medicine and Biology
Laboratory for Structural Analysis of Biomacromolecules
Department of Anthropology

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