Ancient Plasmodium genomes shed light on the history of human malaria
Megan MichelMax Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, . [email protected]Eirini SkourtaniotiDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyFederica PieriniDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyEvelyn K. GuevaraDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyAngela MötschDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyArthur KocherTransmission, Infection, Diversification and Evolution Group, Max Planck Institute of Geoanthropology, Jena, GermanyRodrigo BarqueraDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyRaffaela A. BiancoMax Planck-Harvard Research Center for the Archaeoscience of the Ancient MediterraneanSelina CarlhoffDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyLorenza BoveDepartment of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, SpainSuzanne FreilichDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyKaren GiffinDepartment of Environmental Sciences, University of Basel, Basel, SwitzerlandTaylor R. HermesDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyAlina HißDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyFlorian KnolleDepartment of Medical Engineering and Biotechnology, University of Applied Sciences Jena, Jena, GermanyElizabeth A. NelsonMicrobial Palaeogenomics Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, FranceGunnar U. NeumannMax Planck-Harvard Research Center for the Archaeoscience of the Ancient MediterraneanLuka PapacDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanySandra PenskeDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyAdam B. RohrlachDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyNada SalemMax Planck-Harvard Research Center for the Archaeoscience of the Ancient MediterraneanLena SemerauDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyVanessa Villalba‐MoucoInstituto Universitario de Investigación en Ciencias Ambientales de Aragón, IUCA-Aragosaurus, Universitity of Zaragoza, Zaragoza, SpainIsabelle AbadieCentre Michel de Boüard, Centre de recherches archéologiques et historiques anciennes et médiévales, Université de Caen Normandie, Caen, FranceMark AldenderferDepartment of Anthropology and Heritage Studies, University of California, Merced, Merced, CA, USAJessica BeckettMatthew BrownSociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USAFranco CampusDepartment of History, Human Sciences, and Education, University of Sassari, Sassari, ItalyTsang ChenghwaInstitute of Anthropology, National Tsing Hua University, Hsinchu, TaiwanMaría Cruz BerrocalInstituto de Ciencias del PatrimonioLadislav DamašekInstitute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech RepublicKellie Sara Duffett CarlsonHuman Evolution and Archaeological Sciences, University of Vienna, Vienna, AustriaRaphaël DurandService d'archéologie préventive Bourges plus, Bourges, FranceMichal ErnéeDepartment of Prehistoric Archaeology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech RepublicCristinel FântăneanuH. FrenzelAnatomy Institute, University of Leipzig, Leipzig, GermanyGabriel García AtiénzarInstituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), SpainSonia GuillénEllen HsiehInstitute of Anthropology, National Tsing Hua University, Hsinchu, TaiwanMaciej KarwowskiInstitut für Urgeschichte und Historische Archäologie, University of Vienna, Vienna, AustriaDavid J. KelvinDepartment of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, CanadaNikki KelvinAlexander KhokhlovSamara State University of Social Sciences and Education, Samara, RussiaRebecca KinastonBioArch South, Waitati, New ZealandArkadii KorolevSamara State University of Social Sciences and Education, Samara, RussiaKim-Louise KrettekUniversity of TübingenMario KüßnerThüringer Landesamt für Denkmalpflege und ArchäologieLuca LaiDepartment of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USACory LookSociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USAKerttu MajanderDepartment of Environmental Science, Integrative Prehistory and Archaeological Science, University of Basel, Basel, SwitzerlandKirsten MandlDepartment of Evolutionary Anthropology, University of Vienna, Vienna, AustriaVittorio MazzarelloDepartment of Biomedical Sciences, University of Sassari, Sassari, ItalyMichael McCormickMax Planck-Harvard Research Center for the Archaeoscience of the Ancient MediterraneanMaría Paz de Miguel IbáñezSección de Antropología, Sociedad de Ciencias Aranzadi, Donostia - San Sebastián, SpainReg MurphyUniversity of Nebraska-Lincoln, Lincoln, NE, USARita E. NémethKerkko NordqvistHelsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, FinlandFriederike NovotnyDepartment of Anthropology, Natural History Museum Vienna, Vienna, AustriaMartin ObenausLauro Olmo-EncisoDepartment of History, University of Alcalá, Alcalá de Henares, SpainPäivi OnkamoDepartment of Biology, University of Turku, Turku, FinlandJörg OrschiedtInstitut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, GermanyValerii PatrushevCentre of Archaeological and Ethnographical Investigation, Mari State University, Yoshkar-Ola, RussiaSanni PeltolaFaculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FinlandAlejandro RomeroDepartamento de Biotecnología, Universidad de Alicante, San Vicente del Raspeig, SpainSalvatore RubinoDepartment of Biomedical Sciences, University of Sassari, Sassari, ItalyAntti SajantilaDepartment of Forensic Medicine, University of Helsinki, Helsinki, FinlandDomingo C. Salazar‐GarcíaDepartament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, SpainElena SerranoInstituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, Santander, SpainShapulat ShaydullaevFaculty of History, Termez State University, Termez, UzbekistanEmanuela SiasMario ŠlausAnthropological Center, Croatian Academy of Sciences and Arts, Zagreb, CroatiaLadislav StančoInstitute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech RepublicTreena SwanstonDepartment of Anthropology, Economics and Political Science, MacEwan University, Edmonton, Alberta, CanadaMaria Teschler‐NicolaDepartment of Anthropology, Natural History Museum Vienna, Vienna, AustriaFrédérique ValentinUniversité Paris NanterreKatrien Van de VijverDienst Archeologie - Stad Mechelen, Mechelen, BelgiumTamara L. VarneyDepartment of Anthropology, Lakehead University, Thunder Bay, Ontario, CanadaAlfonso Vigil-Escalera GuiradoDepartamento de Humanidades: Historia, Geografía y Arte, Universidad Carlos III de Madrid, Getafe, SpainChristopher K. WatersHeritage Department, National Parks of Antigua and Barbuda, St. Paul's Parish, Antigua and BarbudaEstella Weiss‐KrejciInstitute for Social AnthropologyEduard WinterDepartment of Anthropology, Natural History Museum Vienna, Vienna, AustriaThiseas C. LamnidisDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyKay PrüferDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyKathrin NägeleDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyMaria A. SpyrouArchaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, GermanyStephan SchiffelsDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyPhilipp W. StockhammerDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyWolfgang HaakDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyCosimo PosthArchaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, GermanyChristina WarinnerDepartment of Anthropology, Harvard University, Cambridge, MA, USAKirsten I. BosDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyAlexander HerbigDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. [email protected]Johannes KrauseMax Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, . [email protected]
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Abstract Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species 1 . Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe 1,2 . To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum , P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia bce , respectively; for P. vivax , this evidence pre-dates textual references by several millennia 3 . Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax , whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.
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