Ancient Plasmodium genomes shed light on the history of human malaria

Megan Michel (), Eirini Skourtanioti, Federica Pierini, Evelyn K. Guevara, Angela Mötsch, Arthur Kocher, Rodrigo Barquera, Raffaela A. Bianco, Selina Carlhoff, Lorenza Coppola Bove, Suzanne Freilich, Karen Giffin, Taylor Hermes, Alina Hiß, Florian Knolle, Elizabeth A. Nelson, Gunnar U. Neumann, Luka Papac, Sandra Penske, Adam B. Rohrlach, Nada Salem, Lena Semerau, Vanessa Villalba-Mouco, Isabelle Abadie, Mark Aldenderfer, Jessica F. Beckett, Matthew Brown, Franco G. R. Campus, Tsang Chenghwa, María Cruz Berrocal, Ladislav Damašek, Kellie Sara Duffett Carlson, Raphaël Durand, Michal Ernée, Cristinel Fântăneanu, Hannah Frenzel, Gabriel García Atiénzar, Sonia Guillén, Ellen Hsieh, Maciej Karwowski, David Kelvin, Nikki Kelvin, Alexander Khokhlov, Rebecca L. Kinaston, Arkadii Korolev, Kim-Louise Krettek, Mario Küßner, Luca Lai, Cory Look, Kerttu Majander, Kirsten Mandl, Vittorio Mazzarello, Michael McCormick, Patxuka Miguel Ibáñez, Reg Murphy, Rita E. Németh, Kerkko Nordqvist, Friederike Novotny, Martin Obenaus, Lauro Olmo-Enciso, Päivi Onkamo, Jörg Orschiedt, Valerii Patrushev, Sanni Peltola, Alejandro Romero, Salvatore Rubino, Antti Sajantila, Domingo C. Salazar-García, Elena Serrano, Shapulat Shaydullaev, Emanuela Sias, Mario Šlaus, Ladislav Stančo, Treena Swanston, Maria Teschler-Nicola, Frederique Valentin, Katrien Vijver, Tamara L. Varney, Alfonso Vigil-Escalera Guirado, Christopher K. Waters, Estella Weiss-Krejci, Eduard Winter, Thiseas C. Lamnidis, Kay Prüfer, Kathrin Nägele, Maria Spyrou, Stephan Schiffels, Philipp W. Stockhammer, Wolfgang Haak, Cosimo Posth, Christina Warinner, Kirsten I. Bos, Alexander Herbig () and Johannes Krause ()
Additional contact information
Megan Michel: Max Planck Institute for Evolutionary Anthropology
Eirini Skourtanioti: Max Planck Institute for Evolutionary Anthropology
Federica Pierini: Max Planck Institute for Evolutionary Anthropology
Evelyn K. Guevara: Max Planck Institute for Evolutionary Anthropology
Angela Mötsch: Max Planck Institute for Evolutionary Anthropology
Arthur Kocher: Max Planck Institute for Evolutionary Anthropology
Rodrigo Barquera: Max Planck Institute for Evolutionary Anthropology
Raffaela A. Bianco: Max Planck Institute for Evolutionary Anthropology
Selina Carlhoff: Max Planck Institute for Evolutionary Anthropology
Lorenza Coppola Bove: Max Planck Institute for Evolutionary Anthropology
Suzanne Freilich: Max Planck Institute for Evolutionary Anthropology
Karen Giffin: Max Planck Institute for Evolutionary Anthropology
Taylor Hermes: Max Planck Institute for Evolutionary Anthropology
Alina Hiß: Max Planck Institute for Evolutionary Anthropology
Florian Knolle: University of Applied Sciences Jena
Elizabeth A. Nelson: Institut Pasteur
Gunnar U. Neumann: Max Planck Institute for Evolutionary Anthropology
Luka Papac: Max Planck Institute for Evolutionary Anthropology
Sandra Penske: Max Planck Institute for Evolutionary Anthropology
Adam B. Rohrlach: Max Planck Institute for Evolutionary Anthropology
Nada Salem: Max Planck Institute for Evolutionary Anthropology
Lena Semerau: Max Planck Institute for Evolutionary Anthropology
Vanessa Villalba-Mouco: Max Planck Institute for Evolutionary Anthropology
Isabelle Abadie: Inrap – Institut national de recherches archéologiques préventives
Mark Aldenderfer: University of California, Merced
Jessica F. Beckett: Cagliari
Matthew Brown: Farmingdale State College
Franco G. R. Campus: University of Sassari
Tsang Chenghwa: National Tsing Hua University
María Cruz Berrocal: Spanish National Research Council (CSIC)
Ladislav Damašek: Charles University
Kellie Sara Duffett Carlson: University of Vienna
Raphaël Durand: Service d’archéologie préventive Bourges plus
Michal Ernée: Institute of Archaeology of the Czech Academy of Sciences
Cristinel Fântăneanu: National Museum of Unification Alba Iulia
Hannah Frenzel: University of Leipzig
Gabriel García Atiénzar: Universidad de Alicante
Sonia Guillén: Centro Mallqui
Ellen Hsieh: National Tsing Hua University
Maciej Karwowski: University of Vienna
David Kelvin: Dalhousie University
Nikki Kelvin: BioForge Canada Limited
Alexander Khokhlov: Samara State University of Social Sciences and Education
Rebecca L. Kinaston: BioArch South
Arkadii Korolev: Samara State University of Social Sciences and Education
Kim-Louise Krettek: University of Tübingen
Mario Küßner: Thuringian State Office for Heritage Management and Archaeology
Luca Lai: University of North Carolina at Charlotte
Cory Look: Farmingdale State College
Kerttu Majander: University of Basel
Kirsten Mandl: University of Vienna
Vittorio Mazzarello: University of Sassari
Michael McCormick: Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
Patxuka Miguel Ibáñez: Universidad de Alicante
Reg Murphy: University of Nebraska-Lincoln
Rita E. Németh: Mureș County Museum
Kerkko Nordqvist: University of Helsinki
Friederike Novotny: Natural History Museum Vienna
Martin Obenaus: Silva Nortica Archäologische Dienstleistungen
Lauro Olmo-Enciso: University of Alcalá
Päivi Onkamo: University of Turku
Jörg Orschiedt: Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt
Valerii Patrushev: Mari State University
Sanni Peltola: Max Planck Institute for Evolutionary Anthropology
Alejandro Romero: Universidad de Alicante
Salvatore Rubino: University of Sassari
Antti Sajantila: University of Helsinki
Domingo C. Salazar-García: Universitat de València
Elena Serrano: Universidad de Cantabria
Shapulat Shaydullaev: Termez State University
Emanuela Sias: Centro Studi sulla Civiltà del Mare
Mario Šlaus: Croatian Academy of Sciences and Arts
Ladislav Stančo: Charles University
Treena Swanston: MacEwan University
Maria Teschler-Nicola: University of Vienna
Frederique Valentin: CNRS
Katrien Vijver: Royal Belgian Institute of Natural Sciences
Tamara L. Varney: Lakehead University
Alfonso Vigil-Escalera Guirado: Universidad Carlos III de Madrid
Christopher K. Waters: National Parks of Antigua and Barbuda
Estella Weiss-Krejci: Austrian Academy of Sciences
Eduard Winter: Natural History Museum Vienna
Thiseas C. Lamnidis: Max Planck Institute for Evolutionary Anthropology
Kay Prüfer: Max Planck Institute for Evolutionary Anthropology
Kathrin Nägele: Max Planck Institute for Evolutionary Anthropology
Maria Spyrou: Max Planck Institute for Evolutionary Anthropology
Stephan Schiffels: Max Planck Institute for Evolutionary Anthropology
Philipp W. Stockhammer: Max Planck Institute for Evolutionary Anthropology
Wolfgang Haak: Max Planck Institute for Evolutionary Anthropology
Cosimo Posth: Max Planck Institute for Evolutionary Anthropology
Christina Warinner: Max Planck Institute for Evolutionary Anthropology
Kirsten I. Bos: Max Planck Institute for Evolutionary Anthropology
Alexander Herbig: Max Planck Institute for Evolutionary Anthropology
Johannes Krause: Max Planck Institute for Evolutionary Anthropology

Nature, 2024, vol. 631, issue 8019, 125-133

Abstract: 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 species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. 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 millennia3. 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.

Date: 2024
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DOI: 10.1038/s41586-024-07546-2

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