The population genomic legacy of the second plague pandemic
Gopalakrishnan, Shyam (University of Copenhagen. The GLOBE Institute)
Ebenesersdóttir, S. Sunna (University of Iceland. Department of Anthropology)
Lundstrøm, Inge K.C. (University of Copenhagen. The GLOBE Institute)
Turner-Walker, Gordon (National Yunlin University of Science & Technology (Taiwan))
Moore, Kristjan H.S. (deCODE Genetics (Reykjavík, Islàndia))
Luisi, Pierre (Universidad Nacional de Córdoba (Argentina))
Margaryan, Ashot (University of Copenhagen. The GLOBE Institute)
Martin, Michael D. (Norwegian University of Science and Technology. NTNU University Museum)
Ellegaard, Martin Rene (Norwegian University of Science and Technology. NTNU University Museum)
Magnússon, Ólafur þ. (deCODE Genetics (Reykjavík, Islàndia))
Sigurðsson, Ásgeir (deCODE Genetics (Reykjavík, Islàndia))
Snorradóttir, Steinunn (deCODE Genetics (Reykjavík, Islàndia))
Magnúsdóttir, Droplaug N. (deCODE Genetics (Reykjavík, Islàndia))
Laffoon, Jason E. (Leiden University. Department of Archaeological Sciences)
van Dorp, Lucy (University College London. Department of Genetics, Evolution and Environment)
Liu, Xiaodong (University of Copenhagen. Department of Biology)
Moltke, Ida (University of Copenhagen. Department of Biology)
Ávila-Arcos, Maria C (Universidad Nacional Autónoma de México. Laboratorio Internacional de Investigación sobre el Genoma Humano)
Schraiber, Joshua G. (Illumina Inc. Illumina Artificial Intelligence Laboratory (USA))
Rasmussen, Simon (University of Copenhagen. Novo Nordisk Foundation Center for Protein Research)
Juan, David (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Gelabert, Pere (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
de-Dios, Toni (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Fotakis, Anna K. (University of Copenhagen. The GLOBE Institute)
Iraeta-Orbegozo, Miren (University of Copenhagen. The GLOBE Institute)
Vågene, Åshild J. (Max Planck Institute for the Science of Human History)
Denham, Sean Dexter (University of Stavanger. Museum of Archaeology)
Christophersen, Axel (Norwegian University of Science and Technology. NTNU University Museum)
Stenøien, Hans K. (Norwegian University of Science and Technology. NTNU University Museum)
Garrett Vieira, Filipe (University of Copenhagen. The GLOBE Institute)
Liu, Shanlin (China National GeneBank)
Günther, Torsten (Evolutionsbiologisk Centrum EBC (Sweden))
Kivisild, Toomas (University of Tartu. Institute of Genomics)
Moseng, Ole Georg (University of South-Eastern Norway. Department of Business, History and Social Sciences)
Skar, Birgitte (Norwegian University of Science and Technology. NTNU University Museum)
Cheung, Christina (Muséum National d'Histoire Naturelle (París, França))
Sandoval-Velasco, Marcela (University of Copenhagen. The GLOBE Institute)
Wales, Nathan (University of York. Department of Archaeology)
Schroeder, Hannes (University of Copenhagen. The GLOBE Institute)
Campos, Paula F. (Universidade do Porto. Centro Interdisciplinar de Investigação Marinha e Ambiental)
Guðmundsdóttir, Valdís B. (University of Iceland. Department of Anthropology)
Sicheritz-Ponten, Thomas (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery)
Petersen, Bent (AIMST University (Malàisia). Centre of Excellence for Omics-Driven Computational Biodiscovery)
Halgunset, Jostein (Biobank1 (Norway))
Gilbert, Edmund (School of Pharmacy and Biomolecular Sciences (Ireland))
Cavalleri, Gianpiero L. (FutureNeuro SFI Research Centre (Ireland))
Hovig, Eivind (University of Oslo. Center for Bioinformatics)
Kockum, Ingrid (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience)
Olsson, Tomas (Karolinska Institutet (Estocolm, Suècia). Department of Clinical Neuroscience)
Alfredsson, Lars (Karolinska Institutet (Estocolm, Suècia))
Hansen, Thomas F. (Copenhagen Mental Health Services. Institute of Biological Psychiatry)
Werge, Thomas (Copenhagen Mental Health Services. Institute of Biological Psychiatry)
Willerslev, Eske (University of Cambridge. Department of Zoology)
Balloux, François (University College London. Department of Genetics, Evolution and Environment)
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
Lalueza-Fox, Carles (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Nielsen, Rasmus (University of California. Department of Integrative Biology)
Stefánsson, Kári (deCODE Genetics (Reykjavík, Islàndia))
Helgason, Agnar (deCODE Genetics (Reykjavík, Islàndia))
Gilbert, M. Thomas P. (Norwegian University of Science and Technology. University Museum)

Data:	2022
Resum:	Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%. It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis). Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
Ajuts:	European Commission 655732 European Commission 681396 European Commission 864203
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Plague ; Second plague pandemic ; Yersinia pestis ; Pandemic genomics ; Population genomics ; Selection ; Population replacement ; Trondheim
Publicat a:	Current Biology, Vol. 32 (November 2022) , p. 1-9/e1-e6, ISSN 1879-0445

DOI: 10.1016/j.cub.2022.09.023
PMID: 36182700

16 p, 3.6 MB

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