Affiliations 

  • 1 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark. Electronic address: shyam.gopalakrishnan@sund.ku.dk
  • 2 deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
  • 3 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
  • 4 National Yunlin University of Science & Technology, 123 University Road, Section 3, 64002 Douliu, Yun-Lin County, Taiwan; Department of Archaeology and Anthropology, National Museum of Natural Science, 1 Guanqian Road, North District Taichung City 404023, Taiwan
  • 5 deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland
  • 6 Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina; Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
  • 7 NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
  • 8 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
  • 9 Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, the Netherlands
  • 10 UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
  • 11 Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
  • 12 International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), 3001 Boulevard Juriquilla, 76230 Querétaro, Mexico
  • 13 Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, USA
  • 14 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
  • 15 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
  • 16 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
  • 17 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
  • 18 Museum of Archaeology, University of Stavanger, Stavanger, Norway
  • 19 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
  • 20 Evolutionsbiologisk Centrum EBC, Norbyv. 18A, 752 36 Uppsala, Sweden
  • 21 KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
  • 22 Department of Business, History and Social Sciences, University of South-Eastern Norway, Notodden, Norway
  • 23 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; EA - Eco-anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
  • 24 Department of Archaeology, Kings Manor and Principals House, University of York, Exhibition Square, York YO1 7EP, UK
  • 25 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
  • 26 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
  • 27 Biobank1, St. Olavs Hospital HF, Trondheim, Norway
  • 28 School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
  • 29 Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
  • 30 Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
  • 31 Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
  • 32 Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
  • 33 Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark; The Globe Institute, Lundbeck Foundation Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
  • 34 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
  • 35 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
  • 36 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain
  • 37 The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
  • 38 deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Faculty of Medicine, University of Iceland, Reykjavík, Iceland
Curr Biol, 2022 Nov 07;32(21):4743-4751.e6.
PMID: 36182700 DOI: 10.1016/j.cub.2022.09.023

Abstract

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%.1 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).2 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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.