The population genomic legacy of the second plague pandemic

Mostra el registre complet Registre parcial de l'ítem

  • dc.contributor.author Gopalakrishnan, Shyam
  • dc.contributor.author Juan, David
  • dc.contributor.author Gelabert Xirinachs, Pere, 1991-
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-
  • dc.contributor.author Lalueza Fox, Carles, 1965-
  • dc.contributor.author Gilbert, M Thomas
  • dc.date.accessioned 2022-11-16T07:37:41Z
  • dc.date.available 2022-11-16T07:37:41Z
  • dc.date.issued 2022
  • dc.description.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.
  • dc.description.sponsorship We acknowledge the following for funding our research: Carlsbergfondet grants CF14-0995 and Marie Skłodowska-Curie Actions grant 655732 (to S.G.), Danish National Research Foundation grant DNRF94, Lundbeckfonden grant R52-5062, Carlsbergfondet grant CF18-1109 and ERC Consolidator grant (681396-ExtinctionGenomics) (to M.T.P.G.), and MEDHEAL600 funded by the Research Council of Norway (FRIHUMSAM) project number is 262424. G.L.C. is supported by the Science Foundation Ireland under grant number 16/RC/3948. T.M.B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 864203).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P et al. The population genomic legacy of the second plague pandemic. Curr Biol. 2022 Nov 7;32(21):4743-51.e6. DOI: 10.1016/j.cub.2022.09.023
  • dc.identifier.doi http://dx.doi.org/10.1016/j.cub.2022.09.023
  • dc.identifier.issn 0960-9822
  • dc.identifier.uri http://hdl.handle.net/10230/54882
  • dc.language.iso eng
  • dc.publisher Elsevier
  • dc.relation.ispartof Curr Biol. 2022 Nov 7;32(21):4743-4751.e6
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/655732
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
  • dc.rights © 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Trondheim
  • dc.subject.keyword Yersinia pestis
  • dc.subject.keyword Pandemic genomics
  • dc.subject.keyword Plague
  • dc.subject.keyword Population genomics
  • dc.subject.keyword Population replacement
  • dc.subject.keyword Second plague pandemic
  • dc.subject.keyword Selection
  • dc.title The population genomic legacy of the second plague pandemic
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion