TY - JOUR

T1 - The population genomic legacy of the second plague pandemic

AU - Gopalakrishnan, Shyam

AU - Ebenesersdóttir, S. Sunna

AU - Lundstrøm, Inge K. C.

AU - Turner-Walker, Gordon

AU - Moore, Kristjan H. S.

AU - Luisi, Pierre

AU - Margaryan, Ashot

AU - Martin, Michael D.

AU - Ellegaard, Martin Rene

AU - Magnússon, Ólafur

AU - Sigurðsson, Ásgeir

AU - Snorradóttir, Steinunn

AU - Magnúsdóttir, Droplaug N.

AU - Laffoon, Jason E.

AU - van Dorp, Lucy

AU - Liu, Xiaodong

AU - Moltke, Ida

AU - Ávila-Arcos, María C.

AU - Schraiber, Joshua G.

AU - Rasmussen, Simon

AU - Juan, David

AU - Gelabert, Pere

AU - de-Dios, Toni

AU - Fotakis, Anna K.

AU - Iraeta-Orbegozo, Miren

AU - Vågene, Åshild J.

AU - Denham, Sean Dexter

AU - Christophersen, Axel

AU - Stenøien, Hans K.

AU - Vieira, Filipe G.

AU - Liu, Shanlin

AU - Günther, Torsten

AU - Kivisild, Toomas

AU - Moseng, Ole Georg

AU - Skar, Birgitte

AU - Cheung, Christina

AU - Sandoval-Velasco, Marcela

AU - Wales, Nathan

AU - Schroeder, Hannes

AU - Campos, Paula F.

AU - Guðmundsdóttir, Valdís B.

AU - Sicheritz-Ponten, Thomas

AU - Petersen, Bent

AU - Halgunset, Jostein

AU - Gilbert, Edmund

AU - Cavalleri, Gianpiero L.

AU - Hovig, Eivind

AU - Kockum, Ingrid

AU - Olsson, Tomas

AU - Alfredsson, Lars

AU - Hansen, Thomas F.

AU - Werge, Thomas

AU - Willerslev, Eske

AU - Balloux, Francois

AU - Marques-Bonet, Tomas

AU - Lalueza-Fox, Carles

AU - Nielsen, Rasmus

AU - Stefánsson, Kári

AU - Helgason, Agnar

AU - Gilbert, M. Thomas P.

N1 - Publisher Copyright: © 2022 The Authors

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - pandemic genomics

KW - plague

KW - population genomics

KW - population replacement

KW - second plague pandemic

KW - selection

KW - Trondheim

KW - Yersinia pestis

U2 - 10.1016/j.cub.2022.09.023

DO - 10.1016/j.cub.2022.09.023

M3 - Journal article

C2 - 36182700

AN - SCOPUS:85139274687

VL - 32

SP - 4743-4751.e6

JO - Current Biology

JF - Current Biology

SN - 0960-9822

IS - 21

ER -