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 -