% pubman genre = report
@techreport{item_3497413,
title = {{The population genomic legacy of the second plague pandemic}},
author = {Gopalakrishnan, Shyam and Ebenesersd{\'o}ttir, S. Sunna and Lundstr{\o}m, Inge K.C. and Turner-Walker, Gordon and Moore, Kristjan H.S. and Luisi, Pierre and Margaryan, Ashot and Martin, Michael D. and Ellegaard, Martin Rene and Magn{\'u}sson, {\'O}lafur {\th}. and Sigur{\dh}sson, {\'A}sgeir and Snorrad{\'o}ttir, Steinunn and Magn{\'u}sd{\'o}ttir, Droplaug N. and Laffoon, Jason E. and van Dorp, Lucy and Liu, Xiaodong and Moltke, Ida and {\'A}vila-Arcos, Mar{\'\i}a C. and Schraiber, Joshua G. and Rasmussen, Simon and Juan, David and Gelabert, Pere and de-Dios, Toni and Fotakis, Anna K. and Iraeta-Orbegozo, Miren and V{\aa}gene, {\AA}shild J. and Denham, Sean Dexter and Christophersen, Axel and Sten{\o}ien, Hans K. and Vieira, Filipe G. and Liu, Shanlin and G{\"u}nther, Torsten and Kivisild, Toomas and Moseng, Ole Georg and Skar, Birgitte and Cheung, Christina and Sandoval-Velasco, Marcela and Wales, Nathan and Schroeder, Hannes and Campos, Paula F. and Gu{\dh}mundsd{\'o}ttir, Vald{\'\i}s B. and Sicheritz-Ponten, Thomas and Petersen, Bent and Halgunset, Jostein and Gilbert, Edmund and Cavalleri, Gianpiero L. and Hovig, Eivind and Kockum, Ingrid and Olsson, Tomas and Alfredsson, Lars and Hansen, Thomas F. and Werge, Thomas and Willerslev, Eske and Balloux, Francois and Marques-Bonet, Tomas and Lalueza-Fox, Carles and Nielsen, Rasmus and Stef{\'a}nsson, K{\'a}ri and Helgason, Agnar and Gilbert, M. Thomas P.},
language = {eng},
issn = {0960-9822},
doi = {10.1016/j.cub.2022.09.023},
institution = {Cell Press},
address = {London, UK},
number = {21},
year = {2022},
date = {2022-11-07},
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{\textpercent}{\textendash}40{\textpercent}.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{\textendash}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.}},
type = {Current Biology},
volume = {32},
pages = {4743--4751},
}