{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:48:49Z","timestamp":1790776129418,"version":"4.1.0"},"reference-count":45,"publisher":"National Academy of Sciences","issue":"36","license":[{"start":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T00:00:00Z","timestamp":1630368000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2021,9,7]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>\n                    Over the last few years, there has been a great deal of scientific debate regarding whether the plague bacterium,\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    , spread from a Western European reservoir during the second plague pandemic, or if it repeatedly came to Europe from Asia. Here, we make a synthesis of the available evidence, including genomes of ancient DNA and historical, archeological, and ecological information. We conclude that the bacterium most likely came to Europe from Asia several times during the second plague pandemic.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2101940118","type":"journal-article","created":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T15:40:14Z","timestamp":1630424414000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":29,"title":["Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information"],"prefix":"10.1073","volume":"118","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5433-663X","authenticated-orcid":false,"given":"Barbara","family":"Bramanti","sequence":"first","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"},{"name":"Department of Neuroscience and Rehabilitation, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 44121 Ferrara, Italy;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4900-315X","authenticated-orcid":false,"given":"Yarong","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3219-7269","authenticated-orcid":false,"given":"Ruifu","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7236-2412","authenticated-orcid":false,"given":"Yujun","family":"Cui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1591-5399","authenticated-orcid":false,"given":"Nils Chr.","family":"Stenseth","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"},{"name":"Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2021,8,31]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001134"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10549"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2016.05.012"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12154-0"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12994"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1812865115"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2009677117"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-71530-9"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2019.0569"},{"key":"e_1_3_4_10_2","volume-title":"Cronaca","author":"Piazza M. D.","year":"1980","unstructured":"M. D. Piazza, Cronaca, A. Giuffrida, Ed. (Renzo Mazzone, Palermo, 1980)."},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-024-0890-4_1"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102383"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1412887112"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(20)30487-4"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/clinids\/6.6.866"},{"key":"e_1_3_4_16_2","first-page":"8","article-title":"Plague persistence in Western Europe: A hypothesis","volume":"1","author":"Carmichael A. G.","year":"2014","unstructured":"A. G. Carmichael, Plague persistence in Western Europe: A hypothesis. Medieval Globe 1, 8 (2014).","journal-title":"Medieval Globe"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2018.2429"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/ereh\/het013"},{"key":"e_1_3_4_19_2","volume-title":"Geschichte der Seuchen, Hungers-und Kriegsnoth zur Zeit des dreissigj\u00e4hrigen Krieges","author":"Lammert G.","year":"1890","unstructured":"G. Lammert, Geschichte der Seuchen, Hungers-und Kriegsnoth zur Zeit des dreissigj\u00e4hrigen Krieges (J. F. Bergmann, 1890)."},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","unstructured":"F. Krauer B. V. Schmid Mapping the plague through natural language processing. medRxiv [Preprint] (2021) https:\/\/www.medrxiv.org\/content\/10.1101\/2021.04.27.21256212v1. Accessed 30 April 2021.","DOI":"10.1101\/2021.04.27.21256212"},{"key":"e_1_3_4_21_2","doi-asserted-by":"crossref","unstructured":"R. Barbieri . Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic. bioRxiv [Preprint] (2021) https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.06.442897v1. Accessed 6 May 2021.","DOI":"10.1101\/2021.05.06.442897"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.181695"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2016.0618"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1080\/00324728.2018.1457794"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1820447116"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-micro-090816-093521"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-14099-w"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1137195"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.3390\/biom10111554"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1715640115"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-021-04805-3"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1902274116"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1015946108"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1202.050651"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaa008"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_4_37_2","unstructured":"H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv (2013) https:\/\/arxiv.org\/abs\/1303.3997. Accessed 26 May 2013."},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"111011","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline","volume":"43","author":"Van der Auwera G. A.","year":"2013","unstructured":"G. A. Van der Auwera ., From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinf. 43, 111011\u2013111033 (2013).","journal-title":"Curr Protoc Bioinf."},{"key":"e_1_3_4_40_2","first-page":"e000074","article-title":"NASP: An accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats","volume":"2","author":"Sahl J. W.","year":"2016","unstructured":"J. W. Sahl ., NASP: An accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb. Genom. 2, e000074 (2016).","journal-title":"Microb. Genom."},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-2-r12"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.2041-210X.2011.00169.x"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2101940118","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T05:31:56Z","timestamp":1673155916000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.2101940118"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,31]]},"references-count":45,"journal-issue":{"issue":"36","published-print":{"date-parts":[[2021,9,7]]}},"alternative-id":["10.1073\/pnas.2101940118"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2101940118","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.04.20.440561","asserted-by":"object"}]},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,31]]},"assertion":[{"value":"2021-08-31","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2101940118"}}