{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T23:28:10Z","timestamp":1793834890100,"version":"4.6.1"},"reference-count":69,"publisher":"National Academy of Sciences","issue":"25","license":[{"start":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T00:00:00Z","timestamp":1559606400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Research Council","award":["APGREID"],"award-info":[{"award-number":["APGREID"]}]},{"name":"Wellcome Trust","award":["2000368\/Z\/15\/Z"],"award-info":[{"award-number":["2000368\/Z\/15\/Z"]}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2019,6,18]]},"abstract":"<jats:p>\n                    The first historically documented pandemic caused by\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    , little is known about the bacterium\u2019s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1820447116","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T17:45:13Z","timestamp":1559670313000},"page":"12363-12372","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":156,"title":["Ancient\n                    <i>Yersinia pestis<\/i>\n                    genomes from across Western Europe reveal early diversification during the First Pandemic (541\u2013750)"],"prefix":"10.1073","volume":"116","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9668-6817","authenticated-orcid":false,"given":"Marcel","family":"Keller","sequence":"first","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"},{"name":"State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria A.","family":"Spyrou","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christiana L.","family":"Scheib","sequence":"additional","affiliation":[{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"},{"name":"Institute of Genomics, University of Tartu, 51010 Tartu, Estonia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar U.","family":"Neumann","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Kr\u00f6pelin","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"},{"name":"Friedrich Schiller University Jena, 07743 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brigitte","family":"Haas-Gebhard","sequence":"additional","affiliation":[{"name":"Archaeological Collection of the Bavarian State, 80538 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"P\u00e4ffgen","sequence":"additional","affiliation":[{"name":"Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen","family":"Haberstroh","sequence":"additional","affiliation":[{"name":"Bavarian State Department of Monuments and Sites, 80539 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Ribera i Lacomba","sequence":"additional","affiliation":[{"name":"Department for Municipal Archaeology, Valencia City Council, 46014 Valencia, Spain;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude","family":"Raynaud","sequence":"additional","affiliation":[{"name":"CNRS, UMR5140, Arch\u00e9ologie des Soci\u00e9t\u00e9s M\u00e9diterran\u00e9ennes, 34199 Montpellier, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig","family":"Cessford","sequence":"additional","affiliation":[{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapha\u00ebl","family":"Durand","sequence":"additional","affiliation":[{"name":"Service d\u2019Arch\u00e9ologie Pr\u00e9ventive de l\u2019Agglom\u00e9ration de Bourges Plus, 18023 Bourges Cedex, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Stadler","sequence":"additional","affiliation":[{"name":"Department of Pre- and Protohistory, University of Vienna, 1190 Vienna, Austria;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathrin","family":"N\u00e4gele","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica S.","family":"Bates","sequence":"additional","affiliation":[{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"Trautmann","sequence":"additional","affiliation":[{"name":"State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah A.","family":"Inskip","sequence":"additional","affiliation":[{"name":"McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joris","family":"Peters","sequence":"additional","affiliation":[{"name":"State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;"},{"name":"ArchaeoBioCenter, Ludwig Maximilian University Munich, 80539 Munich, Germany;"},{"name":"Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, 80539 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John E.","family":"Robb","sequence":"additional","affiliation":[{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6297-7808","authenticated-orcid":false,"given":"Toomas","family":"Kivisild","sequence":"additional","affiliation":[{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom;"},{"name":"Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique","family":"Castex","sequence":"additional","affiliation":[{"name":"UMR 5199, PACEA, CNRS Institute, 33615 Pessac Cedex, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"McCormick","sequence":"additional","affiliation":[{"name":"Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, MA 02138;"},{"name":"Max Planck\u2013Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten I.","family":"Bos","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michaela","family":"Harbeck","sequence":"additional","affiliation":[{"name":"State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-1166","authenticated-orcid":false,"given":"Alexander","family":"Herbig","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9144-3920","authenticated-orcid":false,"given":"Johannes","family":"Krause","sequence":"additional","affiliation":[{"name":"Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;"},{"name":"Max Planck\u2013Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2019,6,4]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-024-0890-4","volume-title":"Yersinia pestis: Retrospective and Perspective","author":"Yang R.","year":"2016","unstructured":"R. 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Anthropol. 126, 48\u201355 (2005).","journal-title":"Am. J. Phys. Anthropol."},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.3201\/eid1009.030933","article-title":"Genotyping, Orientalis-like Yersinia pestis, and plague pandemics","volume":"10","author":"Drancourt M.","year":"2004","unstructured":"M. Drancourt ., Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerg. Infect. Dis. 10, 1585\u20131592 (2004).","journal-title":"Emerg. Infect. Dis."},{"key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"332","DOI":"10.3201\/eid1302.060197","article-title":"Yersinia pestis Orientalis in remains of ancient plague patients","volume":"13","author":"Drancourt M.","year":"2007","unstructured":"M. Drancourt ., Yersinia pestis Orientalis in remains of ancient plague patients. Emerg. Infect. Dis. 13, 332\u2013333 (2007).","journal-title":"Emerg. Infect. 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V\u00e5gene ., Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat. Ecol. Evol. 2, 520\u2013528 (2018).","journal-title":"Nat. Ecol. Evol."},{"key":"e_1_3_4_21_2","doi-asserted-by":"crossref","first-page":"e1004957","DOI":"10.1371\/journal.pcbi.1004957","article-title":"MEGAN community Edition\u2013Interactive exploration and analysis of large-scale microbiome sequencing data","volume":"12","author":"Huson D. H.","year":"2016","unstructured":"D. H. Huson ., MEGAN community Edition\u2013Interactive exploration and analysis of large-scale microbiome sequencing data. PLOS Comput. Biol. 12, e1004957 (2016).","journal-title":"PLOS Comput. Biol."},{"key":"e_1_3_4_22_2","first-page":"49","article-title":"On the generalized distance in statistics","volume":"2","author":"Mahalanobis P. C.","year":"1936","unstructured":"P. C. Mahalanobis, On the generalized distance in statistics. Proc. Natl. Inst. Sci. India 2, 49\u201355 (1936).","journal-title":"Proc. Natl. Inst. Sci. India"},{"key":"e_1_3_4_23_2","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs A. W.","year":"2007","unstructured":"A. W. Briggs ., Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U.S.A. 104, 14616\u201314621 (2007).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","DOI":"10.1146\/annurev-genom-091416-035526","article-title":"A robust framework for microbial archaeology","volume":"18","author":"Warinner C.","year":"2017","unstructured":"C. Warinner ., A robust framework for microbial archaeology. Annu. Rev. Genomics Hum. Genet. 18, 321\u2013356 (2017).","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"e87","DOI":"10.1093\/nar\/gkp1163","article-title":"Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA","volume":"38","author":"Briggs A. W.","year":"2010","unstructured":"A. W. Briggs ., Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1038\/ng.705","article-title":"Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity","volume":"42","author":"Morelli G.","year":"2010","unstructured":"G. Morelli ., Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat. Genet. 42, 1140\u20131143 (2010).","journal-title":"Nat. Genet."},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"6717","DOI":"10.1038\/ncomms7717","article-title":"Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe","volume":"6","author":"Kay G. L.","year":"2015","unstructured":"G. L. Kay ., Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat. Commun. 6, 6717 (2015).","journal-title":"Nat. Commun."},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/s41586-018-0094-2","article-title":"137 ancient human genomes from across the Eurasian steppes","volume":"557","author":"Damgaard P. B.","year":"2018","unstructured":"P. B. Damgaard ., 137 ancient human genomes from across the Eurasian steppes. 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Bacteriol."},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"701","DOI":"10.3389\/fmicb.2014.00701","article-title":"Ypf\u03a6: A filamentous phage acquired by Yersinia pestis","volume":"5","author":"Derbise A.","year":"2014","unstructured":"A. Derbise, E. Carniel, Ypf\u03a6: A filamentous phage acquired by Yersinia pestis. Front. Microbiol. 5, 701 (2014).","journal-title":"Front. Microbiol."},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"2710","DOI":"10.1099\/mic.0.080556-0","article-title":"The importance of the magnesium transporter MgtB for virulence of Yersinia pseudotuberculosis and Yersinia pestis","volume":"160","author":"Ford D. C.","year":"2014","unstructured":"D. C. Ford, G. W. P. Joshua, B. W. Wren, P. C. F. Oyston, The importance of the magnesium transporter MgtB for virulence of Yersinia pseudotuberculosis and Yersinia pestis. Microbiology 160, 2710\u20132717 (2014).","journal-title":"Microbiology"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1128\/JB.00124-06","article-title":"Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: Evidence of gene reduction in an emerging pathogen","volume":"188","author":"Chain P. S. G.","year":"2006","unstructured":"P. S. G. Chain ., Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: Evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188, 4453\u20134463 (2006).","journal-title":"J. Bacteriol."},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1111\/j.1365-2958.1994.tb00463.x","article-title":"The pigmentation locus of Yersinia pestis KIM6+ is flanked by an insertion sequence and includes the structural genes for pesticin sensitivity and HMWP2","volume":"13","author":"Fetherston J. D.","year":"1994","unstructured":"J. D. Fetherston, R. D. Perry, The pigmentation locus of Yersinia pestis KIM6+ is flanked by an insertion sequence and includes the structural genes for pesticin sensitivity and HMWP2. Mol. Microbiol. 13, 697\u2013708 (1994).","journal-title":"Mol. Microbiol."},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","unstructured":"M. A. Spyrou . A phylogeography of the second plague pandemic revealed through the analysis of historical Y. pestis genomes. bioRxiv:https:\/\/doi.org\/10.1101\/481242 (30 November 2018).","DOI":"10.1101\/481242"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1186\/s13104-015-1525-x","article-title":"The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis","volume":"8","author":"H\u00e4nsch S.","year":"2015","unstructured":"S. H\u00e4nsch ., The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Res. Notes 8, 535 (2015).","journal-title":"BMC Res. Notes"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/978-0-387-72124-8_2","article-title":"Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union","volume":"603","author":"Garcia E.","year":"2007","unstructured":"E. Garcia ., Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Adv. Exp. Med. Biol. 603, 17\u201322 (2007).","journal-title":"Adv. Exp. Med. Biol."},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1073\/pnas.1205750110","article-title":"Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis","volume":"110","author":"Cui Y.","year":"2013","unstructured":"Y. Cui ., Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl. Acad. Sci. U.S.A. 110, 577\u2013582 (2013).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","DOI":"10.2307\/j.ctv9b2txr","volume-title":"The Fate of Rome: Climate, Disease, and the End of an Empire","author":"Harper K.","year":"2017","unstructured":"K. Harper, The Fate of Rome: Climate, Disease, and the End of an Empire (Princeton University Press, Princeton, 2017)."},{"key":"e_1_3_4_42_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1162\/002219503322645439","article-title":"Rats, communications, and plague: Toward an ecological history","volume":"34","author":"McCormick M.","year":"2003","unstructured":"M. McCormick, Rats, communications, and plague: Toward an ecological history. J. Interdiscip. Hist. 34, 1\u201325 (2003).","journal-title":"J. Interdiscip. Hist."},{"key":"e_1_3_4_43_2","first-page":"399","article-title":"Le rat noir (Rattus rattus) en Europe antique et medi\u00e9vale: Les voies du commerce et l\u2019expansion de la peste","volume":"25","author":"Audoin-Rouzeau F.","year":"1997","unstructured":"F. Audoin-Rouzeau, J.-D. Vigne, Le rat noir (Rattus rattus) en Europe antique et medi\u00e9vale: Les voies du commerce et l\u2019expansion de la peste. Anthropozoologica 25, 399\u2013404 (1997).","journal-title":"Anthropozoologica"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"e0145194","DOI":"10.1371\/journal.pone.0145194","article-title":"Genotyping Yersinia pestis in historical plague: Evidence for long-term persistence of Y. pestis in Europe from the 14th to the 17th century","volume":"11","author":"Seifert L.","year":"2016","unstructured":"L. Seifert ., Genotyping Yersinia pestis in historical plague: Evidence for long-term persistence of Y. pestis in Europe from the 14th to the 17th century. PLoS One 11, e0145194 (2016).","journal-title":"PLoS One"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"3020","DOI":"10.1073\/pnas.1412887112","article-title":"Climate-driven introduction of the Black Death and successive plague reintroductions into Europe","volume":"112","author":"Schmid B. V.","year":"2015","unstructured":"B. V. Schmid ., Climate-driven introduction of the Black Death and successive plague reintroductions into Europe. Proc. Natl. Acad. Sci. U.S.A. 112, 3020\u20133025 (2015).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"e0187230","DOI":"10.1371\/journal.pone.0187230","article-title":"Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan","volume":"12","author":"Eroshenko G. A.","year":"2017","unstructured":"G. A. Eroshenko ., Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan. PLoS One 12, e0187230 (2017).","journal-title":"PLoS One"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/JB.01518-09","article-title":"Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium","volume":"192","author":"Eppinger M.","year":"2010","unstructured":"M. Eppinger ., Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J. Bacteriol. 192, 1685\u20131699 (2010).","journal-title":"J. Bacteriol."},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","DOI":"10.5040\/9781641899406","volume-title":"Pandemic Disease in the Medieval World: Rethinking the Black Death","author":"Green M. H.","year":"2014","unstructured":"M. H. Green, \u201cTaking \u201cpandemic\u201d seriously: Making the Black Death global\u201d in Pandemic Disease in the Medieval World: Rethinking the Black Death, M. H. Green, Ed. (ARC Humanities Press, Kalamazoo, MI, 2014)."},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1017\/S0268416002004137","article-title":"The Justinianic Plague: Origins and effects","volume":"17","author":"Sarris P.","year":"2002","unstructured":"P. Sarris, The Justinianic Plague: Origins and effects. Contin. Chang. 17, 169\u2013182 (2002).","journal-title":"Contin. Chang."},{"key":"e_1_3_4_50_2","first-page":"5","article-title":"The \u201cJustinianic\u201d Plague","volume":"49","author":"Allen P.","year":"1979","unstructured":"P. Allen, The \u201cJustinianic\u201d Plague. Byzantion 49, 5\u201320 (1979).","journal-title":"Byzantion"},{"key":"e_1_3_4_51_2","volume-title":"Central Eurasia in the Middle Ages. Studies in Honour of Peter B. Golden","author":"Schamiloglu U.","year":"2016","unstructured":"U. Schamiloglu, \u201cThe plague in the time of justinian and central Eurasian history: An agenda for research\u201d in Central Eurasia in the Middle Ages. Studies in Honour of Peter B. Golden, I. Zimonyi, O. Karatay, Eds. (Harrasowitz Verlag, Wiesbaden, 2016)."},{"key":"e_1_3_4_52_2","volume-title":"Plague and the End of Antiquity: The Pandemic of 541\u2013750","author":"Little L. K.","year":"2007","unstructured":"L. K. Little ., Plague and the End of Antiquity: The Pandemic of 541\u2013750, L. K. Little, Ed. (Cambridge University Press, 2007)."},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1353\/jla.2018.0001","article-title":"Indirect evidence for the social impact of the Justinianic pandemic: Episcopal burial and conciliar legislation in Visigothic Hispania","volume":"11","author":"Gruber H.","year":"2018","unstructured":"H. Gruber, Indirect evidence for the social impact of the Justinianic pandemic: Episcopal burial and conciliar legislation in Visigothic Hispania. J. Late Antiq. 11, 193\u2013215 (2018).","journal-title":"J. Late Antiq."},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrmicro.2015.29","article-title":"\u2018Add, stir and reduce\u2019: Yersinia spp. as model bacteria for pathogen evolution","volume":"14","author":"McNally A.","year":"2016","unstructured":"A. McNally, N. R. Thomson, S. Reuter, B. W. Wren, \u2018Add, stir and reduce\u2019: Yersinia spp. as model bacteria for pathogen evolution. Nat. Rev. Microbiol. 14, 177\u2013190 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","article-title":"Genome sequence of Yersinia pestis, the causative agent of plague","volume":"413","author":"Parkhill J.","year":"2001","unstructured":"J. Parkhill ., Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523\u2013527 (2001).","journal-title":"Nature"},{"key":"e_1_3_4_56_2","first-page":"150","volume-title":"Plague and the End of Antiquity: The Pandemic of 541\u2013750","author":"Kulikowski M.","year":"2007","unstructured":"M. Kulikowski, \u201cPlague in Spanish Late Antiquity\u201d in Plague and the End of Antiquity: The Pandemic of 541\u2013750, L. K. Little, Ed. (Cambridge University Press, Cambridge, 2007), pp. 150\u2013170."},{"key":"e_1_3_4_57_2","first-page":"59","volume-title":"Morir en el Mediterr\u00e1neo Medieval: Actas del III Congreso Internacional de Arqueolog\u00eda, Arte e Historia de La Antig\u00fcedad Tard\u00eda y Alta Edad Media Peninsular","author":"Alapont Mart\u00edn L.","year":"2009","unstructured":"L. Alapont Mart\u00edn, A. V. Ribera i Lacomba, (2009) \u201cTopograf\u00eda y jerarqu\u00eda funeraria en la Valencia tardo-antigua\u201d in Morir en el Mediterr\u00e1neo Medieval: Actas del III Congreso Internacional de Arqueolog\u00eda, Arte e Historia de La Antig\u00fcedad Tard\u00eda y Alta Edad Media Peninsular, J. L\u00f3pez Quiroga, A. M. Mart\u00ednez Tejera, Ed. (Oxford), pp 59\u201388."},{"key":"e_1_3_4_58_2","first-page":"135","volume-title":"Plague and the End of Antiquity: The Pandemic of 541\u2013750","author":"Stoclet A. J.","year":"2007","unstructured":"A. J. Stoclet, \u201cConsilia humana, ops divina, superstitio: Seeking succor and solace in times of plague, with particular reference to Gaul in the Early Middle Ages\u201d in Plague and the End of Antiquity: The Pandemic of 541\u2013750, L. K. Little, Ed. (Cambridge University Press, Cambridge, 2007), pp. 135\u2013149."},{"key":"e_1_3_4_59_2","unstructured":"C. Raynaud \u201cLes n\u00e9cropoles de Lunel-Viel (H\u00e9rault) de l\u2019Antiquit\u00e9 au Moyen \u00c2ge.\u201d Revue Arch\u00e9ologique de Narbonnaise Suppl\u00e9ment 40 (Presses Universitaires de la M\u00e9diterran\u00e9e Montpellier France 2010)."},{"key":"e_1_3_4_60_2","volume-title":"Le Pressoir\u2013Rapport Final d\u2019Op\u00e9ration de Fouille Pr\u00e9ventive","author":"Ma\u00e7on P.","year":"2011","unstructured":"P. Ma\u00e7on, R. Durand, M. Salin, F. Dominin, Le Pressoir\u2013Rapport Final d\u2019Op\u00e9ration de Fouille Pr\u00e9ventive (Service d\u2019Arch\u00e9ologie Pr\u00e9ventive de l\u2019Agglom\u00e9ration de Bourges Plus, Bourges, 2011)."},{"key":"e_1_3_4_61_2","doi-asserted-by":"crossref","first-page":"15758","DOI":"10.1073\/pnas.1314445110","article-title":"Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments","volume":"110","author":"Dabney J.","year":"2013","unstructured":"J. Dabney ., Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U.S.A. 110, 15758\u201315763 (2013).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_3_4_62_2","doi-asserted-by":"crossref","first-page":"pdb.prot5448","DOI":"10.1101\/pdb.prot5448","article-title":"Illumina sequencing library preparation for highly multiplexed target capture and sequencing","volume":"2010","author":"Meyer M.","year":"2010","unstructured":"M. Meyer, M. Kircher, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010).","journal-title":"Cold Spring Harb. Protoc."},{"key":"e_1_3_4_63_2","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1093\/nar\/gkr771","article-title":"Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform","volume":"40","author":"Kircher M.","year":"2012","unstructured":"M. Kircher, S. Sawyer, M. Meyer, Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_4_64_2","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/nature13025","article-title":"The genome of a Late Pleistocene human from a Clovis burial site in western Montana","volume":"506","author":"Rasmussen M.","year":"2014","unstructured":"M. Rasmussen ., The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225\u2013229 (2014).","journal-title":"Nature"},{"key":"e_1_3_4_65_2","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1073\/pnas.1221359110","article-title":"DNA analysis of an early modern human from Tianyuan Cave, China","volume":"110","author":"Fu Q.","year":"2013","unstructured":"Q. Fu ., DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. U.S.A. 110, 2223\u20132227 (2013).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"e_1_3_4_66_2","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13059-016-0918-z","article-title":"EAGER: Efficient ancient genome reconstruction","volume":"17","author":"Peltzer A.","year":"2016","unstructured":"A. Peltzer ., EAGER: Efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).","journal-title":"Genome Biol."},{"key":"e_1_3_4_67_2","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature13591","article-title":"Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis","volume":"514","author":"Bos K. I.","year":"2014","unstructured":"K. I. Bos ., Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494\u2013497 (2014).","journal-title":"Nature"},{"key":"e_1_3_4_68_2","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan A. R.","year":"2010","unstructured":"A. R. Quinlan, I. M. Hall, BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_69_2","unstructured":"H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv :1303.3997 (16 March 2013)."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.pnas.org\/syndication\/doi\/10.1073\/pnas.1820447116","content-type":"unspecified","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1820447116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T15:26:52Z","timestamp":1654615612000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1820447116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,4]]},"references-count":69,"journal-issue":{"issue":"25","published-print":{"date-parts":[[2019,6,18]]}},"alternative-id":["10.1073\/pnas.1820447116"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1820447116","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/481226","asserted-by":"object"}]},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,4]]},"assertion":[{"value":"2019-06-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}