{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:35:48Z","timestamp":1791894948691,"version":"4.3.4"},"reference-count":69,"publisher":"National Academy of Sciences","issue":"50","license":[{"start":{"date-parts":[[2018,11,26]],"date-time":"2018-11-26T00:00:00Z","timestamp":1543190400000},"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":[[2018,12,11]]},"abstract":"<jats:p>\n                    Over the last few years, genomic studies on\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    , the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1812865115","type":"journal-article","created":{"date-parts":[[2018,11,26]],"date-time":"2018-11-26T20:45:19Z","timestamp":1543265119000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":87,"title":["Integrative approach using\n                    <i>Yersinia pestis<\/i>\n                    genomes to revisit the historical landscape of plague during the Medieval Period"],"prefix":"10.1073","volume":"115","author":[{"given":"Amine","family":"Namouchi","sequence":"first","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meriam","family":"Guellil","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Kersten","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"H\u00e4nsch","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudio","family":"Ottoni","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris V.","family":"Schmid","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa","family":"Pacciani","sequence":"additional","affiliation":[{"name":"Soprintendenza Archeologia, Belle Arti e Paesaggio di Firenze, Pistoia e Prato, 50125 Florence, Italy;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luisa","family":"Quaglia","sequence":"additional","affiliation":[{"name":"Soprintendenza Archeologia, Belle Arti e Paesaggio di Firenze, Pistoia e Prato, 50125 Florence, Italy;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Vermunt","sequence":"additional","affiliation":[{"name":"Department of Monuments and Archaeology, Municipality of Bergen op Zoom, 4611BT-59 Bergen op Zoom, The Netherlands;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Egil L.","family":"Bauer","sequence":"additional","affiliation":[{"name":"Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Derrick","sequence":"additional","affiliation":[{"name":"Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne \u00d8.","family":"Jensen","sequence":"additional","affiliation":[{"name":"Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sacha","family":"Kacki","sequence":"additional","affiliation":[{"name":"Department of Archaeology, Durham University, DH1 3LE Durham, United Kingdom;"},{"name":"UMR 5199 De la Pr\u00e9histoire \u00e0 l\u2019Actuel: Culture, Environnement et Anthropologie, Centre National de la Recherche Scientifique, University of Bordeaux, 33615 Pessac, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Samuel K.","family":"Cohn","sequence":"additional","affiliation":[{"name":"School of Humanities, University of Glasgow, G12 8QQ Glasgow, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils C.","family":"Stenseth","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"},{"name":"Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Ministry of Education, 100084 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5433-663X","authenticated-orcid":false,"given":"Barbara","family":"Bramanti","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;"},{"name":"Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221 Ferrara, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2018,11,26]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1371\/journal.pmed.0050003","article-title":"Plague: Past, present, and future","volume":"5","author":"Stenseth NC","year":"2008","unstructured":"NC Stenseth, , Plague: Past, present, and future. 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Adv Exp Med Biol 918, 1\u201326 (2016).","journal-title":"Adv Exp Med Biol"},{"key":"e_1_3_4_3_2","volume-title":"The Black Death 1346-1353: The Complete History","author":"Benedictow OJ","year":"2004","unstructured":"OJ Benedictow The Black Death 1346-1353: The Complete History (Boydell Press, Woodbridge, UK, 2004)."},{"key":"e_1_3_4_4_2","volume-title":"Cronaca","author":"Michele da Piazza","year":"1980","unstructured":"; Michele da Piazza Cronaca, ed A Giuffrida (ILA Palma, Palermo, Italy, 1980)."},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139031110","volume-title":"The Great Transition: Climate, Disease and Society in the Late-Medieval World","author":"Campbell BMS","year":"2016","unstructured":"BMS Campbell The Great Transition: Climate, Disease and Society in the Late-Medieval World (Cambridge Univ Press, Cambridge, UK, 2016)."},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"e00623-12","DOI":"10.1128\/mBio.00623-12","article-title":"A decade of plague in Mahajanga, Madagascar: Insights into the global maritime spread of pandemic plague","volume":"4","author":"Vogler AJ","year":"2013","unstructured":"AJ Vogler, , A decade of plague in Mahajanga, Madagascar: Insights into the global maritime spread of pandemic plague. 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Nature 478, 506\u2013510 (2011).","journal-title":"Nature"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/S1473-3099(13)70323-2","article-title":"Yersinia pestis and the plague of Justinian 541-543 AD: A genomic analysis","volume":"14","author":"Wagner DM","year":"2014","unstructured":"DM Wagner, , Yersinia pestis and the plague of Justinian 541-543 AD: A genomic analysis. Lancet Infect Dis 14, 319\u2013326 (2014).","journal-title":"Lancet Infect Dis"},{"key":"e_1_3_4_10_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 BV","year":"2015","unstructured":"BV Schmid, , Climate-driven introduction of the Black Death and successive plague reintroductions into Europe. 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Speculum 39, 1\u201334 (1964).","journal-title":"Speculum"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","unstructured":"AG Carmichael Plague Persistence in Western Europe: A Hypothesis. The Medieval Globe : Vol 1 No 1 Article 8. (2014).","DOI":"10.17302\/TMG.1-1.7"},{"key":"e_1_3_4_29_2","volume-title":"A Treatise of the Plague: Containing an Historical Journal, and Medical Account, of the Plague, at Aleppo, in the Years 1760, 1761, and 1762","author":"Russell P","year":"1791","unstructured":"P Russell A Treatise of the Plague: Containing an Historical Journal, and Medical Account, of the Plague, at Aleppo, in the Years 1760, 1761, and 1762 (G.G.J. and J. Robinson, London, 1791)."},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.meegid.2012.11.016","article-title":"Small oversights that led to the Great Plague of Marseille (1720-1723): Lessons from the past","volume":"14","author":"Devaux CA","year":"2013","unstructured":"CA Devaux, Small oversights that led to the Great Plague of Marseille (1720-1723): Lessons from the past. 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Emerg Infect Dis 8, 971\u2013975 (2002).","journal-title":"Emerg Infect Dis"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1080\/09518967.2017.1314920","article-title":"The transmission of the Black Death to western Europe: A critical review of the existing evidence","volume":"32","author":"Ditrich H","year":"2017","unstructured":"H Ditrich, The transmission of the Black Death to western Europe: A critical review of the existing evidence. Mediterr Hist Rev 32, 25\u201339 (2017).","journal-title":"Mediterr Hist Rev"},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1002\/ajpa.23266","article-title":"The sex-selective impact of the Black Death and recurring plagues in the Southern Netherlands, 1349-1450","volume":"164","author":"Curtis DR","year":"2017","unstructured":"DR Curtis, J Roosen, The sex-selective impact of the Black Death and recurring plagues in the Southern Netherlands, 1349-1450. Am J Phys Anthropol 164, 246\u2013259 (2017).","journal-title":"Am J Phys Anthropol"},{"key":"e_1_3_4_35_2","volume-title":"Portraits of Old Russia: Imagined Lives of Ordinary People, 1300-1745","author":"Donald Ostrowski MTP","year":"2011","unstructured":"MTP Donald Ostrowski Portraits of Old Russia: Imagined Lives of Ordinary People, 1300-1745 (Routledge, London, 2011)."},{"key":"e_1_3_4_36_2","unstructured":"\u0412\u042e \u041a\u043e\u0432\u0430\u043b\u044c \u0422\u043e\u0440\u0433\u043e\u0432\u044b\u0439 \u0438\u043d\u0432\u0435\u043d\u0442\u0430\u0440\u044c \u0438\u0437 \u0440\u0430\u0441\u043a\u043e\u043f\u043e\u043a \u0431\u0430\u0437\u0430\u0440\u0430 \u0441\u0435\u0440\u0435\u0434\u0438\u043d\u044b XIV \u0432\u0435\u043a\u0430 \u0432 \u0411\u043e\u043b\u0433\u0430\u0440\u0435. \u041f\u043e\u0432\u043e\u043b\u0436\u0441\u043a\u0430\u044f \u0410\u0440\u0445\u0435\u043e\u043b\u043e\u0433\u0438\u044f . Available at archaeologie.pro\/ru\/archive\/6\/97\/. Accessed June 11 2018. (2013)."},{"key":"e_1_3_4_37_2","first-page":"9","article-title":"Trade stock from excavation the market of the middle of the XIV century at Bolgar","volume":"4","author":"Yu KV","year":"2013","unstructured":"KV Yu, Trade stock from excavation the market of the middle of the XIV century at Bolgar. Volga River Reg Archaeol 4, 9\u201333 (2013).","journal-title":"Volga River Reg Archaeol"},{"key":"e_1_3_4_38_2","unstructured":"EM Veale The English Fur Trade in the Later Middle Ages (London Record Society London) 2nd Ed Vol 38. Available at https:\/\/www.british-history.ac.uk\/london-record-soc\/vol38. Accessed July 3 2018. (2003)."},{"key":"e_1_3_4_39_2","unstructured":"PF Suhm R Nyerup Historie AF Danmark: Fra AAR 1340 Til 1375 (Nabu Press Charleston SC). Available at https:\/\/www.betterworldbooks.com\/product\/detail\/historie-af-danmark-fra-aar-1340-til-1375-volume-13-1274946565. Accessed July 3 2018. (2012)."},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139004046","volume-title":"Plague and Empire in the Early Modern Mediterranean World: The Ottoman Experience, 1347\u20131600","author":"Varlik N","year":"2015","unstructured":"N Varlik Plague and Empire in the Early Modern Mediterranean World: The Ottoman Experience, 1347\u20131600 (Cambridge Univ Press, Cambridge, UK, 2015)."},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"401","DOI":"10.3406\/cmr.1978.1337","article-title":"The Land of Darkness and the Golden Horde. The fur trade under the Mongols XIII\u2013XIVth centuries","volume":"19","author":"Martin J","year":"1978","unstructured":"J Martin, The Land of Darkness and the Golden Horde. The fur trade under the Mongols XIII\u2013XIVth centuries. 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Proc Natl Acad Sci USA 110, 15758\u201315763 (2013).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"12800","DOI":"10.1073\/pnas.220225197","article-title":"Molecular identification by \u201csuicide PCR\u201d of Yersinia pestis as the agent of medieval Black Death","volume":"97","author":"Raoult D","year":"2000","unstructured":"D Raoult, , Molecular identification by \u201csuicide PCR\u201d of Yersinia pestis as the agent of medieval Black Death. Proc Natl Acad Sci USA 97, 12800\u201312803 (2000).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_47_2","first-page":"368","article-title":"The retrieval of ancient human DNA sequences","volume":"59","author":"Handt O","year":"1996","unstructured":"O Handt, M Krings, RH Ward, S P\u00e4\u00e4bo, The retrieval of ancient human DNA sequences. Am J Hum Genet 59, 368\u2013376 (1996).","journal-title":"Am J Hum Genet"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1126\/science.1118725","article-title":"Ancient DNA from the first European farmers in 7500-year-old Neolithic sites","volume":"310","author":"Haak W","year":"2005","unstructured":"W Haak, , Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310, 1016\u20131018 (2005).","journal-title":"Science"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"db.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, db.prot5448 (2010).","journal-title":"Cold Spring Harb Protoc"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong DT","year":"2015","unstructured":"DT Truong, , MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 12, 902\u2013903 (2015).","journal-title":"Nat Methods"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: Ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood DE","year":"2014","unstructured":"DE Wood, SL Salzberg, Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15, R46 (2014).","journal-title":"Genome Biol"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2013A scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster J","year":"2012","unstructured":"J K\u00f6ster, S Rahmann, Snakemake\u2013A scalable bioinformatics workflow engine. Bioinformatics 28, 2520\u20132522 (2012).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li H","year":"2009","unstructured":"H Li, R Durbin, Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"J\u00f3nsson H","year":"2013","unstructured":"H J\u00f3nsson, A Ginolhac, M Schubert, PLF Johnson, L Orlando, mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682\u20131684 (2013).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li H","year":"2009","unstructured":"H Li, , The sequence alignment\/map format and SAMtools. Bioinformatics; 1000 Genome Project Data Processing Subgroup 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li H","year":"2011","unstructured":"H Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987\u20132993 (2011).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_57_2","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir H","year":"2013","unstructured":"H Thorvaldsd\u00f3ttir, JT Robinson, JP Mesirov, Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform 14, 178\u2013192 (2013).","journal-title":"Brief Bioinform"},{"key":"e_1_3_4_58_2","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson JT","year":"2011","unstructured":"JT Robinson, , Integrative genomics viewer. Nat Biotechnol 29, 24\u201326 (2011).","journal-title":"Nat Biotechnol"},{"key":"e_1_3_4_59_2","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1093\/molbev\/mst024","article-title":"Ultrafast approximation for phylogenetic bootstrap","volume":"30","author":"Minh BQ","year":"2013","unstructured":"BQ Minh, MAT Nguyen, A von Haeseler, Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30, 1188\u20131195 (2013).","journal-title":"Mol Biol Evol"},{"key":"e_1_3_4_60_2","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"Guindon S","year":"2010","unstructured":"S Guindon, , New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 59, 307\u2013321 (2010).","journal-title":"Syst Biol"},{"key":"e_1_3_4_61_2","unstructured":"J Adachi M Hasegawa MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Available at citeseerx.ist.psu.edu\/viewdoc\/summary?doi=10.1.1.476.8552. Accessed September 5 2018. (1996)."},{"key":"e_1_3_4_62_2","doi-asserted-by":"crossref","first-page":"W580","DOI":"10.1093\/nar\/gks498","article-title":"FastML: A web server for probabilistic reconstruction of ancestral sequences","volume":"40","author":"Ashkenazy H","year":"2012","unstructured":"H Ashkenazy, , FastML: A web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res 40, W580\u2013W584 (2012).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_63_2","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut A","year":"2016","unstructured":"A Rambaut, TT Lam, L Max Carvalho, OG Pybus, Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol 2, vew007 (2016).","journal-title":"Virus Evol"},{"key":"e_1_3_4_64_2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/978-94-024-0890-4_6","volume-title":"Yersinia pestis: Retrospective and Perspective","author":"Cui Y","year":"2016","unstructured":"Y Cui, Y Song, Genome and evolution of Yersinia pestis. Yersinia pestis: Retrospective and Perspective, eds R Yang, A Anisimov (Springer, Dordrecht, The Netherlands), pp. 171\u2013192 (2016)."},{"key":"e_1_3_4_65_2","doi-asserted-by":"crossref","first-page":"3683","DOI":"10.1016\/j.cub.2017.10.025","article-title":"The stone age plague and its persistence in Eurasia","volume":"27","author":"Andrades Valtue\u00f1a A","year":"2017","unstructured":"A Andrades Valtue\u00f1a, , The stone age plague and its persistence in Eurasia. Curr Biol 27, 3683\u20133691.e8 (2017).","journal-title":"Curr Biol"},{"key":"e_1_3_4_66_2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139095112","volume-title":"Bayesian Evolutionary Analysis with BEAST 2","author":"Drummond AJ","year":"2015","unstructured":"AJ Drummond, RR Bouckaert Bayesian Evolutionary Analysis with BEAST 2 (Cambridge Univ Press, Cambridge, UK, 2015)."},{"key":"e_1_3_4_67_2","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1111\/1755-0998.12603","article-title":"tipdatingbeast: An R package to assist the implementation of phylogenetic tip-dating tests using beast","volume":"17","author":"Rieux A","year":"2017","unstructured":"A Rieux, CE Khatchikian, tipdatingbeast: An R package to assist the implementation of phylogenetic tip-dating tests using beast. Mol Ecol Resour 17, 608\u2013613 (2017).","journal-title":"Mol Ecol Resour"},{"key":"e_1_3_4_68_2","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1093\/sysbio\/syq099","article-title":"Bayesian estimation of substitution rates from ancient DNA sequences with low information content","volume":"60","author":"Ho SYW","year":"2011","unstructured":"SYW Ho, , Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol 60, 366\u2013375 (2011).","journal-title":"Syst Biol"},{"key":"e_1_3_4_69_2","doi-asserted-by":"crossref","first-page":"e1319","DOI":"10.7717\/peerj.1319","article-title":"Anvi\u2019o: An advanced analysis and visualization platform for \u2018omics data","volume":"3","author":"Eren AM","year":"2015","unstructured":"AM Eren, , Anvi\u2019o: An advanced analysis and visualization platform for \u2018omics data. 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