{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T16:31:42Z","timestamp":1791995502293,"version":"4.4.0"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000155","name":"Gouvernement du Canada | Social Sciences and Humanities Research Council of Canada","doi-asserted-by":"publisher","award":["20008499"],"award-info":[{"award-number":["20008499"]}],"id":[{"id":"10.13039\/501100000155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007631","name":"Canadian Institutes for Advanced Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007631","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium,\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    , regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    -wide molecular clock is unstable. To resolve this, we developed a new approach in which each\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.\n                  <\/jats:p>","DOI":"10.1038\/s42003-022-04394-6","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T12:04:49Z","timestamp":1674129889000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis"],"prefix":"10.1038","volume":"6","author":[{"given":"Katherine","family":"Eaton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leo","family":"Featherstone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2863-0907","authenticated-orcid":false,"given":"Sebastian","family":"Duchene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7516-7460","authenticated-orcid":false,"given":"Ann G.","family":"Carmichael","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"N\u00fckhet","family":"Varl\u0131k","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. Brian","family":"Golding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":false,"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0314-4160","authenticated-orcid":false,"given":"Hendrik N.","family":"Poinar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"4394_CR1","doi-asserted-by":"publisher","first-page":"3683","DOI":"10.1016\/j.cub.2017.10.025","volume":"27","author":"A Andrades Valtue\u00f1a","year":"2017","unstructured":"Andrades Valtue\u00f1a, A. et al. The Stone Age Plague and its persistence in Eurasia. Curr. Biol. 27, 3683\u20133691.e8 (2017).","journal-title":"Curr. Biol."},{"key":"4394_CR2","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1128\/CMR.10.1.35","volume":"10","author":"RD Perry","year":"1997","unstructured":"Perry, R. D. & Fetherston, J. D. Yersinia pestis\u2014etiologic agent of plague. Clin. Microbiol. Rev. 10, 35\u201366 (1997).","journal-title":"Clin. Microbiol. Rev."},{"key":"4394_CR3","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-13481-2","volume":"7","author":"RPH Yue","year":"2017","unstructured":"Yue, R. P. H., Lee, H. F. & Wu, C. Y. H. Trade routes and plague transmission in pre-industrial Europe. Sci. Rep. 7, 12973 (2017).","journal-title":"Sci. Rep."},{"key":"4394_CR4","unstructured":"Plague. World Health Organization https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/plague (2017)."},{"key":"4394_CR5","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/S1473-3099(13)70323-2","volume":"14","author":"DM Wagner","year":"2014","unstructured":"Wagner, D. M. et al. Yersinia pestis and the Plague of Justinian 541\u2013543 AD: a genomic analysis. Lancet Infect. Dis. 14, 319\u2013326 (2014).","journal-title":"Lancet Infect. Dis."},{"key":"4394_CR6","doi-asserted-by":"publisher","first-page":"193","DOI":"10.17302\/TMG.1-1.8","volume":"1","author":"N Varl\u0131k","year":"2014","unstructured":"Varl\u0131k, N. New science and old sources: why the Ottoman experience of plague matters. Medieval Globe 1, 193\u2013227 (2014).","journal-title":"Medieval Globe"},{"key":"4394_CR7","doi-asserted-by":"publisher","first-page":"20133159","DOI":"10.1098\/rspb.2013.3159","volume":"281","author":"L Xu","year":"2014","unstructured":"Xu, L. et al. Wet climate and transportation routes accelerate spread of human plague. Proc. R. Soc. B: Biol. Sci. 281, 20133159 (2014).","journal-title":"Proc. R. Soc. B: Biol. Sci."},{"key":"4394_CR8","doi-asserted-by":"crossref","unstructured":"Benedictow, O. J. The Complete History of the Black Death. (Boydell Press, 2021).","DOI":"10.1017\/9781787449312"},{"key":"4394_CR9","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/j.cell.2015.10.009","volume":"163","author":"S Rasmussen","year":"2015","unstructured":"Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5000 years ago. Cell 163, 571\u2013582 (2015).","journal-title":"Cell"},{"key":"4394_CR10","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nature10549","volume":"478","author":"KI Bos","year":"2011","unstructured":"Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506\u2013510 (2011).","journal-title":"Nature"},{"key":"4394_CR11","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1073\/pnas.1205750110","volume":"110","author":"Y Cui","year":"2013","unstructured":"Cui, Y. et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl Acad. Sci. 110, 577\u2013582 (2013).","journal-title":"Proc. Natl Acad. Sci."},{"key":"4394_CR12","doi-asserted-by":"publisher","first-page":"3007","DOI":"10.1590\/0001-3765201820170977","volume":"90","author":"CG Zeppelini","year":"2018","unstructured":"Zeppelini, C. G., D. E. Almeida, A. M. P. & Cordeiro-Estrela, P. Ongoing quiescence in the Borborema Plateau Plague focus (Paraiba, Brazil). Acad. Bras. Cienc. 90, 3007\u20133015 (2018).","journal-title":"Acad. Bras. Cienc."},{"key":"4394_CR13","doi-asserted-by":"publisher","first-page":"e311","DOI":"10.1016\/S2666-5247(20)30176-2","volume":"1","author":"MH Green","year":"2020","unstructured":"Green, M. H. How a microbe becomes a pandemic: a new story of the Black Death. Lancet Microbe 1, e311\u2013e312 (2020).","journal-title":"Lancet Microbe"},{"key":"4394_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12154-0","volume":"10","author":"MA Spyrou","year":"2019","unstructured":"Spyrou, M. A. et al. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat. Commun. 10, 4470 e000094 (2019).","journal-title":"Nat. Commun."},{"key":"4394_CR15","first-page":"e000094","volume":"2","author":"S Duchene","year":"2016","unstructured":"Duchene, S. et al. Genome-scale rates of evolutionary change in bacteria. Microb. Genom. 2, e000094 (2016).","journal-title":"Microb. Genom."},{"key":"4394_CR16","doi-asserted-by":"publisher","first-page":"3020","DOI":"10.1073\/pnas.1412887112","volume":"112","author":"BV Schmid","year":"2015","unstructured":"Schmid, B. V. et al. Climate-driven introduction of the Black Death and successive plague reintroductions into Europe. PNAS 112, 3020\u20133025 (2015).","journal-title":"PNAS"},{"key":"4394_CR17","doi-asserted-by":"publisher","first-page":"157","DOI":"10.17302\/TMG.1-1.7","volume":"1","author":"AG Carmichael","year":"2015","unstructured":"Carmichael, A. G. Plague persistence in Western Europe: a hypothesis. Medieval Globe 1, 157\u2013191 (2015).","journal-title":"Medieval Globe"},{"key":"4394_CR18","doi-asserted-by":"publisher","first-page":"28328","DOI":"10.1073\/pnas.2009677117","volume":"117","author":"M Guellil","year":"2020","unstructured":"Guellil, M. et al. A genomic and historical synthesis of plague in 18th century Eurasia. PNAS 117, 28328\u201328335 (2020).","journal-title":"PNAS"},{"key":"4394_CR19","doi-asserted-by":"publisher","first-page":"e2101940118","DOI":"10.1073\/pnas.2101940118","volume":"118","author":"B Bramanti","year":"2021","unstructured":"Bramanti, B., Wu, Y., Yang, R., Cui, Y. & Stenseth, N. C. Assessing the origins of the European plagues following the Black Death: A synthesis of genomic, historical, and ecological information. PNAS 118, e2101940118 (2021).","journal-title":"PNAS"},{"key":"4394_CR20","first-page":"247","volume":"4","author":"R Devignat","year":"1951","unstructured":"Devignat, R. Vari\u00e9t\u00e9s de l\u2019esp\u00e8ce Pasteurella pestis. Bull. World Health Organ 4, 247\u2013263 (1951).","journal-title":"Bull. World Health Organ"},{"key":"4394_CR21","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1016\/j.micinf.2004.08.002","volume":"6","author":"D Zhou","year":"2004","unstructured":"Zhou, D., Han, Y., Song, Y., Huang, P. & Yang, R. Comparative and evolutionary genomics of Yersinia pestis. Microbes Infect. 6, 1226\u20131234 (2004).","journal-title":"Microbes Infect."},{"key":"4394_CR22","doi-asserted-by":"publisher","first-page":"e6000","DOI":"10.1371\/journal.pone.0006000","volume":"4","author":"Y Li","year":"2009","unstructured":"Li, Y. et al. Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci. PLoS One 4, e6000 (2009).","journal-title":"PLoS One"},{"key":"4394_CR23","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.3389\/fmicb.2018.01106","volume":"9","author":"VV Kutyrev","year":"2018","unstructured":"Kutyrev, V. V. et al. Phylogeny and classification of Yersinia pestis through the lens of strains from the plague foci of Commonwealth of Independent States. Front. Microbiol. 9, 1106 (2018).","journal-title":"Front. Microbiol."},{"key":"4394_CR24","doi-asserted-by":"publisher","first-page":"1601","DOI":"10.1093\/ahr\/rhaa511","volume":"125","author":"MH Green","year":"2020","unstructured":"Green, M. H. The four Black Deaths. Am. Historical Rev. 125, 1601\u20131631 (2020).","journal-title":"Am. Historical Rev."},{"key":"4394_CR25","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04550-9","volume":"9","author":"MA Spyrou","year":"2018","unstructured":"Spyrou, M. A. et al. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nat. Commun. 9, 2234 (2018).","journal-title":"Nat. Commun."},{"key":"4394_CR26","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1146\/annurev.ento.50.071803.130337","volume":"50","author":"KL Gage","year":"2005","unstructured":"Gage, K. L. & Kosoy, M. Y. Natural history of plague: perspectives from more than a century of research. Annu Rev. Entomol. 50, 505\u2013528 (2005).","journal-title":"Annu Rev. Entomol."},{"key":"4394_CR27","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1017\/S0020743819000667","volume":"51","author":"IA Bola\u00f1os","year":"2019","unstructured":"Bola\u00f1os, I. A. The Ottomans during the global crises of cholera and plague: the view from Iraq and the Gulf. Int. J. Middle East Stud. 51, 603\u2013620 (2019).","journal-title":"Int. J. Middle East Stud."},{"key":"4394_CR28","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1017\/npt.2020.27","volume":"63","author":"N Varl\u0131k","year":"2020","unstructured":"Varl\u0131k, N. The plague that never left: restoring the Second Pandemic to Ottoman and Turkish history in the time of COVID-19. N. Perspect. Turk. 63, 176\u2013189 (2020).","journal-title":"N. Perspect. Turk."},{"key":"4394_CR29","first-page":"1","volume":"23","author":"J Tan","year":"2002","unstructured":"Tan, J. et al. Towards the atlas of plague and its environment in the People\u2019s Republic of China: idea, principle and methodology of design and research results. Huan Jing Ke Xue 23, 1\u20138 (2002).","journal-title":"Huan Jing Ke Xue"},{"key":"4394_CR30","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1016\/j.chom.2016.05.012","volume":"19","author":"A Spyrou, Maria","year":"2016","unstructured":"Spyrou, Maria, A. et al. Historical Y. pestis genomes reveal the European Black Death as the source of ancient and modern plague pandemics. Cell Host Microbe 19, 874\u2013881 (2016).","journal-title":"Cell Host Microbe"},{"key":"4394_CR31","doi-asserted-by":"publisher","first-page":"e0244615","DOI":"10.1371\/journal.pone.0244615","volume":"16","author":"GA Eroshenko","year":"2021","unstructured":"Eroshenko, G. A. et al. Evolution and circulation of Yersinia pestis in the Northern Caspian and Northern Aral Sea regions in the 20th-21st centuries. PLOS ONE 16, e0244615 (2021).","journal-title":"PLOS ONE"},{"key":"4394_CR32","doi-asserted-by":"publisher","first-page":"1140","DOI":"10.1038\/ng.705","volume":"42","author":"G Morelli","year":"2010","unstructured":"Morelli, G. et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat. Genet. 42, 1140\u20131143 (2010).","journal-title":"Nat. Genet."},{"key":"4394_CR33","doi-asserted-by":"publisher","first-page":"1952","DOI":"10.1016\/j.ygeno.2021.04.021","volume":"113","author":"SV Pisarenko","year":"2021","unstructured":"Pisarenko, S. V. et al. Yersinia pestis strains isolated in natural plague foci of Caucasus and Transcaucasia in the context of the global evolution of species. Genomics 113, 1952\u20131961 (2021).","journal-title":"Genomics"},{"key":"4394_CR34","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1093\/molbev\/msaa163","volume":"37","author":"S Duch\u00eane","year":"2020","unstructured":"Duchene, S. et al. Bayesian evaluation of temporal signal in measurably evolving populations. Mol. Biol. Evolution 37, 3363\u20133379 (2020).","journal-title":"Mol. Biol. Evolution"},{"key":"4394_CR35","doi-asserted-by":"crossref","unstructured":"Duchene, S. et al. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evolution 6, veaa061 (2020).","DOI":"10.1093\/ve\/veaa061"},{"key":"4394_CR36","doi-asserted-by":"publisher","first-page":"79","DOI":"10.3390\/v13010079","volume":"13","author":"A Lam","year":"2021","unstructured":"Lam, A. & Duchene, S. The impacts of low diversity sequence data on phylodynamic inference during an emerging epidemic. Viruses 13, 79 (2021).","journal-title":"Viruses"},{"key":"4394_CR37","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.1111\/2041-210X.13620","volume":"12","author":"LA Featherstone","year":"2021","unstructured":"Featherstone, L. A., Di Giallonardo, F., Holmes, E. C., Vaughan, T. G. & Duch\u00eane, S. Infectious disease phylodynamics with occurrence data. Methods Ecol. Evolution 12, 1498\u20131507 (2021).","journal-title":"Methods Ecol. Evolution"},{"key":"4394_CR38","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1126\/science.abc5746","volume":"368","author":"SYW Ho","year":"2020","unstructured":"Ho, S. Y. W. & Duch\u00eane, S. Dating the emergence of human pathogens. Science 368, 1310\u20131311 (2020).","journal-title":"Science"},{"key":"4394_CR39","doi-asserted-by":"publisher","first-page":"e0007761","DOI":"10.1371\/journal.pntd.0007761","volume":"13","author":"A Munyenyiwa","year":"2019","unstructured":"Munyenyiwa, A., Zimba, M., Nhiwatiwa, T. & Barson, M. Plague in Zimbabwe from 1974 to 2018: a review article. PLOS Neglected Tropical Dis. 13, e0007761 (2019).","journal-title":"PLOS Neglected Tropical Dis."},{"key":"4394_CR40","doi-asserted-by":"publisher","unstructured":"Green, M. H. Putting Africa on the Black Death map: narratives from genetics and history. Afriques 9, https:\/\/doi.org\/10.4000\/afriques.2125 (2018).","DOI":"10.4000\/afriques.2125"},{"key":"4394_CR41","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/s12866-017-1146-8","volume":"18","author":"SS Nyirenda","year":"2018","unstructured":"Nyirenda, S. S. et al. Molecular epidemiological investigations of plague in Eastern Province of Zambia. BMC Microbiol. 18, 2 (2018).","journal-title":"BMC Microbiol"},{"key":"4394_CR42","doi-asserted-by":"crossref","unstructured":"Little, L. K. Plague and the End of Antiquity: The Pandemic of 541-750. (Cambridge University Press, 2007).","DOI":"10.1017\/CBO9780511812934"},{"key":"4394_CR43","doi-asserted-by":"publisher","first-page":"e2016033","DOI":"10.4178\/epih.e2016033","volume":"38","author":"A Hashemi Shahraki","year":"2016","unstructured":"Hashemi Shahraki, A., Carniel, E. & Mostafavi, E. Plague in Iran: its history and current status. Epidemiol Health 38, e2016033 (2016).","journal-title":"Epidemiol Health"},{"key":"4394_CR44","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1017\/mdh.2021.3","volume":"65","author":"N Fancy","year":"2021","unstructured":"Fancy, N. & Green, M. Plague and the fall of Baghdad (1258). Med. Hist. 65, 155\u2013177 (2021).","journal-title":"Med. Hist."},{"key":"4394_CR45","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1038\/s41586-022-04800-3","volume":"606","author":"MA Spyrou","year":"2022","unstructured":"Spyrou, M. A. et al. The source of the Black Death in fourteenth-century central Eurasia. Nature 606, 718\u2013724 (2022).","journal-title":"Nature"},{"key":"4394_CR46","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1177\/009770048801400201","volume":"14","author":"C Benedict","year":"1988","unstructured":"Benedict, C. Bubonic plague in nineteenth-century China. Mod. China 14, 107\u2013155 (1988).","journal-title":"Mod. China"},{"key":"4394_CR47","doi-asserted-by":"publisher","first-page":"11833","DOI":"10.1073\/pnas.1901366116","volume":"116","author":"L Xu","year":"2019","unstructured":"Xu, L. et al. Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic. PNAS 116, 11833\u201311838 (2019).","journal-title":"PNAS"},{"key":"4394_CR48","doi-asserted-by":"publisher","first-page":"e1003","DOI":"10.1371\/journal.pntd.0001003","volume":"5","author":"ET Ryan","year":"2011","unstructured":"Ryan, E. T. The cholera pandemic, still with us after half a century: time to rethink. PLOS Neglected Tropical Dis. 5, e1003 (2011).","journal-title":"PLOS Neglected Tropical Dis."},{"key":"4394_CR49","doi-asserted-by":"publisher","first-page":"2244","DOI":"10.1111\/1751-7915.13916","volume":"14","author":"H Br\u00fcssow","year":"2021","unstructured":"Br\u00fcssow, H. What we can learn from the dynamics of the 1889 \u2018Russian flu\u2019 pandemic for the future trajectory of COVID-19. Microbial Biotechnol. 14, 2244\u20132253 (2021).","journal-title":"Microbial Biotechnol."},{"key":"4394_CR50","doi-asserted-by":"publisher","first-page":"631736","DOI":"10.3389\/fmicb.2020.631736","volume":"11","author":"J Piret","year":"2021","unstructured":"Piret, J. & Boivin, G. Pandemics throughout history. Front. Microbiol. 11, 631736 (2021).","journal-title":"Front. Microbiol."},{"key":"4394_CR51","doi-asserted-by":"publisher","first-page":"vex042","DOI":"10.1093\/ve\/vex042","volume":"4","author":"P Sagulenko","year":"2018","unstructured":"Sagulenko, P., Puller, V. & Neher, R. A. TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol. 4, vex042 (2018).","journal-title":"Virus Evol."},{"key":"4394_CR52","first-page":"15","volume":"16","author":"J Cantlie","year":"1897","unstructured":"Cantlie, J. The spread of plague. Trans. Epidemiol. Soc. Lond. 16, 15\u201363 (1897).","journal-title":"Trans. Epidemiol. Soc. Lond."},{"key":"4394_CR53","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1353\/jwh.2002.0033","volume":"13","author":"M Echenberg","year":"2002","unstructured":"Echenberg, M. Pestis redux: the initial years of the third bubonic plague pandemic, 1894\u20131901. J. World Hist. 13, 429\u2013449 (2002).","journal-title":"J. World Hist."},{"key":"4394_CR54","doi-asserted-by":"publisher","first-page":"e1008561","DOI":"10.1371\/journal.pcbi.1008561","volume":"17","author":"A Kalkauskas","year":"2021","unstructured":"Kalkauskas, A. et al. Sampling bias and model choice in continuous phylogeography: getting lost on a random walk. PLOS Computational Biol. 17, e1008561 (2021).","journal-title":"PLOS Computational Biol."},{"key":"4394_CR55","unstructured":"Benedictow, O. J. The Black Death, 1346-1353: The Complete History. (Boydell Press, 2004)."},{"key":"4394_CR56","unstructured":"Shadwell, A. The plague in Oporto. Nineteenth Century: a monthly Rev. 46, 833\u2013847 (1899)."},{"key":"4394_CR57","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/pastj\/gtaa028","volume":"252","author":"P Slavin","year":"2021","unstructured":"Slavin, P. Out of the West: formation of a permanent plague reservoir in south-central Germany (1349\u20131356) and its implications. Present 252, 3\u201351 (2021).","journal-title":"Present"},{"key":"4394_CR58","doi-asserted-by":"publisher","first-page":"103","DOI":"10.3201\/eid2401.170477","volume":"24","author":"J Roosen","year":"2018","unstructured":"Roosen, J. & Curtis, D. R. Dangers of noncritical use of historical plague data. Emerg. Infect. Dis. 24, 103\u2013110 (2018).","journal-title":"Emerg. Infect. Dis."},{"key":"4394_CR59","doi-asserted-by":"publisher","first-page":"1990","DOI":"10.21105\/joss.01990","volume":"5","author":"K Eaton","year":"2020","unstructured":"Eaton, K. NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases. J. Open Source Softw. 5, 1990 (2020).","journal-title":"J. Open Source Softw."},{"key":"4394_CR60","doi-asserted-by":"publisher","first-page":"e10947","DOI":"10.7717\/peerj.10947","volume":"9","author":"JAF Yates","year":"2021","unstructured":"Yates, J. A. F. et al. Reproducible, portable, and efficient ancient genome reconstruction with nf-core\/eager. PeerJ 9, e10947 (2021).","journal-title":"PeerJ"},{"key":"4394_CR61","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","volume":"14","author":"S Kalyaanamoorthy","year":"2017","unstructured":"Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587\u2013589 (2017).","journal-title":"Nat. Methods"},{"key":"4394_CR62","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"4394_CR63","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","volume":"35","author":"DT Hoang","year":"2018","unstructured":"Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evolution 35, 518\u2013522 (2018).","journal-title":"Mol. Biol. Evolution"},{"key":"4394_CR64","doi-asserted-by":"publisher","first-page":"vey016","DOI":"10.1093\/ve\/vey016","volume":"4","author":"MA Suchard","year":"2018","unstructured":"Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).","journal-title":"Virus Evol."},{"key":"4394_CR65","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1093\/jole\/lzz005","volume":"4","author":"AM Ritchie","year":"2019","unstructured":"Ritchie, A. M. & Ho, S. Y. W. Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families. J. Lang. Evol. 4, 108\u2013123 (2019).","journal-title":"J. Lang. Evol."},{"key":"4394_CR66","doi-asserted-by":"publisher","first-page":"4200","DOI":"10.1073\/pnas.1713314115","volume":"115","author":"S M\u00f6ller","year":"2018","unstructured":"M\u00f6ller, S., du Plessis, L. & Stadler, T. Impact of the tree prior on estimating clock rates during epidemic outbreaks. Proc. Natl Acad. Sci. 115, 4200\u20134205 (2018).","journal-title":"Proc. Natl Acad. Sci."},{"key":"4394_CR67","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1093\/molbev\/mss243","volume":"30","author":"G Baele","year":"2013","unstructured":"Baele, G., Li, W. L. S., Drummond, A. J., Suchard, M. A. & Lemey, P. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 30, 239\u2013243 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"4394_CR68","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1002\/cjs.5550360302","volume":"36","author":"MAR Ferreira","year":"2008","unstructured":"Ferreira, M. A. R. & Suchard, M. A. Bayesian analysis of elapsed times in continuous-time Markov chains. Can. J. Stat. 36, 355\u2013368 (2008).","journal-title":"Can. J. Stat."},{"key":"4394_CR69","doi-asserted-by":"publisher","first-page":"e1000520","DOI":"10.1371\/journal.pcbi.1000520","volume":"5","author":"P Lemey","year":"2009","unstructured":"Lemey, P., Rambaut, A., Drummond, A. J. & Suchard, M. A. Bayesian phylogeography finds its roots. PLOS Computational Biol. 5, e1000520 (2009).","journal-title":"PLOS Computational Biol."},{"key":"4394_CR70","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","volume":"4","author":"AJ Drummond","year":"2006","unstructured":"Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).","journal-title":"PLoS Biol."},{"key":"4394_CR71","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-7-214","volume":"7","author":"AJ Drummond","year":"2007","unstructured":"Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolut. Biol. 7, 214 (2007).","journal-title":"BMC Evolut. Biol."},{"key":"4394_CR72","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.21105\/joss.03021","volume":"6","author":"ML Waskom","year":"2021","unstructured":"Waskom, M. L. Seaborn: statistical data visualization. J. Open Source Softw. 6, 3021 (2021).","journal-title":"J. Open Source Softw."},{"key":"4394_CR73","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","volume":"34","author":"J Hadfield","year":"2018","unstructured":"Hadfield, J. et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34, 4121\u20134123 (2018).","journal-title":"Bioinformatics"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-04394-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-04394-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-04394-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T12:25:41Z","timestamp":1674131141000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-022-04394-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,19]]},"references-count":73,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["4394"],"URL":"https:\/\/doi.org\/10.1038\/s42003-022-04394-6","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-1146895\/v1","asserted-by":"object"}]},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,19]]},"assertion":[{"value":"17 December 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 December 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 January 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"23"}}