{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T22:44:41Z","timestamp":1791326681600,"version":"4.3.1"},"reference-count":54,"publisher":"National Academy of Sciences","issue":"2","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2013,1,8]]},"abstract":"<jats:p>\n                    The genetic diversity of\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    , the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    strains that were isolated in China and elsewhere. These SNPs define the genealogy of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1205750110","type":"journal-article","created":{"date-parts":[[2012,12,27]],"date-time":"2012-12-27T22:33:25Z","timestamp":1356647605000},"page":"577-582","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":376,"title":["Historical variations in mutation rate in an epidemic pathogen,\n                    <i>Yersinia pestis<\/i>"],"prefix":"10.1073","volume":"110","author":[{"given":"Yujun","family":"Cui","sequence":"first","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"},{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang","family":"Yu","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanfeng","family":"Yan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"},{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongfang","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanjun","family":"Li","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"}]},{"given":"Thibaut","family":"Jombart","sequence":"additional","affiliation":[{"name":"Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucy A.","family":"Weinert","sequence":"additional","affiliation":[{"name":"University College London Genetics Institute, Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuyun","family":"Wang","sequence":"additional","affiliation":[{"name":"Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaobiao","family":"Guo","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"}]},{"given":"Lizhi","family":"Xu","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Xinjiang Center for Disease Control and Prevention, Urumiqi 830002, Xijiang province, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hancheng","family":"Zheng","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Qin","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Xiao","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"}]},{"given":"Mingshou","family":"Wu","sequence":"additional","affiliation":[{"name":"Yunnan Institute for Epidemic Diseases Control and Research, Dali 671000, Yunnan Province, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyi","family":"Wang","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"}]},{"given":"Dongsheng","family":"Zhou","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"}]},{"given":"Zhizhen","family":"Qi","sequence":"additional","affiliation":[{"name":"Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongmin","family":"Du","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"}]},{"given":"Honglong","family":"Wu","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianwei","family":"Yang","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongzhi","family":"Cao","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hu","family":"Wang","sequence":"additional","affiliation":[{"name":"Qinghai Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Health Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100025, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shusen","family":"Yao","sequence":"additional","affiliation":[{"name":"Military Center for Disease Control and Prevention, Beijing 100850, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Rakin","sequence":"additional","affiliation":[{"name":"Max von Pettenkofer Institute, Ludwig-Maximilians-University, Munich 80336, Germany; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Falush","sequence":"additional","affiliation":[{"name":"Environmental Research Institute, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francois","family":"Balloux","sequence":"additional","affiliation":[{"name":"University College London Genetics Institute, Department of Genetics Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Achtman","sequence":"additional","affiliation":[{"name":"Environmental Research Institute, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajun","family":"Song","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"},{"name":"Environmental Research Institute, University College Cork, Cork, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruifu","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;"},{"name":"Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2012,12,27]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1146\/annurev.ento.50.071803.130337","article-title":"Natural history of plague: Perspectives from more than a century of research","volume":"50","author":"Gage KL","year":"2005","unstructured":"KL Gage, MY Kosoy, 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":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1371\/journal.pmed.0050003","article-title":"Plague: Past, present, and future","volume":"5","author":"Stenseth NC","year":"2008","unstructured":"NC Stenseth, et al., Plague: Past, present, and future. PLoS Med 5, e3 (2008).","journal-title":"PLoS Med"},{"key":"e_1_3_4_3_2","first-page":"428","article-title":"La peste bubonique \u00e0 Hong-Kong [Bubonic plague in Hong Kong]","volume":"2","author":"Yersin A","year":"1894","unstructured":"A Yersin, La peste bubonique \u00e0 Hong-Kong [Bubonic plague in Hong Kong]. Ann Inst Pasteur (Paris) 2, 428\u2013430 (1894).","journal-title":"Ann Inst Pasteur (Paris)"},{"key":"e_1_3_4_4_2","volume-title":"The Black Death 1346\u20131353","author":"Benedictow OJ","year":"2004","unstructured":"OJ Benedictow The Black Death 1346\u20131353 (Boydell Press, Woodbridge, 2004)."},{"key":"e_1_3_4_5_2","first-page":"xiv","volume-title":"Plague and the End of Antiquity: The Pandemic of 541-750","author":"Little LK","year":"2007","unstructured":"LK Little Plague and the End of Antiquity: The Pandemic of 541-750 (Cambridge Univ Press, New York), pp. xiv, 360. (2007)."},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"xiv","DOI":"10.1017\/CBO9780511542527.002","volume-title":"Biology of Plagues: Evidence from Historical Populations","author":"Scott S","year":"2001","unstructured":"S Scott, CJ Duncan Biology of Plagues: Evidence from Historical Populations (Cambridge Univ Press, Cambridge, New York), pp. xiv, 420. (2001)."},{"key":"e_1_3_4_7_2","first-page":"x","volume-title":"The Back Death Transformed: Disease and Culture in Early Renaissance Europe","author":"Cohn SK","year":"2002","unstructured":"SK Cohn The Back Death Transformed: Disease and Culture in Early Renaissance Europe (Arnold and Oxford Univ Press, London, New York), pp. x, 318. (2002)."},{"key":"e_1_3_4_8_2","volume-title":"The Black Death: A Biological Reappraisal","author":"Twigg G","year":"1984","unstructured":"G Twigg The Black Death: A Biological Reappraisal (Batsford, London, 1984)."},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"e1001134","DOI":"10.1371\/journal.ppat.1001134","article-title":"Distinct clones of Yersinia pestis caused the black death","volume":"6","author":"Haensch S","year":"2010","unstructured":"S Haensch, et al., Distinct clones of Yersinia pestis caused the black death. PLoS Pathog 6, e1001134 (2010).","journal-title":"PLoS Pathog"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"e16735","DOI":"10.1371\/journal.pone.0016735","article-title":"High throughput, multiplexed pathogen detection authenticates plague waves in medieval Venice, Italy","volume":"6","author":"Tran TN","year":"2011","unstructured":"TN Tran, et al., High throughput, multiplexed pathogen detection authenticates plague waves in medieval Venice, Italy. PLoS ONE 6, e16735 (2011).","journal-title":"PLoS ONE"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature10549","article-title":"A draft genome of Yersinia pestis from victims of the Black Death","volume":"478","author":"Bos KI","year":"2011","unstructured":"KI Bos, et al., A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506\u2013510 (2011).","journal-title":"Nature"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1146\/annurev.micro.62.081307.162832","article-title":"Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens","volume":"62","author":"Achtman M","year":"2008","unstructured":"M Achtman, Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 62, 53\u201370 (2008).","journal-title":"Annu Rev Microbiol"},{"key":"e_1_3_4_13_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, et al., 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_14_2","doi-asserted-by":"crossref","first-page":"e2166","DOI":"10.1371\/journal.pone.0002166","article-title":"Different region analysis for genotyping Yersinia pestis isolates from China","volume":"3","author":"Li Y","year":"2008","unstructured":"Y Li, et al., Different region analysis for genotyping Yersinia pestis isolates from China. PLoS ONE 3, e2166 (2008).","journal-title":"PLoS ONE"},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"e6000","DOI":"10.1371\/journal.pone.0006000","article-title":"Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: Insights into the worldwide expansion of Central Asia plague foci","volume":"4","author":"Li Y","year":"2009","unstructured":"Y Li, 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":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1101\/gr.097261.109","article-title":"De novo assembly of human genomes with massively parallel short read sequencing","volume":"20","author":"Li R","year":"2010","unstructured":"R Li, et al., De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20, 265\u2013272 (2010).","journal-title":"Genome Res"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"7628","DOI":"10.1128\/JB.01227-09","article-title":"Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China","volume":"191","author":"Eppinger M","year":"2009","unstructured":"M Eppinger, et al., Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J Bacteriol 191, 7628\u20137629 (2009).","journal-title":"J Bacteriol"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","first-page":"14043","DOI":"10.1073\/pnas.96.24.14043","article-title":"Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis","volume":"96","author":"Achtman M","year":"1999","unstructured":"M Achtman, et al., Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci USA 96, 14043\u201314048 (1999).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"17837","DOI":"10.1073\/pnas.0408026101","article-title":"Microevolution and history of the plague bacillus, Yersinia pestis","volume":"101","author":"Achtman M","year":"2004","unstructured":"M Achtman, et al., Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci USA 101, 17837\u201317842 (2004).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"3114","DOI":"10.1111\/j.1462-2920.2011.02588.x","article-title":"Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing","volume":"13","author":"Laukkanen-Ninios R","year":"2011","unstructured":"R Laukkanen-Ninios, et al., Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing. Environ Microbiol 13, 3114\u20133127 (2011).","journal-title":"Environ Microbiol"},{"key":"e_1_3_4_21_2","unstructured":"; WHO WHO Report on Global Surveillance of Epidemic-Prone Infectious Disease (WHO Geneva) pp. 25\u201337 Available at http:\/\/www.who.int\/csr\/resources\/publications\/surveillance\/WHO_CDS_CSR_ISR_2000_1\/en. (2000)."},{"key":"e_1_3_4_22_2","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/dnares\/11.3.179","article-title":"Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans","volume":"11","author":"Song Y","year":"2004","unstructured":"Y Song, et al., Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res 11, 179\u2013197 (2004).","journal-title":"DNA Res"},{"key":"e_1_3_4_23_2","doi-asserted-by":"crossref","first-page":"5147","DOI":"10.1128\/JB.186.15.5147-5152.2004","article-title":"Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus","volume":"186","author":"Zhou D","year":"2004","unstructured":"D Zhou, et al., Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J Bacteriol 186, 5147\u20135152 (2004).","journal-title":"J Bacteriol"},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1038\/nature08182","article-title":"Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic","volume":"459","author":"Smith GJ","year":"2009","unstructured":"GJ Smith, et al., Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459, 1122\u20131125 (2009).","journal-title":"Nature"},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread","volume":"327","author":"Harris SR","year":"2010","unstructured":"SR Harris, et al., Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469\u2013474 (2010).","journal-title":"Science"},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"e1000855","DOI":"10.1371\/journal.ppat.1000855","article-title":"A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus","volume":"6","author":"N\u00fcbel U","year":"2010","unstructured":"U N\u00fcbel, et al., A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog 6, e1000855 (2010).","journal-title":"PLoS Pathog"},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"Drummond AJ","year":"2007","unstructured":"AJ Drummond, A Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214 (2007).","journal-title":"BMC Evol Biol"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/1741-7007-8-114","article-title":"Bayesian random local clocks, or one rate to rule them all","volume":"8","author":"Drummond AJ","year":"2010","unstructured":"AJ Drummond, MA Suchard, Bayesian random local clocks, or one rate to rule them all. BMC Biol 8, 114 (2010).","journal-title":"BMC Biol"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"Drummond AJ","year":"2006","unstructured":"AJ Drummond, SY Ho, MJ Phillips, A Rambaut, Relaxed phylogenetics and dating with confidence. PLoS Biol 4, e88 (2006).","journal-title":"PLoS Biol"},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1093\/molbev\/msi145","article-title":"Time dependency of molecular rate estimates and systematic overestimation of recent divergence times","volume":"22","author":"Ho SY","year":"2005","unstructured":"SY Ho, MJ Phillips, A Cooper, AJ Drummond, Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22, 1561\u20131568 (2005).","journal-title":"Mol Biol Evol"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1080\/10635150600865567","article-title":"Detecting the node-density artifact in phylogeny reconstruction","volume":"55","author":"Venditti C","year":"2006","unstructured":"C Venditti, A Meade, M Pagel, Detecting the node-density artifact in phylogeny reconstruction. Syst Biol 55, 637\u2013643 (2006).","journal-title":"Syst Biol"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1038\/nature08480","article-title":"Genome evolution and adaptation in a long-term experiment with Escherichia coli","volume":"461","author":"Barrick JE","year":"2009","unstructured":"JE Barrick, et al., Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243\u20131247 (2009).","journal-title":"Nature"},{"key":"e_1_3_4_33_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, et al., 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_34_2","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1126\/science.1134933","article-title":"Evolutionary history of Salmonella typhi","volume":"314","author":"Roumagnac P","year":"2006","unstructured":"P Roumagnac, et al., Evolutionary history of Salmonella typhi. Science 314, 1301\u20131304 (2006).","journal-title":"Science"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"e1001301","DOI":"10.1371\/journal.pgen.1001301","article-title":"Prevalence of epistasis in the evolution of influenza A surface proteins","volume":"7","author":"Kryazhimskiy S","year":"2011","unstructured":"S Kryazhimskiy, J Dushoff, GA Bazykin, JB Plotkin, Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet 7, e1001301 (2011).","journal-title":"PLoS Genet"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1099\/mic.0.021170-0","article-title":"Attenuated enzootic (pestoides) isolates of Yersinia pestis express active aspartase","volume":"155","author":"Bearden SW","year":"2009","unstructured":"SW Bearden, et al., Attenuated enzootic (pestoides) isolates of Yersinia pestis express active aspartase. Microbiology 155, 198\u2013209 (2009).","journal-title":"Microbiology"},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/S1473-3099(06)70438-8","article-title":"Yersinia pestis as a telluric, human ectoparasite-borne organism","volume":"6","author":"Drancourt M","year":"2006","unstructured":"M Drancourt, L Houhamdi, D Raoult, Yersinia pestis as a telluric, human ectoparasite-borne organism. Lancet Infect Dis 6, 234\u2013241 (2006).","journal-title":"Lancet Infect Dis"},{"key":"e_1_3_4_38_2","first-page":"197","article-title":"The evolution of flea-borne transmission in Yersinia pestis","volume":"7","author":"Hinnebusch BJ","year":"2005","unstructured":"BJ Hinnebusch, The evolution of flea-borne transmission in Yersinia pestis. Curr Issues Mol Biol 7, 197\u2013212 (2005).","journal-title":"Curr Issues Mol Biol"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1086\/429931","article-title":"Poor vector competence of fleas and the evolution of hypervirulence in Yersinia pestis","volume":"191","author":"Lorange EA","year":"2005","unstructured":"EA Lorange, BL Race, F Sebbane, B Joseph Hinnebusch, Poor vector competence of fleas and the evolution of hypervirulence in Yersinia pestis. J Infect Dis 191, 1907\u20131912 (2005).","journal-title":"J Infect Dis"},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"8408","DOI":"10.1073\/pnas.0401561101","article-title":"Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales","volume":"101","author":"Girard JM","year":"2004","unstructured":"JM Girard, et al., Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proc Natl Acad Sci USA 101, 8408\u20138413 (2004).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/224149a0","article-title":"Rate of fixation of nucleotide substitutions in evolution","volume":"224","author":"Laird CD","year":"1969","unstructured":"CD Laird, BL McConaughy, BJ McCarthy, Rate of fixation of nucleotide substitutions in evolution. Nature 224, 149\u2013154 (1969).","journal-title":"Nature"},{"key":"e_1_3_4_42_2","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin H","year":"2005","unstructured":"H Tettelin, et al., Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u201cpan-genome\u201d. Proc Natl Acad Sci USA 102, 13950\u201313955 (2005).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","article-title":"Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths","volume":"5","author":"Touchon M","year":"2009","unstructured":"M Touchon, et al., Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5, e1000344 (2009).","journal-title":"PLoS Genet"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/ng.195","article-title":"High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi","volume":"40","author":"Holt KE","year":"2008","unstructured":"KE Holt, et al., High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 40, 987\u2013993 (2008).","journal-title":"Nat Genet"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1126\/science.1167140","article-title":"The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria","volume":"323","author":"Moran NA","year":"2009","unstructured":"NA Moran, HJ McLaughlin, R Sorek, The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323, 379\u2013382 (2009).","journal-title":"Science"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1111\/j.1365-2958.2006.05570.x","article-title":"A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus","volume":"63","author":"Derbise A","year":"2007","unstructured":"A Derbise, et al., A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus. Mol Microbiol 63, 1145\u20131157 (2007).","journal-title":"Mol Microbiol"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1002\/ajpa.10276","article-title":"Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.)","volume":"126","author":"Wiechmann I","year":"2005","unstructured":"I Wiechmann, G Grupe, Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). Am J Phys Anthropol 126, 48\u201355 (2005).","journal-title":"Am J Phys Anthropol"},{"key":"e_1_3_4_48_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, et al., 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_49_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, et al., Yersinia pestis Orientalis in remains of ancient plague patients. Emerg Infect Dis 13, 332\u2013333 (2007).","journal-title":"Emerg Infect Dis"},{"key":"e_1_3_4_50_2","first-page":"1317","article-title":"Yersinia pestis genotyping","volume":"11","author":"Vergnaud G","year":"2005","unstructured":"G Vergnaud, Yersinia pestis genotyping. Emerg Infect Dis 11, 1317\u20131318, author reply 1318\u20131319 (2005).","journal-title":"Emerg Infect Dis"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrmicro2219","article-title":"Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases","volume":"7","author":"Keim PS","year":"2009","unstructured":"PS Keim, DM Wagner, Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nat Rev Microbiol 7, 813\u2013821 (2009).","journal-title":"Nat Rev Microbiol"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"8648","DOI":"10.1128\/AEM.06538-11","article-title":"A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type","volume":"77","author":"Bakker HC","year":"2011","unstructured":"HC Bakker, et al., A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type. Appl Environ Microbiol 77, 8648\u20138655 (2011).","journal-title":"Appl Environ Microbiol"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"13110","DOI":"10.1073\/pnas.0602447103","article-title":"Plague dynamics are driven by climate variation","volume":"103","author":"Stenseth NC","year":"2006","unstructured":"NC Stenseth, et al., Plague dynamics are driven by climate variation. Proc Natl Acad Sci USA 103, 13110\u201313115 (2006).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"10214","DOI":"10.1073\/pnas.1019486108","article-title":"Nonlinear effect of climate on plague during the third pandemic in China","volume":"108","author":"Xu L","year":"2011","unstructured":"L Xu, et al., Nonlinear effect of climate on plague during the third pandemic in China. Proc Natl Acad Sci USA 108, 10214\u201310219 (2011).","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1205750110","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T06:12:38Z","timestamp":1654582358000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1205750110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12,27]]},"references-count":54,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2013,1,8]]}},"alternative-id":["10.1073\/pnas.1205750110"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1205750110","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718302099.793491844","asserted-by":"object"}]},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,27]]},"assertion":[{"value":"2012-12-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}