{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T12:08:33Z","timestamp":1783512513898,"version":"3.55.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T00:00:00Z","timestamp":1548028800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Methods"],"published-print":{"date-parts":[[2019,2]]},"DOI":"10.1038\/s41592-018-0293-7","type":"journal-article","created":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T19:46:44Z","timestamp":1546976804000},"page":"199-204","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":85,"title":["Inferring bacterial recombination rates from large-scale sequencing datasets"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8435-3780","authenticated-orcid":false,"given":"Mingzhi","family":"Lin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0590-4036","authenticated-orcid":false,"given":"Edo","family":"Kussell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,1,21]]},"reference":[{"key":"293_CR1","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1098\/rspb.1991.0085","volume":"245","author":"J Maynard Smith","year":"1991","unstructured":"Maynard Smith, J. The population genetics of bacteria. Proc. Biol. Sci. 245, 37\u201341 (1991).","journal-title":"Proc. Biol. Sci."},{"key":"293_CR2","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/nrmicro1234","volume":"3","author":"CM Thomas","year":"2005","unstructured":"Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711\u2013721 (2005).","journal-title":"Nat. Rev. Microbiol."},{"key":"293_CR3","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1126\/science.1127573","volume":"315","author":"C Fraser","year":"2007","unstructured":"Fraser, C., Hanage, W. P. & Spratt, B. G. Recombination and the nature of bacterial speciation. Science 315, 476\u2013480 (2007).","journal-title":"Science"},{"key":"293_CR4","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1126\/science.1218198","volume":"336","author":"BJ Shapiro","year":"2012","unstructured":"Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48\u201351 (2012).","journal-title":"Science"},{"key":"293_CR5","doi-asserted-by":"publisher","first-page":"a018069","DOI":"10.1101\/cshperspect.a018069","volume":"8","author":"WP Hanage","year":"2016","unstructured":"Hanage, W. P. Not so simple after all: bacteria, their population genetics, and recombination. Cold Spring Harb. Perspect. Biol. 8, a018069 (2016).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"293_CR6","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1128\/MMBR.00039-14","volume":"79","author":"HH Chang","year":"2015","unstructured":"Chang, H. H. et al. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol. Mol. Biol. Rev. 79, 101\u2013116 (2015).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"293_CR7","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1038\/nrmicro.2015.13","volume":"14","author":"X Didelot","year":"2016","unstructured":"Didelot, X., Walker, A. S., Peto, T. E., Crook, D. W. & Wilson, D. J. Within-host evolution of bacterial pathogens. Nat. Rev. Microbiol. 14, 150\u2013162 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"293_CR8","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1534\/genetics.113.157172","volume":"196","author":"MA Ansari","year":"2014","unstructured":"Ansari, M. A. & Didelot, X. Inference of the properties of the recombination process from whole bacterial genomes. Genetics 196, 253 (2014).","journal-title":"Genetics"},{"key":"293_CR9","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).","journal-title":"Nucleic Acids Res."},{"key":"293_CR10","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1534\/genetics.106.063305","volume":"175","author":"X Didelot","year":"2007","unstructured":"Didelot, X. & Falush, D. Inference of bacterial microevolution using multilocus sequence data. Genetics 175, 1251\u20131266 (2007).","journal-title":"Genetics"},{"key":"293_CR11","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1534\/genetics.110.120121","volume":"186","author":"X Didelot","year":"2010","unstructured":"Didelot, X., Lawson, D., Darling, A. & Falush, D. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 186, 1435\u20131449 (2010).","journal-title":"Genetics"},{"key":"293_CR12","doi-asserted-by":"publisher","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","volume":"11","author":"X Didelot","year":"2015","unstructured":"Didelot, X. & Wilson, D. J. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput. Biol. 11, e1004041 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"293_CR13","doi-asserted-by":"publisher","first-page":"e6","DOI":"10.1093\/nar\/gkr928","volume":"40","author":"P Marttinen","year":"2012","unstructured":"Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).","journal-title":"Nucleic Acids Res."},{"key":"293_CR14","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1093\/molbev\/msx066","volume":"34","author":"R Mostowy","year":"2017","unstructured":"Mostowy, R. et al. Efficient inference of recent and ancestral recombination within bacterial populations. Mol. Biol. Evol. 34, 1167\u20131182 (2017).","journal-title":"Mol. Biol. Evol."},{"key":"293_CR15","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1534\/genetics.117.300662","volume":"208","author":"BJ Arnold","year":"2018","unstructured":"Arnold, B. J. et al. Weak epistasis may drive adaptation in recombining bacteria. Genetics 208, 1247\u20131260 (2018).","journal-title":"Genetics"},{"key":"293_CR16","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1126\/science.aad2545","volume":"351","author":"F Maixner","year":"2016","unstructured":"Maixner, F. et al. The 5300-year-old Helicobacter pylori genome of the Iceman. Science 351, 162\u2013165 (2016).","journal-title":"Science"},{"key":"293_CR17","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":"293_CR18","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1534\/genetics.116.189621","volume":"205","author":"M Lin","year":"2017","unstructured":"Lin, M. & Kussell, E. Correlated mutations and homologous recombination within bacterial populations. Genetics 205, 891\u2013917 (2017).","journal-title":"Genetics"},{"key":"293_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11995","volume":"7","author":"S Bubendorfer","year":"2016","unstructured":"Bubendorfer, S. et al. Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nat. Commun. 7, 11995 (2016).","journal-title":"Nat. Commun."},{"key":"293_CR20","doi-asserted-by":"publisher","first-page":"e1002745","DOI":"10.1371\/journal.ppat.1002745","volume":"8","author":"NJ Croucher","year":"2012","unstructured":"Croucher, N. J., Harris, S. R., Barquist, L., Parkhill, J. & Bentley, S. D. A high-resolution view of genome-wide pneumococcal transformation. PLoS Pathog. 8, e1002745 (2012).","journal-title":"PLoS Pathog."},{"key":"293_CR21","doi-asserted-by":"publisher","first-page":"e1006546","DOI":"10.1371\/journal.pgen.1006546","volume":"13","author":"K Thorell","year":"2017","unstructured":"Thorell, K. et al. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genet. 13, e1006546 (2017).","journal-title":"PLoS Genet."},{"key":"293_CR22","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/ng.3767","volume":"49","author":"AL Manson","year":"2017","unstructured":"Manson, A. L. et al. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat. Genet. 49, 395\u2013402 (2017).","journal-title":"Nat. Genet."},{"key":"293_CR23","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1136\/gutjnl-2014-307345","volume":"64","author":"QZ Cao","year":"2015","unstructured":"Cao, Q. Z. et al. Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut 64, 554\u2013561 (2015).","journal-title":"Gut"},{"key":"293_CR24","doi-asserted-by":"publisher","first-page":"5033","DOI":"10.1073\/pnas.1018444108","volume":"108","author":"L Kennemann","year":"2011","unstructured":"Kennemann, L. et al. Helicobacter pylori genome evolution during human infection. Proc. Natl Acad. Sci. USA 108, 5033\u20135038 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"293_CR25","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593\u2013594 (2012).","journal-title":"Bioinformatics"},{"key":"293_CR26","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.1093\/nar\/gkr344","volume":"39","author":"K Nakamura","year":"2011","unstructured":"Nakamura, K. et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 39, e90 (2011).","journal-title":"Nucleic Acids Res."},{"key":"293_CR27","doi-asserted-by":"publisher","first-page":"2912","DOI":"10.1016\/j.celrep.2016.03.015","volume":"14","author":"DV Ward","year":"2016","unstructured":"Ward, D. V. et al. Metagenomic sequencing with strain-level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and mortality in preterm infants. Cell Rep. 14, 2912\u20132924 (2016).","journal-title":"Cell Rep."},{"key":"293_CR28","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"293_CR29","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691\u20133693 (2015).","journal-title":"Bioinformatics"},{"key":"293_CR30","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792\u20131797 (2004).","journal-title":"Nucleic Acids Res."},{"key":"293_CR31","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"293_CR32","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/nmeth.3802","volume":"13","author":"M Scholz","year":"2016","unstructured":"Scholz, M. et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat. Methods 13, 435\u2013438 (2016).","journal-title":"Nat. Methods"},{"key":"293_CR33","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"}],"container-title":["Nature Methods"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s41592-018-0293-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41592-018-0293-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41592-018-0293-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T22:07:44Z","timestamp":1684620464000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41592-018-0293-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,21]]},"references-count":33,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2019,2]]}},"alternative-id":["293"],"URL":"https:\/\/doi.org\/10.1038\/s41592-018-0293-7","relation":{},"ISSN":["1548-7091","1548-7105"],"issn-type":[{"value":"1548-7091","type":"print"},{"value":"1548-7105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,21]]},"assertion":[{"value":"12 November 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 November 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 January 2019","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"}}]}}