{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T22:36:00Z","timestamp":1793658960322,"version":"4.5.1"},"reference-count":90,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2016,10,31]],"date-time":"2016-10-31T00:00:00Z","timestamp":1477872000000},"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 Genet"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1038\/ng.3704","type":"journal-article","created":{"date-parts":[[2016,10,31]],"date-time":"2016-10-31T19:27:30Z","timestamp":1477942050000},"page":"1535-1543","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":420,"title":["Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages"],"prefix":"10.1038","volume":"48","author":[{"given":"David","family":"Stucki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Brites","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le\u00efla","family":"Jeljeli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mireia","family":"Coscolla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrej","family":"Trauner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas","family":"Fenner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liliana","family":"Rutaihwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Borrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Midori","family":"Kato-Maeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Ballif","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Egger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rita","family":"Macedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helmi","family":"Mardassi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milagros","family":"Moreno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Griselda Tudo","family":"Vilanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet","family":"Fyfe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Globan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jackson","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frances","family":"Jamieson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8565-203X","authenticated-orcid":false,"given":"Jennifer L","family":"Guthrie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adwoa","family":"Asante-Poku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorothy","family":"Yeboah-Manu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eddie","family":"Wampande","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willy","family":"Ssengooba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moses","family":"Joloba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W Henry","family":"Boom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Indira","family":"Basu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Bower","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarida","family":"Saraiva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sidra E G","family":"Vasconcellos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Suffys","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Koch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2753-1800","authenticated-orcid":false,"given":"Robert","family":"Wilkinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Gail-Bekker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bijaya","family":"Malla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serej D","family":"Ley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8326-4834","authenticated-orcid":false,"given":"Hans-Peter","family":"Beck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bouke C","family":"de Jong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kadri","family":"Toit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Sanchez-Padilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryline","family":"Bonnet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Gil-Brusola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Frank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronique N","family":"Penlap Beng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen","family":"Eisenach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4084-9442","authenticated-orcid":false,"given":"Issam","family":"Alani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Perpetual Wangui","family":"Ndung'u","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunturu","family":"Revathi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Gehre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suriya","family":"Akter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francine","family":"Ntoumi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynsey","family":"Stewart-Isherwood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nyanda E","family":"Ntinginya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Rachow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hoelscher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela Maria","family":"Cirillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Girts","family":"Skenders","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Hoffner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daiva","family":"Bakonyte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petras","family":"Stakenas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland","family":"Diel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeriu","family":"Crudu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Moldovan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sahal","family":"Al-Hajoj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larissa","family":"Otero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Barletta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E Jane","family":"Carter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lameck","family":"Diero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Supply","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5504-9408","authenticated-orcid":false,"given":"I\u00f1aki","family":"Comas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Niemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastien","family":"Gagneux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,10,31]]},"reference":[{"key":"BFng3704_CR1","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1146\/annurev.es.19.110188.001231","volume":"19","author":"DJ Futuyma","year":"1988","unstructured":"Futuyma, D.J. & Moreno, G. The evolution of ecological specialization. Annu. Rev. Ecol. Syst. 19, 207\u2013233 (1988).","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"BFng3704_CR2","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/ng1202-569","volume":"32","author":"ME Woolhouse","year":"2002","unstructured":"Woolhouse, M.E., Webster, J.P., Domingo, E., Charlesworth, B. & Levin, B.R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569\u2013577 (2002).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR3","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1126\/science.1059026","volume":"292","author":"ME Woolhouse","year":"2001","unstructured":"Woolhouse, M.E., Taylor, L.H. & Haydon, D.T. Population biology of multihost pathogens. Science 292, 1109\u20131112 (2001).","journal-title":"Science"},{"key":"BFng3704_CR4","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.tim.2011.11.006","volume":"20","author":"MW Kirzinger","year":"2012","unstructured":"Kirzinger, M.W. & Stavrinides, J. Host specificity determinants as a genetic continuum. Trends Microbiol. 20, 88\u201393 (2012).","journal-title":"Trends Microbiol."},{"key":"BFng3704_CR5","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.cmi.2015.10.010","volume":"22","author":"M Vouga","year":"2016","unstructured":"Vouga, M. & Greub, G. Emerging bacterial pathogens: the past and beyond. Clin. Microbiol. Infect. 22, 12\u201321 (2016).","journal-title":"Clin. Microbiol. Infect."},{"key":"BFng3704_CR6","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1111\/imr.12264","volume":"264","author":"D Brites","year":"2015","unstructured":"Brites, D. & Gagneux, S. Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunol. Rev. 264, 6\u201324 (2015).","journal-title":"Immunol. Rev."},{"key":"BFng3704_CR7","first-page":"1456","volume":"13","author":"S Borrell","year":"2009","unstructured":"Borrell, S. & Gagneux, S. Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis. 13, 1456\u20131466 (2009).","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"BFng3704_CR8","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/ng.3195","volume":"47","author":"M Merker","year":"2015","unstructured":"Merker, M. et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat. Genet. 47, 242\u2013249 (2015).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR9","doi-asserted-by":"publisher","first-page":"8136","DOI":"10.1073\/pnas.1424063112","volume":"112","author":"T Luo","year":"2015","unstructured":"Luo, T. et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc. Natl. Acad. Sci. USA 112, 8136\u20138141 (2015).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3704_CR10","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1086\/592575","volume":"47","author":"D Cowley","year":"2008","unstructured":"Cowley, D. et al. Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa. Clin. Infect. Dis. 47, 1252\u20131259 (2008).","journal-title":"Clin. Infect. Dis."},{"key":"BFng3704_CR11","doi-asserted-by":"publisher","first-page":"e744","DOI":"10.1371\/journal.pntd.0000744","volume":"4","author":"BC de Jong","year":"2010","unstructured":"de Jong, B.C., Antonio, M. & Gagneux, S. Mycobacterium africanum\u2014review of an important cause of human tuberculosis in West Africa. PLoS Negl. Trop. Dis. 4, e744 (2010).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"BFng3704_CR12","doi-asserted-by":"publisher","first-page":"460","DOI":"10.3201\/eid1903.120256","volume":"19","author":"R Firdessa","year":"2013","unstructured":"Firdessa, R. et al. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg. Infect. Dis. 19, 460\u2013463 (2013).","journal-title":"Emerg. Infect. Dis."},{"key":"BFng3704_CR13","doi-asserted-by":"publisher","first-page":"850","DOI":"10.1098\/rstb.2011.0316","volume":"367","author":"S Gagneux","year":"2012","unstructured":"Gagneux, S. Host\u2013pathogen coevolution in human tuberculosis. Phil. Trans. R. Soc. Lond. B 367, 850\u2013859 (2012).","journal-title":"Phil. Trans. R. Soc. Lond. B"},{"key":"BFng3704_CR14","doi-asserted-by":"publisher","first-page":"e1003318","DOI":"10.1371\/journal.pgen.1003318","volume":"9","author":"L Fenner","year":"2013","unstructured":"Fenner, L. et al. HIV infection disrupts the sympatric host\u2013pathogen relationship in human tuberculosis. PLoS Genet. 9, e1003318 (2013).","journal-title":"PLoS Genet."},{"key":"BFng3704_CR15","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1073\/pnas.0511240103","volume":"103","author":"S Gagneux","year":"2006","unstructured":"Gagneux, S. et al. Variable host\u2013pathogen compatibility in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103, 2869\u20132873 (2006).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3704_CR16","doi-asserted-by":"publisher","first-page":"1568","DOI":"10.3201\/eid1009.040046","volume":"10","author":"L Baker","year":"2004","unstructured":"Baker, L., Brown, T., Maiden, M.C. & Drobniewski, F. Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg. Infect. Dis. 10, 1568\u20131577 (2004).","journal-title":"Emerg. Infect. Dis."},{"key":"BFng3704_CR17","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1128\/JCM.02142-08","volume":"47","author":"MB Reed","year":"2009","unstructured":"Reed, M.B. et al. Major Mycobacterium tuberculosis lineages associate with patient country of origin. J. Clin. Microbiol. 47, 1119\u20131128 (2009).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR18","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1016\/j.meegid.2012.02.004","volume":"12","author":"C Demay","year":"2012","unstructured":"Demay, C. et al. SITVITWEB\u2014a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect. Genet. Evol. 12, 755\u2013766 (2012).","journal-title":"Infect. Genet. Evol."},{"key":"BFng3704_CR19","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/j.smim.2014.09.012","volume":"26","author":"M Coscolla","year":"2014","unstructured":"Coscolla, M. & Gagneux, S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin. Immunol. 26, 431\u2013444 (2014).","journal-title":"Semin. Immunol."},{"key":"BFng3704_CR20","doi-asserted-by":"publisher","first-page":"e43","DOI":"10.1016\/j.ddmec.2010.09.004","volume":"7","author":"M Coscolla","year":"2010","unstructured":"Coscolla, M. & Gagneux, S. Does M. tuberculosis genomic diversity explain disease diversity? Drug Discov. Today Dis. Mech. 7, e43\u2013e59 (2010).","journal-title":"Drug Discov. Today Dis. Mech."},{"key":"BFng3704_CR21","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1038\/ng.2744","volume":"45","author":"I Comas","year":"2013","unstructured":"Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 45, 1176\u20131182 (2013).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR22","doi-asserted-by":"publisher","first-page":"969","DOI":"10.3201\/eid1906.121012","volume":"19","author":"M Coscolla","year":"2013","unstructured":"Coscolla, M. et al. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg. Infect. Dis. 19, 969\u2013976 (2013).","journal-title":"Emerg. Infect. Dis."},{"key":"BFng3704_CR23","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1016\/j.meegid.2010.07.006","volume":"10","author":"E Abadia","year":"2010","unstructured":"Abadia, E. et al. Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method. Infect. Genet. Evol. 10, 1066\u20131074 (2010).","journal-title":"Infect. Genet. Evol."},{"key":"BFng3704_CR24","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1128\/JB.188.2.759-772.2006","volume":"188","author":"I Filliol","year":"2006","unstructured":"Filliol, I. et al. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J. Bacteriol. 188, 759\u2013772 (2006).","journal-title":"J. Bacteriol."},{"key":"BFng3704_CR25","doi-asserted-by":"publisher","first-page":"9869","DOI":"10.1073\/pnas.94.18.9869","volume":"94","author":"S Sreevatsan","year":"1997","unstructured":"Sreevatsan, S. et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94, 9869\u20139874 (1997).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3704_CR26","doi-asserted-by":"publisher","first-page":"e39855","DOI":"10.1371\/journal.pone.0039855","volume":"7","author":"S Homolka","year":"2012","unstructured":"Homolka, S. et al. High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms. PLoS One 7, e39855 (2012).","journal-title":"PLoS One"},{"key":"BFng3704_CR27","doi-asserted-by":"publisher","first-page":"4812","DOI":"10.1038\/ncomms5812","volume":"5","author":"F Coll","year":"2014","unstructured":"Coll, F. et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat. Commun. 5, 4812 (2014).","journal-title":"Nat. Commun."},{"key":"BFng3704_CR28","doi-asserted-by":"publisher","first-page":"4865","DOI":"10.1073\/pnas.0305634101","volume":"101","author":"AG Tsolaki","year":"2004","unstructured":"Tsolaki, A.G. et al. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc. Natl. Acad. Sci. USA 101, 4865\u20134870 (2004).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3704_CR29","doi-asserted-by":"publisher","first-page":"e7815","DOI":"10.1371\/journal.pone.0007815","volume":"4","author":"I Comas","year":"2009","unstructured":"Comas, I., Homolka, S., Niemann, S. & Gagneux, S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One 4, e7815 (2009).","journal-title":"PLoS One"},{"key":"BFng3704_CR30","doi-asserted-by":"publisher","first-page":"e21906","DOI":"10.1371\/journal.pone.0021906","volume":"6","author":"D Yeboah-Manu","year":"2011","unstructured":"Yeboah-Manu, D. et al. Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana. PLoS One 6, e21906 (2011).","journal-title":"PLoS One"},{"key":"BFng3704_CR31","doi-asserted-by":"publisher","first-page":"e52297","DOI":"10.1371\/journal.pone.0052297","volume":"7","author":"B Malla","year":"2012","unstructured":"Malla, B. et al. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal. PLoS One 7, e52297 (2012).","journal-title":"PLoS One"},{"key":"BFng3704_CR32","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1128\/JCM.05392-11","volume":"50","author":"L Fenner","year":"2012","unstructured":"Fenner, L. et al. Mycobacterium tuberculosis transmission in a country with low tuberculosis incidence: role of immigration and HIV infection. J. Clin. Microbiol. 50, 388\u2013395 (2012).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR33","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.5588\/ijtld.11.0779","volume":"16","author":"M Ballif","year":"2012","unstructured":"Ballif, M. et al. Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea. Int. J. Tuberc. Lung Dis. 16, 1100\u20131107 (2012).","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"BFng3704_CR34","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1186\/1471-2334-13-484","volume":"13","author":"EM Wampande","year":"2013","unstructured":"Wampande, E.M. et al. Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease. BMC Infect. Dis. 13, 484 (2013).","journal-title":"BMC Infect. Dis."},{"key":"BFng3704_CR35","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1186\/s12866-014-0307-2","volume":"14","author":"SD Ley","year":"2014","unstructured":"Ley, S.D. et al. Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea. BMC Microbiol. 14, 307 (2014).","journal-title":"BMC Microbiol."},{"key":"BFng3704_CR36","doi-asserted-by":"publisher","first-page":"e41253","DOI":"10.1371\/journal.pone.0041253","volume":"7","author":"D Stucki","year":"2012","unstructured":"Stucki, D. et al. Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One 7, e41253 (2012).","journal-title":"PLoS One"},{"key":"BFng3704_CR37","doi-asserted-by":"publisher","first-page":"3292","DOI":"10.1128\/JCM.00744-11","volume":"49","author":"C Bouakaze","year":"2011","unstructured":"Bouakaze, C. et al. Matrix-assisted laser desorption ionization\u2013time of flight mass spectrometry\u2013based single nucleotide polymorphism genotyping assay using iPLEX gold technology for identification of Mycobacterium tuberculosis complex species and lineages. J. Clin. Microbiol. 49, 3292\u20133299 (2011).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR38","unstructured":"World Health Organization. Global Tuberculosis Control\u2014Surveillance, Planning, Financing (WHO, 2015)."},{"key":"BFng3704_CR39","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1111\/j.1574-695X.2009.00600.x","volume":"58","author":"M M\u00f6ller","year":"2010","unstructured":"M\u00f6ller, M., de Wit, E. & Hoal, E.G. Past, present and future directions in human genetic susceptibility to tuberculosis. FEMS Immunol. Med. Microbiol. 58, 3\u201326 (2010).","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"BFng3704_CR40","doi-asserted-by":"publisher","first-page":"e1000034","DOI":"10.1371\/journal.ppat.1000034","volume":"4","author":"M Caws","year":"2008","unstructured":"Caws, M. et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog. 4, e1000034 (2008).","journal-title":"PLoS Pathog."},{"key":"BFng3704_CR41","doi-asserted-by":"publisher","first-page":"e3370","DOI":"10.1371\/journal.pntd.0003370","volume":"9","author":"A Asante-Poku","year":"2015","unstructured":"Asante-Poku, A. et al. Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS Negl. Trop. Dis. 9, e3370 (2015).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"BFng3704_CR42","doi-asserted-by":"publisher","first-page":"3812","DOI":"10.1093\/nar\/gkg509","volume":"31","author":"PC Ng","year":"2003","unstructured":"Ng, P.C. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812\u20133814 (2003).","journal-title":"Nucleic Acids Res."},{"key":"BFng3704_CR43","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1146\/annurev.es.24.110193.001245","volume":"24","author":"NC Ellstrand","year":"1993","unstructured":"Ellstrand, N.C. & Elam, D.R. Population genetic consequences of small population size: implications for plant conservation. Annu. Rev. Ecol. Syst. 24, 217\u2013242 (1993).","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"BFng3704_CR44","doi-asserted-by":"publisher","first-page":"3277","DOI":"10.1128\/JCM.01122-13","volume":"51","author":"F Lanzas","year":"2013","unstructured":"Lanzas, F., Karakousis, P.C., Sacchettini, J.C. & Ioerger, T.R. Multidrug-resistant tuberculosis in Panama is driven by clonal expansion of a multidrug-resistant Mycobacterium tuberculosis strain related to the KZN extensively drug-resistant M. tuberculosis strain from South Africa. J. Clin. Microbiol. 51, 3277\u20133285 (2013).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR45","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/1471-2334-13-110","volume":"13","author":"JM Bryant","year":"2013","unstructured":"Bryant, J.M. et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect. Dis. 13, 110 (2013).","journal-title":"BMC Infect. Dis."},{"key":"BFng3704_CR46","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/S2213-2600(13)70231-5","volume":"1","author":"JM Bryant","year":"2013","unstructured":"Bryant, J.M. et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir. Med. 1, 786\u2013792 (2013).","journal-title":"Lancet Respir. Med."},{"key":"BFng3704_CR47","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1056\/NEJMoa1003176","volume":"364","author":"JL Gardy","year":"2011","unstructured":"Gardy, J.L. et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 364, 730\u2013739 (2011).","journal-title":"N. Engl. J. Med."},{"key":"BFng3704_CR48","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1038\/ng.2878","volume":"46","author":"N Casali","year":"2014","unstructured":"Casali, N. et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat. Genet. 46, 279\u2013286 (2014).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR49","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","volume":"13","author":"TM Walker","year":"2013","unstructured":"Walker, T.M. et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect. Dis. 13, 137\u2013146 (2013).","journal-title":"Lancet Infect. Dis."},{"key":"BFng3704_CR50","doi-asserted-by":"publisher","first-page":"e1001387","DOI":"10.1371\/journal.pmed.1001387","volume":"10","author":"A Roetzer","year":"2013","unstructured":"Roetzer, A. et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med. 10, e1001387 (2013).","journal-title":"PLoS Med."},{"key":"BFng3704_CR51","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/ng.2747","volume":"45","author":"MR Farhat","year":"2013","unstructured":"Farhat, M.R. et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet. 45, 1183\u20131189 (2013).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR52","doi-asserted-by":"publisher","first-page":"e83012","DOI":"10.1371\/journal.pone.0083012","volume":"8","author":"TG Clark","year":"2013","unstructured":"Clark, T.G. et al. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 8, e83012 (2013).","journal-title":"PLoS One"},{"key":"BFng3704_CR53","doi-asserted-by":"publisher","first-page":"3795","DOI":"10.1128\/JCM.01726-14","volume":"52","author":"FB Jamieson","year":"2014","unstructured":"Jamieson, F.B. et al. Whole-genome sequencing of the Mycobacterium tuberculosis Manila sublineage results in less clustering and better resolution than mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping. J. Clin. Microbiol. 52, 3795\u20133798 (2014).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR54","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1093\/infdis\/jit439","volume":"209","author":"L P\u00e9rez-Lago","year":"2014","unstructured":"P\u00e9rez-Lago, L. et al. Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J. Infect. Dis. 209, 98\u2013108 (2014).","journal-title":"J. Infect. Dis."},{"key":"BFng3704_CR55","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1093\/infdis\/jiu574","volume":"211","author":"JA Guerra-Assun\u00e7\u00e3o","year":"2015","unstructured":"Guerra-Assun\u00e7\u00e3o, J.A. et al. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J. Infect. Dis. 211, 1154\u20131163 (2015).","journal-title":"J. Infect. Dis."},{"key":"BFng3704_CR56","doi-asserted-by":"publisher","first-page":"e05166","DOI":"10.7554\/eLife.05166","volume":"4","author":"JA Guerra-Assun\u00e7\u00e3o","year":"2015","unstructured":"Guerra-Assun\u00e7\u00e3o, J.A. et al. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 4, e05166 (2015).","journal-title":"eLife"},{"key":"BFng3704_CR57","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/ng.590","volume":"42","author":"I Comas","year":"2010","unstructured":"Comas, I. et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat. Genet. 42, 498\u2013503 (2010).","journal-title":"Nat. Genet."},{"key":"BFng3704_CR58","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.chom.2015.10.008","volume":"18","author":"M Coscolla","year":"2015","unstructured":"Coscolla, M. et al. M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens. Cell Host Microbe 18, 538\u2013548 (2015).","journal-title":"Cell Host Microbe"},{"key":"BFng3704_CR59","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nrmicro2145","volume":"7","author":"KW Deitsch","year":"2009","unstructured":"Deitsch, K.W., Lukehart, S.A. & Stringer, J.R. Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens. Nat. Rev. Microbiol. 7, 493\u2013503 (2009).","journal-title":"Nat. Rev. Microbiol."},{"key":"BFng3704_CR60","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.tube.2007.11.002","volume":"88","author":"JD Ernst","year":"2008","unstructured":"Ernst, J.D. et al. Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database. Tuberculosis (Edinb.) 88, 366\u2013370 (2008).","journal-title":"Tuberculosis (Edinb.)"},{"key":"BFng3704_CR61","doi-asserted-by":"publisher","first-page":"e1003543","DOI":"10.1371\/journal.ppat.1003543","volume":"9","author":"CS Pepperell","year":"2013","unstructured":"Pepperell, C.S. et al. The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog. 9, e1003543 (2013).","journal-title":"PLoS Pathog."},{"key":"BFng3704_CR62","doi-asserted-by":"publisher","first-page":"e1002946","DOI":"10.1371\/journal.ppat.1002946","volume":"8","author":"YJ Zhang","year":"2012","unstructured":"Zhang, Y.J. et al. Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog. 8, e1002946 (2012).","journal-title":"PLoS Pathog."},{"key":"BFng3704_CR63","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1111\/sji.12249","volume":"81","author":"M Esparza","year":"2015","unstructured":"Esparza, M. et al. PstS-1, the 38-kDa Mycobacterium tuberculosis glycoprotein, is an adhesin, which binds the macrophage mannose receptor and promotes phagocytosis. Scand. J. Immunol. 81, 46\u201355 (2015).","journal-title":"Scand. J. Immunol."},{"key":"BFng3704_CR64","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.tube.2013.03.003","volume":"93","author":"A Bekmurzayeva","year":"2013","unstructured":"Bekmurzayeva, A., Sypabekova, M. & Kanayeva, D. Tuberculosis diagnosis using immunodominant, secreted antigens of Mycobacterium tuberculosis. Tuberculosis (Edinb.) 93, 381\u2013388 (2013).","journal-title":"Tuberculosis (Edinb.)"},{"key":"BFng3704_CR65","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1128\/IAI.59.1.372-382.1991","volume":"59","author":"S Nagai","year":"1991","unstructured":"Nagai, S., Wiker, H.G., Harboe, M. & Kinomoto, M. Isolation and partial characterization of major protein antigens in the culture fluid of Mycobacterium tuberculosis. Infect. Immun. 59, 372\u2013382 (1991).","journal-title":"Infect. Immun."},{"key":"BFng3704_CR66","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1111\/j.1574-6968.2001.tb10826.x","volume":"203","author":"MD Ju\u00e1rez","year":"2001","unstructured":"Ju\u00e1rez, M.D., Torres, A. & Espitia, C. Characterization of the Mycobacterium tuberculosis region containing the mpt83 and mpt70 genes. FEMS Microbiol. Lett. 203, 95\u2013102 (2001).","journal-title":"FEMS Microbiol. Lett."},{"key":"BFng3704_CR67","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1128\/CVI.00271-15","volume":"22","author":"M Coppola","year":"2015","unstructured":"Coppola, M. et al. Synthetic long peptide derived from Mycobacterium tuberculosis latency antigen Rv1733c protects against tuberculosis. Clin. Vaccine Immunol. 22, 1060\u20131069 (2015).","journal-title":"Clin. Vaccine Immunol."},{"key":"BFng3704_CR68","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1016\/j.tube.2015.08.002","volume":"95","author":"LS Araujo","year":"2015","unstructured":"Araujo, L.S. et al. Profile of interferon-\u03b3 response to latency-associated and novel in vivo expressed antigens in a cohort of subjects recently exposed to Mycobacterium tuberculosis. Tuberculosis (Edinb.) 95, 751\u2013757 (2015).","journal-title":"Tuberculosis (Edinb.)"},{"key":"BFng3704_CR69","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.ympev.2015.03.008","volume":"87","author":"Y Yu","year":"2015","unstructured":"Yu, Y., Harris, A.J., Blair, C. & He, X. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Mol. Phylogenet. Evol. 87, 46\u201349 (2015).","journal-title":"Mol. Phylogenet. Evol."},{"key":"BFng3704_CR70","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/1471-2180-6-23","volume":"6","author":"K Brudey","year":"2006","unstructured":"Brudey, K. et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6, 23 (2006).","journal-title":"BMC Microbiol."},{"key":"BFng3704_CR71","doi-asserted-by":"publisher","first-page":"3260","DOI":"10.1016\/j.cub.2015.10.061","volume":"25","author":"I Comas","year":"2015","unstructured":"Comas, I. et al. Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in sub-Saharan Africa. Curr. Biol. 25, 3260\u20133266 (2015).","journal-title":"Curr. Biol."},{"key":"BFng3704_CR72","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/nature13591","volume":"514","author":"KI Bos","year":"2014","unstructured":"Bos, K.I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494\u2013497 (2014).","journal-title":"Nature"},{"key":"BFng3704_CR73","doi-asserted-by":"publisher","first-page":"6717","DOI":"10.1038\/ncomms7717","volume":"6","author":"GL Kay","year":"2015","unstructured":"Kay, G.L. et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat. Commun. 6, 6717 (2015).","journal-title":"Nat. Commun."},{"key":"BFng3704_CR74","doi-asserted-by":"publisher","first-page":"3891","DOI":"10.1128\/JCM.01394-07","volume":"45","author":"LC Lazzarini","year":"2007","unstructured":"Lazzarini, L.C. et al. Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J. Clin. Microbiol. 45, 3891\u20133902 (2007).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3704_CR75","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1186\/1471-2164-15-991","volume":"15","author":"J Perdig\u00e3o","year":"2014","unstructured":"Perdig\u00e3o, J. et al. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics 15, 991 (2014).","journal-title":"BMC Genomics"},{"key":"BFng3704_CR76","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.ympev.2016.03.020","volume":"99","author":"I Mokrousov","year":"2016","unstructured":"Mokrousov, I. et al. Latin-American\u2013Mediterranean lineage of Mycobacterium tuberculosis: human traces across pathogen's phylogeography. Mol. Phylogenet. Evol. 99, 133\u2013143 (2016).","journal-title":"Mol. Phylogenet. Evol."},{"key":"BFng3704_CR77","unstructured":"Baily, S.L. & Miguez, E.J. Mass Migration to Modern Latin America. (Scholarly Resources,1993)."},{"key":"BFng3704_CR78","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1016\/S0025-7125(16)30188-2","volume":"77","author":"JH Bates","year":"1993","unstructured":"Bates, J.H. & Stead, W.W. The history of tuberculosis as a global epidemic. Med. Clin. North Am. 77, 1205\u20131217 (1993).","journal-title":"Med. Clin. North Am."},{"key":"BFng3704_CR79","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/S1473-3099(07)70108-1","volume":"7","author":"S Gagneux","year":"2007","unstructured":"Gagneux, S. & Small, P.M. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect. Dis. 7, 328\u2013337 (2007).","journal-title":"Lancet Infect. Dis."},{"key":"BFng3704_CR80","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1186\/1471-2164-15-881","volume":"15","author":"A Steiner","year":"2014","unstructured":"Steiner, A., Stucki, D., Coscolla, M., Borrell, S. & Gagneux, S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics 15, 881 (2014).","journal-title":"BMC Genomics"},{"key":"BFng3704_CR81","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"BFng3704_CR82","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).","journal-title":"Nucleic Acids Res."},{"key":"BFng3704_CR83","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731\u20132739 (2011).","journal-title":"Mol. Biol. Evol."},{"key":"BFng3704_CR84","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","volume":"20","author":"E Paradis","year":"2004","unstructured":"Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289\u2013290 (2004).","journal-title":"Bioinformatics"},{"key":"BFng3704_CR85","first-page":"47","volume":"1","author":"L Excoffier","year":"2007","unstructured":"Excoffier, L., Laval, G. & Schneider, S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47\u201350 (2007).","journal-title":"Evol. Bioinform. Online"},{"key":"BFng3704_CR86","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","volume":"25","author":"AM Waterhouse","year":"2009","unstructured":"Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. & Barton, G.J. Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189\u20131191 (2009).","journal-title":"Bioinformatics"},{"key":"BFng3704_CR87","unstructured":"Hartl, D. & Clarck, A.G. Principles of Population Genetics (Sinauer, 2007)."},{"key":"BFng3704_CR88","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.tube.2010.09.008","volume":"91","author":"JM Lew","year":"2011","unstructured":"Lew, J.M., Kapopoulou, A., Jones, L.M. & Cole, S.T. TubercuList\u201410 years after. Tuberculosis (Edinb.) 91, 1\u20137 (2011).","journal-title":"Tuberculosis (Edinb.)"},{"key":"BFng3704_CR89","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","volume":"19","author":"F Ronquist","year":"2003","unstructured":"Ronquist, F. & Huelsenbeck, J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572\u20131574 (2003).","journal-title":"Bioinformatics"},{"key":"BFng3704_CR90","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/ng.3704.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ng.3704","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ng.3704.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T21:18:48Z","timestamp":1684444728000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ng.3704"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10,31]]},"references-count":90,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["BFng3704"],"URL":"https:\/\/doi.org\/10.1038\/ng.3704","relation":{},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10,31]]},"assertion":[{"value":"3 August 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 October 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}