{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T07:15:53Z","timestamp":1722842153641},"reference-count":99,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2014,10,9]],"date-time":"2014-10-09T00:00:00Z","timestamp":1412812800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0109840","type":"journal-article","created":{"date-parts":[[2014,10,9]],"date-time":"2014-10-09T18:16:40Z","timestamp":1412878600000},"page":"e109840","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Intragenic Recombination Has a Critical Role on the Evolution of Legionella pneumophila Virulence-Related Effector sidJ"],"prefix":"10.1371","volume":"9","author":[{"given":"Joana","family":"Costa","sequence":"first","affiliation":[]},{"given":"Paulo Gon\u00e7alves","family":"Teixeira","sequence":"additional","affiliation":[]},{"given":"Ana Filipa","family":"d'Av\u00f3","sequence":"additional","affiliation":[]},{"given":"C\u00e9lio Santos","family":"J\u00fanior","sequence":"additional","affiliation":[]},{"given":"Ant\u00f3nio","family":"Ver\u00edssimo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,10,9]]},"reference":[{"key":"ref1","unstructured":"Fields BS (2008) <italic>Legionella<\/italic> in the environment. In: Hoffman P, Friedman H, Bendinelli M, editors. <italic>Legionella pneumophila<\/italic>: pathogenesis and immunity. New York: Springer Science and Business Media. pp 85\u201391."},{"key":"ref2","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1016\/j.micinf.2013.09.007","article-title":"Molecular mimicry and original biochemical strategies for the biogenesis of a <italic>Legionella pneumophila<\/italic> replicative niche in phagocytic cells","volume":"15(14\u201315)","author":"J Allombert","year":"2013","journal-title":"Microbes Infect"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"307","DOI":"10.4161\/viru.24290","article-title":"Cellular microbiology and molecular ecology of Legionella-amoeba interaction","volume":"15(4)","author":"AM Richards","year":"2013","journal-title":"Virulence"},{"key":"ref4","first-page":"19","article-title":"<italic>Legionella<\/italic> secreted effectors and innate immune responses","volume":"14(1)","author":"ZQ Luo","year":"2012","journal-title":"Cell Microbiol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1128\/CMR.00052-09","article-title":"Molecular pathogenesis of infections caused by Legionella pneumophila","volume":"23","author":"HJ Newton","year":"2010","journal-title":"Clin Microbiol Rev"},{"key":"ref6","first-page":"182","article-title":"<italic>Legionella<\/italic>: from protozoa to humans","volume":"12(2)","author":"C Buchrieser","year":"2011","journal-title":"Front Microbiol"},{"key":"ref7","first-page":"1","article-title":"From amoeba to macrophages: exploring the molecular mechanisms of <italic>Legionella pneumophila<\/italic> infection in both hosts","volume":"376","author":"P Escoll","year":"2013","journal-title":"Curr Top Microbiol Immunol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.tim.2012.03.005","article-title":"Exploitation of evolutionarily conserved amoeba and mammalian processes by <italic>Legionella<\/italic>","volume":"20(6)","author":"T Al-Quadan","year":"2012","journal-title":"Trends Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1146\/annurev-cellbio-100109-104034","article-title":"Modulation of host cell function by <italic>Legionella pneumophila<\/italic> type IV effectors","volume":"26","author":"A Hubber","year":"2010","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/j.1574-6976.2009.00209.x","article-title":"Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution","volume":"34","author":"C Moliner","year":"2010","journal-title":"FEMS Microbiol Rev"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1159\/000312910","article-title":"Amoeba\/amoebal symbiont genetic transfers: lessons from giant virus neighbours","volume":"53(5)","author":"V Thomas","year":"2010","journal-title":"Intervirology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1186\/1471-2164-12-536","article-title":"Extensive recombination events and horizontal gene transfer shaped the <italic>Legionella pneumophila<\/italic> genomes","volume":"12","author":"L Gomez-Valero","year":"2011","journal-title":"BMC Genomics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e1002731","DOI":"10.1371\/journal.ppat.1002731","article-title":"Experimental evolution of <italic>Legionella pneumophila<\/italic> in mouse macrophages leads to strains with altered determinants of environmental survival","volume":"8(5)","author":"AW Ensminger","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/j.1469-0691.2006.01558.x","article-title":"Comparison of clinical and environmental isolates of <italic>Legionella pneumophila<\/italic> obtained in the UK over 19 years","volume":"213","author":"TG Harrison","year":"2007","journal-title":"Clin Microbiol Infect"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1007\/s10096-009-0705-9","article-title":"Distribution of <italic>Legionella pneumophila<\/italic> serogroups, monoclonal antibody subgroups and DNA sequence types in recent clinical and environmental isolates from England and Wales (2000\u20132008)","volume":"28","author":"TG Harrison","year":"2009","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/j.meegid.2009.05.013","article-title":"Comparison of clinical and environmental samples of <italic>Legionella pneumophila<\/italic> at the nucleotide sequence level","volume":"9","author":"M Coscoll\u00e1","year":"2009","journal-title":"Infect Genet Evol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1128\/AEM.71.2.663-671.2005","article-title":"Presence and persistence of <italic>Legionella<\/italic> spp. in groundwater","volume":"71","author":"J Costa","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2711","DOI":"10.1111\/j.1462-2920.2010.02240.x","article-title":"Molecular evolution of <italic>Legionella pneumophila dotA<\/italic> gene, the contribution of natural environmental strains","volume":"12","author":"J Costa","year":"2010","journal-title":"Environ Microbiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1111\/j.1462-2920.2011.02646.x","article-title":"A Molecular evolution of key genes for type II secretion in <italic>Legionella pneumophila<\/italic>","volume":"14(8)","author":"J Costa","year":"2012","journal-title":"Environ Microbiol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.mib.2008.12.004","article-title":"<italic>Legionella pneumophila<\/italic> Dot\/Icm translocated substrates: a sum of parts","volume":"12","author":"AW Ensminger","year":"2009","journal-title":"Curr Opin Microbiol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1146\/annurev-cellbio-100109-104034","article-title":"Modulation of host cell function by <italic>Legionella pneumophila<\/italic> type IV effectors","volume":"26","author":"A Hubber","year":"2010","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"E707","DOI":"10.1073\/pnas.1215278110","article-title":"Computational modeling and experimental validation of the <italic>Legionella<\/italic> and <italic>Coxiella<\/italic> virulence-related type-IVB secretion signal","volume":"110(8)","author":"Z Lifshitz","year":"2013","journal-title":"Proc Natl Acad Sci USA 19"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"14733","DOI":"10.1073\/pnas.1111678108","article-title":"Minimization of the <italic>Legionella pneumophila<\/italic> genome reveals chromosomal regions involved in host range expansion","volume":"108","author":"TJ O'Connor","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"691","DOI":"10.2217\/fmb.09.47","article-title":"Molecular mimicry: an important virulence strategy employed by <italic>Legionella pneumophila<\/italic> to subvert host functions","volume":"4(6)","author":"T Nora","year":"2009","journal-title":"Future Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.micinf.2003.11.004","article-title":"Cell biology of the intracellular infection by <italic>Legionella pneumophila<\/italic>","volume":"6(1)","author":"M Molmeret","year":"2004","journal-title":"Microbes Infect"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"18745","DOI":"10.1073\/pnas.0609012103","article-title":"A <italic>Legionella pneumophila<\/italic>-translocated substrate that is required for growth within macrophages and protection from host cell death","volume":"103","author":"RK Laguna","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1128\/IAI.01278-06","article-title":"The <italic>Legionella pneumophila<\/italic> effector SidJ is required for efficient recruitment of endoplasmic reticulum proteins to the bacterial phagosome","volume":"75(2)","author":"Y Liu","year":"2007","journal-title":"Infect Immun"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1111\/j.1365-2958.2008.06453.x","article-title":"A Dot\/Icm translocated ankyrin protein of <italic>Legionella pneumophila<\/italic> is required for intracellular proliferation within human macrophages and protozoa","volume":"70(4)","author":"S Al-Khodor","year":"2008","journal-title":"Mol Microbiol"},{"key":"ref29","first-page":"208","article-title":"Comparative and functional genomics of legionella identified eukaryotic like proteins as key players in host-pathogen interactions. Front Microbiol","volume":"2","author":"L Gomez-Valero","year":"2011","journal-title":"28"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1128\/JB.06626-11","article-title":"Whole-genome sequence of the human pathogen <italic>Legionella pneumophila<\/italic> serogroup 12 strain 570-CO-H","volume":"194(6)","author":"F Amaro","year":"2012","journal-title":"J Bacteriol"},{"key":"ref31","first-page":"e00320","article-title":"Genome sequence of an environmental isolate of the bacterial pathogen <italic>Legionella pneumophila<\/italic>","volume":"1(3)","author":"J Ma","year":"2013","journal-title":"Genome Announc"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e67298","DOI":"10.1371\/journal.pone.0067298","article-title":"Comparative genomics reveal that host-innate immune responses influence the clinical prevalence of <italic>Legionella pneumophila<\/italic> serogroups","volume":"8(6)","author":"MA Khan","year":"2013","journal-title":"PLoS One"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1111\/j.1365-2958.2005.04539.x","article-title":"IcmS-dependent translocation of SdeA into macrophages by the <italic>Legionella pneumophila<\/italic> type IV secretion system","volume":"56","author":"JP Bardill","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1073\/pnas.0304916101","article-title":"Multiple substrates of the <italic>Legionella pneumophila<\/italic> Dot\/Icm system identified by interbacterial protein transfer","volume":"101","author":"ZQ Luo","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1126\/science.1099776","article-title":"The genomic sequence of the accidental pathogen <italic>Legionella pneumophila<\/italic>","volume":"305","author":"M Chien","year":"2004","journal-title":"Science"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1038\/ng1447","article-title":"Evidence in the <italic>Legionella pneumophila<\/italic> genome for exploitation of host cell functions and high genome plasticity","volume":"36","author":"C Cazalet","year":"2004","journal-title":"Nat Genet"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.ijmm.2007.07.012","article-title":"Identification and characterization of a new conjugation\/type IVA secretion system (trb\/tra) of <italic>Legionella pneumophila<\/italic> Corby localized on two mobile genomic islands","volume":"298","author":"G Gl\u00f6ckner","year":"2008","journal-title":"Int J Med Microbiol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/1471-2164-11-181","article-title":"<italic>Legionella pneumophila<\/italic> pangenome reveals strain-specific virulence factors","volume":"17","author":"G D'Auria","year":"2010","journal-title":"BMC Genomics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"6001","DOI":"10.1128\/JB.00778-10","article-title":"<italic>Legionella pneumophila<\/italic> strain 130b possesses a unique combination of type IV secretion systems and novel Dot\/Icm secretion system effector proteins","volume":"192","author":"GN Schroeder","year":"2010","journal-title":"J Bacteriol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.resmic.2009.10.005","article-title":"Colonization of a therapeutic spa with <italic>Legionella<\/italic> spp.: a public health issue","volume":"161","author":"J Costa","year":"2010","journal-title":"Res Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28(10)","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref42","first-page":"307","article-title":"CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol Biol","volume":"25","author":"DG Higgins","year":"1994"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"F Sievers","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"J Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA","volume":"22(2)","author":"M Hasegawa","year":"1985","journal-title":"J Mol Evol"},{"key":"ref47","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"K Tamura","year":"1993","journal-title":"Mol Biol Evol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1093\/bioinformatics\/bth155","article-title":"TOPALi: Software for automatic identification of recombinant sequences within DNA multiple alignments","volume":"20","author":"I Milne","year":"2004","journal-title":"Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: phylogenetic model averaging","volume":"25","author":"D Posada","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Trans Autom Control"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1080\/10635150490522304","article-title":"Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests","volume":"53","author":"D Posada","year":"2004","journal-title":"Syst Biol"},{"key":"ref52","first-page":"275","article-title":"The rapid generation of mutation data matrices from protein sequences","volume":"8","author":"DT Jones","year":"1992","journal-title":"Comp Apps Biosc"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1093\/bioinformatics\/bti263","article-title":"ProtTest: Selection of best-fit models of protein evolution","volume":"21","author":"F Abascal","year":"2005","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: A software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"P Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"ref55","first-page":"255","article-title":"Neighbor-net: an agglomerative method for the construction of phylogenetic networks","volume":"21(2)","author":"D Bryant","year":"2004","journal-title":"Mol Biol Evol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"DH Huson","year":"2006","journal-title":"Mol Bio Evol"},{"key":"ref57","doi-asserted-by":"crossref","unstructured":"Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. pp 21\u2013132.","DOI":"10.1016\/B978-1-4832-3211-9.50009-7"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2462","DOI":"10.1093\/bioinformatics\/btq467","article-title":"RDP3: a flexible and fast computer program for analyzing recombination","volume":"26","author":"DP Martin","year":"2010","journal-title":"Bioinformatics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/bioinformatics\/16.6.562","article-title":"RDP: detection of recombination amongst aligned sequences","volume":"16","author":"DP Martin","year":"2000","journal-title":"Bioinformatics"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/viro.1999.0056","article-title":"Possible emergence of new geminiviruses by frequent recombination","volume":"265","author":"M Padidam","year":"1999","journal-title":"Virology"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1089\/aid.2005.21.98","article-title":"A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints","volume":"21","author":"DP Martin","year":"2005","journal-title":"AIDS Res Hum Retrovir"},{"key":"ref62","first-page":"126","article-title":"Analysing the mosaic structure of genes","volume":"34","author":"J Maynard Smith","year":"1992","journal-title":"J Mol Evol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"13757","DOI":"10.1073\/pnas.241370698","article-title":"Evaluation of methods for detecting recombination from DNA sequences: computer simulations","volume":"98","author":"D Posada","year":"2001","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/bioinformatics\/16.7.573","article-title":"Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences","volume":"16","author":"MJ Gibbs","year":"2000","journal-title":"Bioinformatics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1093\/bioinformatics\/btl474","article-title":"GARD: a genetic algorithm for recombination detection","volume":"22","author":"SL Kosakovsky Pond","year":"2006","journal-title":"Bioinformatics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology","volume":"26","author":"W Delport","year":"2010","journal-title":"Bioinformatics"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism","volume":"123","author":"F Tajima","year":"1989","journal-title":"Genetics"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1093\/genetics\/134.4.1261","article-title":"Maximum likelihood estimation of population parameters","volume":"134","author":"YX Fu","year":"1993","journal-title":"Genetics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/genetics\/147.2.915","article-title":"Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection","volume":"147","author":"YX Fu","year":"1997","journal-title":"Genetics"},{"key":"ref70","doi-asserted-by":"crossref","unstructured":"Kimura M (1983) The neutral theory of molecular evolution. Cambridge: Cambridge University Press. 384 p.","DOI":"10.1017\/CBO9780511623486"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1111\/j.1462-2920.2006.00997.x","article-title":"Genetic variation in environmental samples of <italic>Legionella pneumophila<\/italic> from the Comunidad Valenciana (Spain)","volume":"4","author":"M Coscoll\u00e1","year":"2006","journal-title":"Environ Microbiol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Statis Soc B"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1198\/016214504000001907","article-title":"False discovery rate \u2013 adjusted multiple confidence intervals for selected parameters","volume":"100","author":"Y Benjamini","year":"2005","journal-title":"J Am Stat Assoc"},{"key":"ref74","first-page":"418","article-title":"Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions","volume":"3","author":"M Nei","year":"1986","journal-title":"Mol Biol Evol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1093\/bioinformatics\/bti259","article-title":"Selecton: a server for detecting evolutionary forces at a single amino-acid site","volume":"21","author":"A Doron-Faigenboim","year":"2005","journal-title":"Bioinformatics"},{"key":"ref76","doi-asserted-by":"crossref","unstructured":"Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, <etal>et al<\/etal>. (2007) Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res 35(Web Server issue): W506\u2013W511.","DOI":"10.1093\/nar\/gkm382"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1093\/oxfordjournals.molbev.a004233","article-title":"Pervasive adaptive evolution in mammalian fertilization proteins","volume":"20","author":"WJ Swanson","year":"2003","journal-title":"Mol Biol Evol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution models for heterogeneous selection pressure at amino acid sites","volume":"155","author":"Z Yang","year":"2000","journal-title":"Genetics"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/BF01732948","article-title":"Evolution of the amino acid substitution in the mammalian myoglobin gene","volume":"15","author":"RA Bogardt","year":"1980","journal-title":"J Mol Evol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/28.1.374","article-title":"AAIndex: amino acid index database","volume":"28","author":"S Kawashima","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/BF01732340","article-title":"Two types of amino acid substitutions in protein evolution","volume":"12","author":"T Miyata","year":"1979","journal-title":"J Mol Evol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.plasmid.2003.12.004","article-title":"Comparative sequence analysis of the <italic>icm\/dot<\/italic> genes in <italic>Legionella<\/italic>","volume":"51","author":"I Morozova","year":"2004","journal-title":"Plasmid"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1128\/JB.184.8.2123-2130.2002","article-title":"Population genetic structure of <italic>Legionella pneumophila<\/italic> inferred from RNA polymerase gene (<italic>rpoB<\/italic>) and DotA gene (<italic>dotA<\/italic>) sequences","volume":"184","author":"KS Ko","year":"2002","journal-title":"J Bacteriol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1128\/JCM.26.9.1695-1703.1988","article-title":"<italic>Legionella pneumophila<\/italic> serogroup Lansing 3 isolated from a patient with fatal pneumonia, and descriptions of <italic>L. pneumophila<\/italic> subsp. <italic>pneumophila<\/italic> subsp. <italic>nov<\/italic>., <italic>L. pneumophila<\/italic> subsp. <italic>fraseri<\/italic> subsp. <italic>nov<\/italic>., and <italic>L. pneumophila<\/italic> subsp. <italic>pascullei<\/italic> subsp. <italic>nov<\/italic>","volume":"26","author":"DJ Brenner","year":"1988","journal-title":"J Clin Microbiol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1099\/00207713-46-2-526","article-title":"Phylogeny of <italic>Legionellaceae<\/italic> based on small-subunit ribosomal DNA sequences and proposal of <italic>Legionella lytica<\/italic> comb. nov. for <italic>Legionella<\/italic>-like amoebal pathogens","volume":"46","author":"JV Hookey","year":"1996","journal-title":"Int J Syst Bacteriol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1099\/00207713-46-1-41","article-title":"Characterization of <italic>Legionella<\/italic> species by numerical analysis of whole-cell protein electrophoresis","volume":"46","author":"A Ver\u00edssimo","year":"1996","journal-title":"Int J Syst Bacteriol"},{"key":"ref87","first-page":"81","article-title":"Type II Secretion and <italic>Legionella<\/italic> Virulence","volume":"376","author":"NP Cianciotto","year":"2013"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1111\/j.1462-2920.2006.01184.x","article-title":"Population structure and recombination in environmental isolates of <italic>Legionella pneumophila<\/italic>","volume":"9","author":"M Coscoll\u00e1","year":"2007","journal-title":"Environ Microbiol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1099\/mic.0.2007\/012336-0","article-title":"Clonal population structure of <italic>Legionella pneumophila<\/italic> inferred from allelic profiling","volume":"154","author":"MT Edwards","year":"2008","journal-title":"Microbiol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"2525","DOI":"10.1128\/JCM.02410-08","article-title":"Distribution of lag-1 alleles and sequence-based types among <italic>Legionella pneumophila<\/italic> serogroup 1 clinical and environmental isolates in the United States","volume":"47","author":"NA Kozak","year":"2009","journal-title":"J Clin Microbiol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"3077","DOI":"10.1128\/IAI.00252-13","article-title":"Induction of rapid cell death by an environmental isolate of <italic>Legionella pneumophila<\/italic> in mouse macrophages","volume":"81(9)","author":"L Tao","year":"2013","journal-title":"Infect Immun"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"2011","DOI":"10.1534\/genetics.105.052183","article-title":"Positive selection can create false hotspots of recombination","volume":"172","author":"FA Reed","year":"2006","journal-title":"Genetics"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1128\/AEM.57.10.2921-2927.1991","article-title":"Distribution of <italic>Legionella<\/italic> spp. in hydrothermal areas in continental Portugal and the island of S\u00e3o Miguel, Azores","volume":"57","author":"A Ver\u00edssimo","year":"1991","journal-title":"Appl Environ Microbiol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1111\/j.1574-6941.1993.tb00013.x","article-title":"Biofilms as major sources of <italic>Legionella<\/italic> spp. in hydrothermal areas and their dispersion into stream water","volume":"12","author":"G Marr\u00e3o","year":"1993","journal-title":"FEMS Microbiol Ecol"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/0195-6701(90)90033-K","article-title":"A hot water supply as the source of <italic>Legionella pneumophila<\/italic> in incubators of a neonatology unit","volume":"15","author":"A Ver\u00edssimo","year":"1990","journal-title":"J Hosp Infect"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1128\/JCM.23.6.1146-1147.1986","article-title":"11th serogroup of <italic>Legionella pneumophila<\/italic> isolated from a patient with fatal pneumonia","volume":"23","author":"WL Thacker","year":"1986","journal-title":"J Clin Microbiol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1128\/JCM.12.3.395-401.1980","article-title":"<italic>Legionella pneumophila<\/italic> serogroup six: isolated from cases of Legionellosis, identification by immunofluirescence staining, and immunological response to infection","volume":"12","author":"RM McKinney","year":"1980","journal-title":"J Clin Microbiol"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1128\/JCM.17.5.887-891.1983","article-title":"New serogroup of <italic>Legionella pneumophila<\/italic>, serogroup 8","volume":"17","author":"ML Bissett","year":"1983","journal-title":"J Clin Microbiol"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"621","DOI":"10.7326\/0003-4819-90-4-621","article-title":"Four serogroups of Legionnaires&apos; disease bacteria defined by direct immunofluorescence","volume":"90","author":"RM McKinney","year":"1979","journal-title":"Ann Inter Med"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0109840","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T19:03:48Z","timestamp":1717441428000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0109840"}},"subtitle":[],"editor":[{"given":"Yousef Abu","family":"Kwaik","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,10,9]]},"references-count":99,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2014,10,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0109840","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,9]]}}}