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Volumn 11, Issue 1, 2011, Pages

Obscured phylogeny and possible recombinational dormancy in Escherichia coli

Author keywords

Definition of Species; Phylogeny; Recombination

Indexed keywords

CHROMOSOME; COALESCENCE; COLIFORM BACTERIUM; DORMANCY; EVOLUTIONARY BIOLOGY; NEW SPECIES; PHYLOGENETICS; PHYLOGENY; POLYMORPHISM; TOPOLOGY;

EID: 79959573534     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-183     Document Type: Article
Times cited : (24)

References (46)
  • 1
    • 0015917096 scopus 로고
    • Electrophoretic variation in Escherichia coli from natural sources
    • 10.1126/science.182.4116.1024 4584002
    • Electrophoretic variation in Escherichia coli from natural sources. R Milkman, Science 1973 182 116 1024 1026 10.1126/science.182.4116.1024 4584002
    • (1973) Science , vol.182 , Issue.116 , pp. 1024-1026
    • Milkman, R.1
  • 2
    • 0021367325 scopus 로고
    • Standard reference strains of Escherichia coli from natural populations
    • Standard reference strains of Escherichia coli from natural populations. H Ochman, RK Selander, J Bacteriol 1984 157 2 690 693 6363394 (Pubitemid 14190968)
    • (1984) Journal of Bacteriology , vol.157 , Issue.2 , pp. 690-693
    • Ochman, H.1    Selander, R.K.2
  • 4
    • 0020960815 scopus 로고
    • Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella
    • Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. H Ochman, TS Whittam, DA Caugant, RK Selander, J Gen Microbiol 1983 129 9 2715 2726 6355392 (Pubitemid 13024810)
    • (1983) Journal of General Microbiology , vol.129 , Issue.9 , pp. 2715-2726
    • Ochman, H.1    Whittam, T.S.2    Caugant, D.A.3    Selander, R.K.4
  • 5
    • 0025096192 scopus 로고
    • Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli
    • Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. PJ Herzer, S Inouye, M Inouye, TS Whittam, J Bacteriol 1990 172 11 6175 6181 1699928 (Pubitemid 20372753)
    • (1990) Journal of Bacteriology , vol.172 , Issue.11 , pp. 6175-6181
    • Herzer, P.J.1    Inouye, S.2    Inouye, M.3    Whittam, T.S.4
  • 6
    • 0025788069 scopus 로고
    • Recombination in Escherichia coli and the definition of biological species
    • 1938920
    • Recombination in Escherichia coli and the definition of biological species. DE Dykhuizen, L Green, J Bacteriol 1991 173 22 7257 7268 1938920
    • (1991) J Bacteriol , vol.173 , Issue.22 , pp. 7257-7268
    • Dykhuizen, D.E.1    Green, L.2
  • 7
    • 0347093471 scopus 로고    scopus 로고
    • Decreasing the effects of horizontal gene transfer on bacterial phylogeny: The Escherichia coli case study
    • DOI 10.1016/S1055-7903(03)00181-7
    • Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study. P Escobar-Paramo, A Sabbagh, P Darlu, O Pradillon, C Vaury, E Denamur, G Lecointre, Mol Phylogenet Evol 2004 30 1 243 250 10.1016/S1055-7903(03)00181-7 15022774 (Pubitemid 38092532)
    • (2004) Molecular Phylogenetics and Evolution , vol.30 , Issue.1 , pp. 243-250
    • Escobar-Paramo, P.1    Sabbagh, A.2    Darlu, P.3    Pradillon, O.4    Vaury, C.5    Denamur, E.6    Lecointre, G.7
  • 9
    • 0030722947 scopus 로고    scopus 로고
    • Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica
    • Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. FS Wang, TS Whittam, RK Selander, J Bacteriol 1997 179 21 6551 6559 9352899 (Pubitemid 27465284)
    • (1997) Journal of Bacteriology , vol.179 , Issue.21 , pp. 6551-6559
    • Wang, F.-S.1    Whittam, T.S.2    Selander, R.K.3
  • 10
    • 0026728291 scopus 로고
    • Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli
    • 1400239
    • Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. K Nelson, RK Selander, J Bacteriol 1992 174 21 6886 6895 1400239
    • (1992) J Bacteriol , vol.174 , Issue.21 , pp. 6886-6895
    • Nelson, K.1    Selander, R.K.2
  • 11
    • 0025992890 scopus 로고
    • Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli
    • Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. K Nelson, TS Whittam, RK Selander, Proc Natl Acad Sci USA 1991 88 15 6667 6671 10.1073/pnas.88.15.6667 1862091 (Pubitemid 21915010)
    • (1991) Proceedings of the National Academy of Sciences of the United States of America , vol.88 , Issue.15 , pp. 6667-6671
    • Nelson, K.1    Whittam, T.S.2    Selander, R.K.3
  • 12
    • 0030834799 scopus 로고    scopus 로고
    • Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli
    • Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli. K Nelson, FS Wang, EF Boyd, RK Selander, Genetics 1997 147 4 1509 1520 9409817 (Pubitemid 27525449)
    • (1997) Genetics , vol.147 , Issue.4 , pp. 1509-1520
    • Nelson, K.1    Wang, F.-S.2    Boyd, E.F.3    Seiander, R.K.4
  • 14
    • 34547702305 scopus 로고    scopus 로고
    • Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches
    • DOI 10.1111/j.1462-2920.2007.01341.x
    • Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. ST Walk, EW Alm, LM Calhoun, JM Mladonicky, TS Whittam, Environ Microbiol 2007 9 9 2274 2288 10.1111/j.1462-2920.2007.01341.x 17686024 (Pubitemid 47222119)
    • (2007) Environmental Microbiology , vol.9 , Issue.9 , pp. 2274-2288
    • Walk, S.T.1    Alm, E.W.2    Calhoun, L.M.3    Mladonicky, J.M.4    Whittam, T.S.5
  • 16
    • 33746438839 scopus 로고    scopus 로고
    • Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis
    • DOI 10.1016/j.micinf.2006.02.007, PII S1286457906001134
    • Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis. JR Johnson, KL Owens, CR Clabots, SJ Weissman, SB Cannon, Microbes Infect 2006 8 7 1702 1713 10.1016/j.micinf.2006.02.007 16820314 (Pubitemid 44128872)
    • (2006) Microbes and Infection , vol.8 , Issue.7 , pp. 1702-1713
    • Johnson, J.R.1    Owens, K.L.2    Clabots, C.R.3    Weissman, S.J.4    Cannon, S.B.5
  • 17
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • 10.1371/journal.pgen.1000344 19165319
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. M Touchon, C Hoede, O Tenaillon, V Barbe, S Baeriswyl, P Bidet, E Bingen, S Bonacorsi, C Bouchier, O Bouvet, et al. PLoS Genet 2009 5 1 1000344 10.1371/journal.pgen.1000344 19165319
    • (2009) PLoS Genet , vol.5 , Issue.1 , pp. 51000344
    • Touchon, M.1    Hoede, C.2    Tenaillon, O.3    Barbe, V.4    Baeriswyl, S.5    Bidet, P.6    Bingen, E.7    Bonacorsi, S.8    Bouchier, C.9    Bouvet, O.10
  • 18
    • 51649120558 scopus 로고    scopus 로고
    • Assigning Escherichia coli strains to phylogenetic groups: Multi-locus sequence typing versus the PCR triplex method
    • 10.1111/j.1462-2920.2008.01669.x 18518895
    • Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. DM Gordon, O Clermont, H Tolley, E Denamur, Environ Microbiol 2008 10 10 2484 2496 10.1111/j.1462-2920.2008. 01669.x 18518895
    • (2008) Environ Microbiol , vol.10 , Issue.10 , pp. 2484-2496
    • Gordon, D.M.1    Clermont, O.2    Tolley, H.3    Denamur, E.4
  • 21
    • 0033758756 scopus 로고    scopus 로고
    • Pathogenicity islands and the evolution of microbes
    • 10.1146/annurev.micro.54.1.641 11018140
    • Pathogenicity islands and the evolution of microbes. J Hacker, JB Kaper, Annu Rev Microbiol 2000 54 641 679 10.1146/annurev.micro.54.1.641 11018140
    • (2000) Annu Rev Microbiol , vol.54 , pp. 641-679
    • Hacker, J.1    Kaper, J.B.2
  • 22
    • 0031741481 scopus 로고    scopus 로고
    • Escherichia coli molecular phylogeny using the incongruence length difference test
    • Escherichia coli molecular phylogeny using the incongruence length difference test. G Lecointre, L Rachdi, P Darlu, E Denamur, Mol Biol Evol 1998 15 12 1685 1695 9866203 (Pubitemid 28550992)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.12 , pp. 1685-1695
    • LeCointre, G.1    Rachdi, L.2    Darlu, P.3    Denamur, E.4
  • 23
    • 35848958139 scopus 로고    scopus 로고
    • Extraintestinal virulence is a coincidental by-product of commensalism in b2 phylogenetic group Escherichia coli strains
    • DOI 10.1093/molbev/msm172
    • Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. T Le Gall, O Clermont, S Gouriou, B Picard, X Nassif, E Denamur, O Tenaillon, Mol Biol Evol 2007 24 11 2373 2384 10.1093/molbev/msm172 17709333 (Pubitemid 350060443)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.11 , pp. 2373-2384
    • Le Gall, T.1    Clermont, O.2    Gouriou, S.3    Picard, B.4    Nassif, X.5    Denamur, E.6    Tenaillon, O.7
  • 24
    • 2442667673 scopus 로고    scopus 로고
    • A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli
    • DOI 10.1093/molbev/msh118
    • A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. P Escobar-Paramo, O Clermont, AB Blanc-Potard, H Bui, C Le Bouguenec, E Denamur, Mol Biol Evol 2004 21 6 1085 1094 10.1093/molbev/msh118 15014151 (Pubitemid 38658217)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.6 , pp. 1085-1094
    • Escobar-Paramo, P.1    Clermont, O.2    Blanc-Potard, A.-B.3    Bui, H.4    Le Bouguenec, C.5    Denamur, E.6
  • 26
    • 0003651227 scopus 로고    scopus 로고
    • Distributed by the author, Department of Mathematics, Washington University in St. Louis http://www.math.wustl.edu/∼sawyer
    • GENECONV: A computer package for the statistical detection of gene conversion. SA Sawyer, Distributed by the author, Department of Mathematics, Washington University in St. Louis 1999 http://www.math.wustl.edu/∼sawyer
    • (1999) GENECONV: A Computer Package for the Statistical Detection of Gene Conversion
    • Sawyer, S.A.1
  • 27
    • 33745112085 scopus 로고    scopus 로고
    • Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli
    • DOI 10.1186/gb-2006-7-5-r44
    • Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. B Mau, JD Glasner, AE Darling, NT Perna, Genome Biol 2006 7 5 44 10.1186/gb-2006-7-5-r44 16737554 (Pubitemid 43885060)
    • (2006) Genome Biology , vol.7 , Issue.5
    • Mau, B.1    Glasner, J.D.2    Darling, A.E.3    Perna, N.T.4
  • 29
    • 34548246020 scopus 로고    scopus 로고
    • Temporal fragmentation of speciation in bacteria
    • DOI 10.1126/science.1144876
    • Temporal fragmentation of speciation in bacteria. AC Retchless, JG Lawrence, Science 2007 317 5841 1093 1096 10.1126/science.1144876 17717188 (Pubitemid 47330195)
    • (2007) Science , vol.317 , Issue.5841 , pp. 1093-1096
    • Retchless, A.C.1    Lawrence, J.G.2
  • 31
    • 67149119196 scopus 로고    scopus 로고
    • Hyper-recombination, diversity, and antibiotic resistance in pneumococcus
    • 10.1126/science.1171908 19520963
    • Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. WP Hanage, C Fraser, J Tang, TR Connor, J Corander, Science 2009 324 5933 1454 1457 10.1126/science.1171908 19520963
    • (2009) Science , vol.324 , Issue.5933 , pp. 1454-1457
    • Hanage, W.P.1    Fraser, C.2    Tang, J.3    Connor, T.R.4    Corander, J.5
  • 34
    • 0036407157 scopus 로고    scopus 로고
    • What are bacterial species?
    • DOI 10.1146/annurev.micro.56.012302.160634
    • What are bacterial species? FM Cohan, Annu Rev Microbiol 2002 56 457 487 10.1146/annurev.micro.56.012302.160634 12142474 (Pubitemid 35217463)
    • (2002) Annual Review of Microbiology , vol.56 , pp. 457-487
    • Cohan, F.M.1
  • 36
    • 77954912139 scopus 로고    scopus 로고
    • Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
    • 10.1073/pnas.1001291107 20534528
    • Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. AC Retchless, JG Lawrence, Proc Natl Acad Sci USA 2010 107 25 11453 11458 10.1073/pnas.1001291107 20534528
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.25 , pp. 11453-11458
    • Retchless, A.C.1    Lawrence, J.G.2
  • 38
    • 0028605344 scopus 로고
    • Clonal divergence in Escherichia coli as a result of recombination, not mutation
    • 10.1126/science.7973728 7973728
    • Clonal divergence in Escherichia coli as a result of recombination, not mutation. DS Guttman, DE Dykhuizen, Science 1994 266 5189 1380 1383 10.1126/science.7973728 7973728
    • (1994) Science , vol.266 , Issue.5189 , pp. 1380-1383
    • Guttman, D.S.1    Dykhuizen, D.E.2
  • 39
    • 66649094404 scopus 로고    scopus 로고
    • A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis
    • 19439656
    • A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis. SR Leopold, V Magrini, NJ Holt, N Shaikh, ER Mardis, J Cagno, Y Ogura, A Iguchi, T Hayashi, A Mellmann, et al. Proc Natl Acad Sci USA 2009 106 21 8713 8718 19439656
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.21 , pp. 8713-8718
    • Leopold, S.R.1    Magrini, V.2    Holt, N.J.3    Shaikh, N.4    Mardis, E.R.5    Cagno, J.6    Ogura, Y.7    Iguchi, A.8    Hayashi, T.9    Mellmann, A.10
  • 40
    • 33645827531 scopus 로고    scopus 로고
    • Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach
    • 10.1073/pnas.0600938103 16585510
    • Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. SL Chen, CS Hung, J Xu, CS Reigstad, V Magrini, A Sabo, D Blasiar, T Bieri, RR Meyer, P Ozersky, et al. Proc Natl Acad Sci USA 2006 103 15 5977 5982 10.1073/pnas.0600938103 16585510
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.15 , pp. 5977-5982
    • Chen, S.L.1    Hung, C.S.2    Xu, J.3    Reigstad, C.S.4    Magrini, V.5    Sabo, A.6    Blasiar, D.7    Bieri, T.8    Meyer, R.R.9    Ozersky, P.10
  • 41
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • DOI 10.1093/nar/25.17.3389
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul, TL Madden, AA Schaffer, J Zhang, Z Zhang, W Miller, DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 42
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson, DG Higgins, TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 43
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • DOI 10.1093/molbev/msm092
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura, J Dudley, M Nei, S Kumar, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 44
    • 74549125386 scopus 로고    scopus 로고
    • SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
    • SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. M Gouy, S Guindon, O Gascuel, Mol Biol Evol 27 2 221 224
    • Mol Biol Evol , vol.27 , Issue.2 , pp. 221-224
    • Gouy, M.1    Guindon, S.2    Gascuel, O.3
  • 45
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • DOI 10.1093/molbev/msj030
    • Application of phylogenetic networks in evolutionary studies. DH Huson, D Bryant, Mol Biol Evol 2006 23 2 254 267 16221896 (Pubitemid 43100040)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2


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