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Volumn 107, Issue 25, 2010, Pages 11453-11458

Phylogenetic incongruence arising from fragmented speciation in enteric bacteria

Author keywords

Incomplete lineage sorting; Population structure; Recombination; Species; Tree of life

Indexed keywords

ARTICLE; BACTERIAL GENE; CHROMOSOME ANALYSIS; DNA POLYMORPHISM; ENTEROBACTERIACEAE; ESCHERICHIA COLI; GENE LOCUS; GENETIC RECOMBINATION; NONHUMAN; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; BACTERIUM; BIOLOGICAL MODEL; CELL LINEAGE; CODON; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; SALMONELLA ENTERICA;

EID: 77954912139     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1001291107     Document Type: Article
Times cited : (55)

References (32)
  • 1
    • 0025788069 scopus 로고
    • Recombination in Escherichia coli and the definition of biological species
    • Dykhuizen DE, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173:7257-7268.
    • (1991) J Bacteriol , vol.173 , pp. 7257-7268
    • Dykhuizen, D.E.1    Green, L.2
  • 3
    • 0242627658 scopus 로고    scopus 로고
    • A molecular phylogeny of enteric bacteria and implications for a bacterial species concept
    • DOI 10.1046/j.1420-9101.2003.00612.x
    • Wertz JE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16:1236-1248. (Pubitemid 37379291)
    • (2003) Journal of Evolutionary Biology , vol.16 , Issue.6 , pp. 1236-1248
    • Wertz, J.E.1    Goldstone, C.2    Gordon, D.M.3    Riley, M.A.4
  • 5
    • 57749178593 scopus 로고    scopus 로고
    • Reproductive isolation in Saccharomyces
    • Greig D (2009) Reproductive isolation in Saccharomyces. Heredity 102:39-44.
    • (2009) Heredity , vol.102 , pp. 39-44
    • Greig, D.1
  • 6
    • 0022689021 scopus 로고
    • Homologous recombination in Escherichia coli: Dependence on substrate length and homology
    • Shen P, Huang HV (1986) Homologous recombination in Escherichia coli: Dependence on substrate length and homology. Genetics 112:441-457.
    • (1986) Genetics , vol.112 , pp. 441-457
    • Shen, P.1    Huang, H.V.2
  • 7
    • 70350150370 scopus 로고    scopus 로고
    • Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome
    • Ray JL, et al. (2009) Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics 182:1165-1181.
    • (2009) Genetics , vol.182 , pp. 1165-1181
    • Ray, J.L.1
  • 8
    • 0036598066 scopus 로고    scopus 로고
    • Gene transfer in bacteria: Speciation without species?
    • Lawrence JG (2002) Gene transfer in bacteria: Speciation without species? Theor Popul Biol 61:449-460.
    • (2002) Theor Popul Biol , vol.61 , pp. 449-460
    • Lawrence, J.G.1
  • 9
    • 0026776971 scopus 로고
    • Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species
    • Spratt BG, Bowler LD, Zhang QY, Zhou J, Smith JM (1992) Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species. J Mol Evol 34:115-125.
    • (1992) J Mol Evol , vol.34 , pp. 115-125
    • Spratt, B.G.1    Bowler, L.D.2    Zhang, Q.Y.3    Zhou, J.4    Smith, J.M.5
  • 10
    • 22144486947 scopus 로고    scopus 로고
    • Fuzzy species among recombinogenic bacteria
    • Hanage WP, Fraser C, Spratt BG (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3:6.
    • (2005) BMC Biol , vol.3 , pp. 6
    • Hanage, W.P.1    Fraser, C.2    Spratt, B.G.3
  • 11
    • 34548246020 scopus 로고    scopus 로고
    • Temporal fragmentation of speciation in bacteria
    • Retchless AC, Lawrence JG (2007) Temporal fragmentation of speciation in bacteria. Science 317:1093-1096.
    • (2007) Science , vol.317 , pp. 1093-1096
    • Retchless, A.C.1    Lawrence, J.G.2
  • 12
    • 33846625056 scopus 로고    scopus 로고
    • Recombination and the nature of bacterial speciation
    • Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315:476-480.
    • (2007) Science , vol.315 , pp. 476-480
    • Fraser, C.1    Hanage, W.P.2    Spratt, B.G.3
  • 13
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • Touchon M, et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344.
    • (2009) PLoS Genet , vol.5
    • Touchon, M.1
  • 15
    • 0034235228 scopus 로고    scopus 로고
    • Yersinia pestis: An instant species?
    • Dykhuizen DE (2000) Yersinia pestis: An instant species? Trends Microbiol 8:296-298.
    • (2000) Trends Microbiol , vol.8 , pp. 296-298
    • Dykhuizen, D.E.1
  • 16
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
    • DOI 10.1093/molbev/msh018
    • Bryant D, Moulton V (2004) Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255-265. (Pubitemid 38314614)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.2 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 17
    • 77955410887 scopus 로고    scopus 로고
    • The myth of bacterial species and speciation
    • press
    • Lawrence JG, Retchless AC (2010) The myth of bacterial species and speciation. Biol Philos, in press.
    • (2010) Biol Philos
    • Lawrence, J.G.1    Retchless, A.C.2
  • 18
    • 70349944351 scopus 로고    scopus 로고
    • Cryptic lineages of the genus Escherichia
    • Walk ST, et al. (2009) Cryptic lineages of the genus Escherichia. Appl Environ Microbiol 75:6534-6544.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 6534-6544
    • Walk, S.T.1
  • 19
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5:568-583.
    • (1988) Mol Biol Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 20
    • 3242795999 scopus 로고    scopus 로고
    • An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data
    • Taylor DJ, Piel WH (2004) An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol Biol Evol 21:1534-1537.
    • (2004) Mol Biol Evol , vol.21 , pp. 1534-1537
    • Taylor, D.J.1    Piel, W.H.2
  • 21
    • 12044253190 scopus 로고
    • An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
    • Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42:182-192.
    • (1993) Syst Biol , vol.42 , pp. 182-192
    • Hillis, D.M.1    Bull, J.J.2
  • 22
    • 22844438847 scopus 로고    scopus 로고
    • Hidden likelihood support in genomic data: Can forty-five wrongs make a right?
    • Gatesy J, Baker RH (2005) Hidden likelihood support in genomic data: Can forty-five wrongs make a right? Syst Biol 54:483-492.
    • (2005) Syst Biol , vol.54 , pp. 483-492
    • Gatesy, J.1    Baker, R.H.2
  • 23
    • 0031981808 scopus 로고    scopus 로고
    • Santa Rosalia revisited: Why are there so many species of bacteria?
    • Dykhuizen DE (1998) Santa Rosalia revisited: Why are there so many species of bacteria? Antonie Van Leeuwenhoek 73:25-33.
    • (1998) Antonie Van Leeuwenhoek , vol.73 , pp. 25-33
    • Dykhuizen, D.E.1
  • 24
    • 33847790997 scopus 로고    scopus 로고
    • Pattern pluralism and the Tree of Life hypothesis
    • Doolittle WF, Bapteste E (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104:2043-2049.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 2043-2049
    • Doolittle, W.F.1    Bapteste, E.2
  • 25
    • 42049090179 scopus 로고    scopus 로고
    • Convergence of Campylobacter species: Implications for bacterial evolution
    • DOI 10.1126/science.1155532
    • Sheppard SK, McCarthy ND, Falush D, Maiden MC (2008) Convergence of Campylobacter species: Implications for bacterial evolution. Science 320:237-239. (Pubitemid 351521420)
    • (2008) Science , vol.320 , Issue.5873 , pp. 237-239
    • Sheppard, S.K.1    McCarthy, N.D.2    Falush, D.3    Maiden, M.C.J.4
  • 26
    • 66049089612 scopus 로고    scopus 로고
    • On the origin of prokaryotic species
    • Doolittle WF, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19:744-756.
    • (2009) Genome Res , vol.19 , pp. 744-756
    • Doolittle, W.F.1    Zhaxybayeva, O.2
  • 27
    • 65549140696 scopus 로고    scopus 로고
    • Epistemological impacts of horizontal gene transfer on classification in microbiology
    • Bapteste E, Boucher Y (2009) Epistemological impacts of horizontal gene transfer on classification in microbiology. Methods Mol Biol 532:55-72.
    • (2009) Methods Mol Biol , vol.532 , pp. 55-72
    • Bapteste, E.1    Boucher, Y.2
  • 28
    • 0036719291 scopus 로고    scopus 로고
    • Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches
    • Lawrence JG, Hatfull GF, Hendrix RW (2002) Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches. J Bacteriol 184:4891-4905.
    • (2002) J Bacteriol , vol.184 , pp. 4891-4905
    • Lawrence, J.G.1    Hatfull, G.F.2    Hendrix, R.W.3
  • 29
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • DOI 10.1093/bioinformatics/btg180
    • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 30
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 31
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116. (Pubitemid 29368141)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.8 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 32
    • 31344433677 scopus 로고    scopus 로고
    • An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
    • DOI 10.1080/10635150500354688
    • Ren F, Tanaka H, Yang Z (2005) An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol 54:808-818. (Pubitemid 43142296)
    • (2005) Systematic Biology , vol.54 , Issue.5 , pp. 808-818
    • Ren, F.1    Tanaka, H.2    Yang, Z.3


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