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Volumn 29, Issue 12, 2012, Pages 3669-3683

Ecological adaptation in bacteria: Speciation driven by codon selection

Author keywords

codon selection; codon usage bias; recombination interference; speciation

Indexed keywords

ADAPTIVE CODON ENRICHMENT METRIC; ANIMAL EXPERIMENT; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATE; BIOMETRY; CODON; CODON USAGE; CONFERENCE PAPER; CONTROLLED STUDY; ENTEROBACTERIACEAE; EVOLUTIONARY ADAPTATION; GENE LOCUS; GENE MUTATION; GENETIC VARIABILITY; HABITAT; HOUSEKEEPING GENE; HUMAN; NATURAL SELECTION; NONHUMAN; OPERON; PHYLOGENY; STRAIN DIFFERENCE;

EID: 84869026028     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss171     Document Type: Conference Paper
Times cited : (17)

References (54)
  • 1
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 2
    • 0036407157 scopus 로고    scopus 로고
    • What are bacterial species?
    • Cohan FM. 2002. What are bacterial species? Annu Rev Microbiol. 56: 457-487.
    • (2002) Annu Rev Microbiol. , vol.56 , pp. 457-487
    • Cohan, F.M.1
  • 3
    • 33846668510 scopus 로고    scopus 로고
    • Operon prediction using both genome-specific and general genomic information
    • Dam P, Olman V, Harris K, Su Z, Xu Y. 2007. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res. 35:288-298.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 288-298
    • Dam, P.1    Olman, V.2    Harris, K.3    Su, Z.4    Xu, Y.5
  • 4
    • 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
  • 5
    • 0032733829 scopus 로고    scopus 로고
    • The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis
    • Feil EJ, Maiden MC, Achtman M, Spratt BG. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol Biol Evol. 16:1496-1502.
    • (1999) Mol Biol Evol. , vol.16 , pp. 1496-1502
    • Feil, E.J.1    Maiden, M.C.2    Achtman, M.3    Spratt, B.G.4
  • 6
    • 0034128665 scopus 로고    scopus 로고
    • Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data
    • Feil EJ, Smith JM, Enright MC, Spratt BG. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:1439-1450.
    • (2000) Genetics , vol.154 , pp. 1439-1450
    • Feil, E.J.1    Smith, J.M.2    Enright, M.C.3    Spratt, B.G.4
  • 7
    • 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
  • 9
    • 0036264202 scopus 로고    scopus 로고
    • The genetic structure of Escherichia coli populations in primary and secondary habitats
    • Gordon DM, Bauer S, Johnson JR. 2002. The genetic structure of Escherichia coli populations in primary and secondary habitats. Microbiology 148:1513-1522.
    • (2002) Microbiology , vol.148 , pp. 1513-1522
    • Gordon, D.M.1    Bauer, S.2    Johnson, J.R.3
  • 10
    • 0346882653 scopus 로고    scopus 로고
    • The distribution and genetic structure of Escherichia coli in Australian vertebrates: Host and geographic effects
    • Gordon DM, Cowling A. 2003. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology 149:3575-3586.
    • (2003) Microbiology , vol.149 , pp. 3575-3586
    • Gordon, D.M.1    Cowling, A.2
  • 11
    • 70449713952 scopus 로고    scopus 로고
    • The NIH Human Microbiome Project
    • Group NHW, Peterson J, Garges S, et al. (40 co-authors). 2009. The NIH Human Microbiome Project. Genome Res. 19:2317-2323.
    • (2009) Genome Res. , vol.19 , pp. 2317-2323
    • Group, N.H.W.1    Peterson, J.2    Garges, S.3
  • 12
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
    • (2003) Syst Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 13
    • 0034980876 scopus 로고    scopus 로고
    • Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes
    • Hacker J, Carniel E. 2001. Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2:376-381.
    • (2001) EMBO Rep. , vol.2 , pp. 376-381
    • Hacker, J.1    Carniel, E.2
  • 15
    • 33947231236 scopus 로고    scopus 로고
    • Mutational bias suggests that replication termination occurs near the dif site, not at ter sites
    • Hendrickson H, Lawrence JG. 2007. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol Microbiol. 64:42-56.
    • (2007) Mol Microbiol. , vol.64 , pp. 42-56
    • Hendrickson, H.1    Lawrence, J.G.2
  • 16
    • 0019474499 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrance of the respective codons in its protein genes
    • Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrance of the respective codons in its protein genes. J Mol Biol. 146:1-21.
    • (1981) J Mol Biol. , vol.146 , pp. 1-21
    • Ikemura, T.1
  • 17
    • 0033816775 scopus 로고    scopus 로고
    • Predicted highly expressed genes of diverse prokaryotic genomes
    • Karlin S, Mrazek J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol. 182:5238-5250.
    • (2000) J Bacteriol. , vol.182 , pp. 5238-5250
    • Karlin, S.1    Mrazek, J.2
  • 18
    • 78651076675 scopus 로고    scopus 로고
    • Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes
    • Kono N, Arakawa K, Tomita M. 2011. Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics 12:19.
    • (2011) BMC Genomics , vol.12 , pp. 19
    • Kono, N.1    Arakawa, K.2    Tomita, M.3
  • 19
    • 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
  • 20
    • 0030809629 scopus 로고    scopus 로고
    • Selfish operons and speciation by gene transfer
    • Lawrence JG. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol. 5:355-359.
    • (1997) Trends Microbiol. , vol.5 , pp. 355-359
    • Lawrence, J.G.1
  • 21
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 44:383-397.
    • (1997) J Mol Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 22
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • Lawrence JG, Ochman H. 1998. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A. 95:9413-9417.
    • (1998) Proc Natl Acad Sci U S A. , vol.95 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 23
    • 65549114090 scopus 로고    scopus 로고
    • The interplay of homologous recombination and horizontal gene transfer in bacterial speciation
    • Lawrence JG, Retchless AC. 2009. The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol. 532:29-53.
    • (2009) Methods Mol Biol. , vol.532 , pp. 29-53
    • Lawrence, J.G.1    Retchless, A.C.2
  • 24
    • 77955410887 scopus 로고    scopus 로고
    • The myth of bacterial species and speciation
    • Lawrence JG, Retchless AC. 2010. The myth of bacterial species and speciation. Biol Phil. 25:569-588.
    • (2010) Biol Phil. , vol.25 , pp. 569-588
    • Lawrence, J.G.1    Retchless, A.C.2
  • 25
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li WH,Wu CI, Luo CC. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 2:150-174.
    • (1985) Mol Biol Evol. , vol.2 , pp. 150-174
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 26
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry JR. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 13:660-665.
    • (1996) Mol Biol Evol. , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 27
    • 79955559191 scopus 로고    scopus 로고
    • Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
    • Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. 2011. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A. 108:7200-7205.
    • (2011) Proc Natl Acad Sci U S A. , vol.108 , pp. 7200-7205
    • Luo, C.1    Walk, S.T.2    Gordon, D.M.3    Feldgarden, M.4    Tiedje, J.M.5    Konstantinidis, K.T.6
  • 28
    • 0034539018 scopus 로고    scopus 로고
    • Population structure and evolutionary dynamics of pathogenic bacteria
    • Maynard Smith J, Feil EJ, Smith NH. 2000. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22: 1115-1122.
    • (2000) BioEssays , vol.22 , pp. 1115-1122
    • Maynard Smith, J.1    Feil, E.J.2    Smith, N.H.3
  • 32
    • 0035312272 scopus 로고    scopus 로고
    • Highly expressed and alien genes of the Synechocystis genome
    • Mrazek J, Bhaya D, Grossman AR, Karlin S. 2001. Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29: 1590-1601.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1590-1601
    • Mrazek, J.1    Bhaya, D.2    Grossman, A.R.3    Karlin, S.4
  • 33
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 34
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H, Lawrence JG, Groisman E. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.3
  • 35
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: The causes and consequences of codon bias
    • Plotkin JB, Kudla G. 2010. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 12:32-42.
    • (2010) Nat Rev Genet. , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 36
    • 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
  • 37
    • 77954912139 scopus 로고    scopus 로고
    • Phylogenetic incongruence arising from fragmented speciation in enteric bacteria
    • Retchless AC, Lawrence JG. 2010. Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. Proc Natl Acad Sci U S A. 107:11453-11458.
    • (2010) Proc Natl Acad Sci U S A. , vol.107 , pp. 11453-11458
    • Retchless, A.C.1    Lawrence, J.G.2
  • 38
    • 79960573669 scopus 로고    scopus 로고
    • Quantification of codon selection for comparative bacterial genomics
    • Retchless AC, Lawrence JG. 2011. Quantification of codon selection for comparative bacterial genomics. BMC Genomics 12:374.
    • (2011) BMC Genomics , vol.12 , pp. 374
    • Retchless, A.C.1    Lawrence, J.G.2
  • 39
    • 3142679507 scopus 로고    scopus 로고
    • The replication-related organization of bacterial genomes
    • Rocha EP. 2004. The replication-related organization of bacterial genomes. Microbiology 150:1609-1627.
    • (2004) Microbiology , vol.150 , pp. 1609-1627
    • Rocha, E.P.1
  • 40
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
    • (1987) Mol Biol Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 41
    • 25444453726 scopus 로고    scopus 로고
    • Salmonella flagellin, a microbial target of the innate and adaptive immune system
    • Salazar-Gonzalez RM, McSorley SJ. 2005. Salmonella flagellin, a microbial target of the innate and adaptive immune system. Immunol Lett. 101:117-122.
    • (2005) Immunol Lett. , vol.101 , pp. 117-122
    • Salazar-Gonzalez, R.M.1    McSorley, S.J.2
  • 43
    • 0023762645 scopus 로고
    • Codon usage patterns in Escherichia coli, Bacillus subtilus, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens; A review of the considerable within-species diversity
    • Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilus, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16:8207-8211.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 8207-8211
    • Sharp, P.M.1    Cowe, E.2    Higgins, D.G.3    Shields, D.C.4    Wolfe, K.H.5    Wright, F.6
  • 44
    • 0023274170 scopus 로고
    • The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias
    • Sharp PM, Li W-H. 1987a. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol. 4:222-230.
    • (1987) Mol Biol Evol. , vol.4 , pp. 222-230
    • Sharp, P.M.1    Li, W.-H.2
  • 45
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li W-H. 1987b. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.-H.2
  • 46
    • 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.
    • (1999) Mol Biol Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 47
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki Y, Gojobori T. 1999. A method for detecting positive selection at single amino acid sites. Mol Biol Evol. 16:1315-1328.
    • (1999) Mol Biol Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 48
    • 0000314099 scopus 로고
    • Ecological species, multispecies, oaks
    • Van Valen L. 1976. Ecological species, multispecies, oaks. Taxon 25: 223-239.
    • (1976) Taxon , vol.25 , pp. 223-239
    • Van Valen, L.1
  • 49
    • 0030924545 scopus 로고    scopus 로고
    • Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in Enterobacteria
    • Vulic M, Dionisio F, Taddei F, Radman M. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in Enterobacteria. Proc Natl Acad Sci U S A. 94:9763-9767.
    • (1997) Proc Natl Acad Sci U S A. , vol.94 , pp. 9763-9767
    • Vulic, M.1    Dionisio, F.2    Taddei, F.3    Radman, M.4
  • 50
    • 0033594973 scopus 로고    scopus 로고
    • Mutation, recombination, and incipient speciation of bacteria in the laboratory
    • Vulic M, Lenski RE, Radman M. 1999. Mutation, recombination, and incipient speciation of bacteria in the laboratory. Proc Natl Acad Sci U S A. 96:7348-7351.
    • (1999) Proc Natl Acad Sci U S A. , vol.96 , pp. 7348-7351
    • Vulic, M.1    Lenski, R.E.2    Radman, M.3
  • 52
    • 3242695831 scopus 로고    scopus 로고
    • Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella
    • Wildschutte H, Wolfe DM, Tamewitz A, Lawrence JG. 2004. Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella. Proc Natl Acad Sci U S A. 101: 10644-10649.
    • (2004) Proc Natl Acad Sci U S A. , vol.101 , pp. 10644-10649
    • Wildschutte, H.1    Wolfe, D.M.2    Tamewitz, A.3    Lawrence, J.G.4
  • 53
    • 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
  • 54
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.Mol Biol Evol. 17:32-43.
    • (2000) Mol Biol Evol. , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2


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