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Volumn 186, Issue 19, 2004, Pages 6575-6585

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS; BACTERIAL GENOME; CLOSTRIDIUM; COMPARATIVE STUDY; CONTROLLED STUDY; EVOLUTION; GENE IDENTIFICATION; GENE TRANSFER; GENETIC ANALYSIS; GRAM NEGATIVE BACTERIUM; MOLECULAR CLOCK; NONHUMAN; ORTHOLOGY; PHYLOGENY; PRIORITY JOURNAL;

EID: 4544298806     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.19.6575-6585.2004     Document Type: Article
Times cited : (87)

References (57)
  • 2
    • 0031736121 scopus 로고    scopus 로고
    • Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
    • Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:442-444.
    • (1998) Trends Genet. , vol.14 , pp. 442-444
    • Aravind, L.1    Tatusov, R.L.2    Wolf, Y.I.3    Walker, D.R.4    Koonin, E.V.5
  • 3
    • 0036137155 scopus 로고    scopus 로고
    • Eubacterial phylogeny based on translational apparatus proteins
    • Brochier, C., E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5.
    • (2002) Trends Genet. , vol.18 , pp. 1-5
    • Brochier, C.1    Bapteste, E.2    Moreira, D.3    Philippe, H.4
  • 4
    • 0034565944 scopus 로고    scopus 로고
    • The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
    • Brochier, C., H. Philippe, and D. Moreira. 2000. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:529-533.
    • (2000) Trends Genet. , vol.16 , pp. 529-533
    • Brochier, C.1    Philippe, H.2    Moreira, D.3
  • 5
    • 0037373563 scopus 로고    scopus 로고
    • The modern molecular clock
    • Bromham, L., and D. Penny. 2003. The modern molecular clock. Nat. Rev. Genet. 4:216-224.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 216-224
    • Bromham, L.1    Penny, D.2
  • 6
    • 0037306453 scopus 로고    scopus 로고
    • Ancient horizontal gene transfer
    • Brown, J. R. 2003. Ancient horizontal gene transfer. Nat. Rev. Genet. 4:121-132.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 121-132
    • Brown, J.R.1
  • 7
    • 0036210883 scopus 로고    scopus 로고
    • Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
    • Clarke, G. D., R. G. Beiko, M. A. Ragan, and R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:2072-2080.
    • (2002) J. Bacteriol. , vol.184 , pp. 2072-2080
    • Clarke, G.D.1    Beiko, R.G.2    Ragan, M.A.3    Charlebois, R.L.4
  • 8
    • 0034100202 scopus 로고    scopus 로고
    • Understanding the overdispersed molecular clock
    • Cutler, D. J. 2000. Understanding the overdispersed molecular clock. Genetics 154:1403-1417.
    • (2000) Genetics , vol.154 , pp. 1403-1417
    • Cutler, D.J.1
  • 9
    • 0042027842 scopus 로고    scopus 로고
    • Phylogenetics and the cohesion of bacterial genomes
    • Daubin, V., N. A. Moran, and H. Ochntan. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832.
    • (2003) Science , vol.301 , pp. 829-832
    • Daubin, V.1    Moran, N.A.2    Ochntan, H.3
  • 10
    • 0031769997 scopus 로고    scopus 로고
    • Evolutionary anomalies among the aminoacyl-tRNA synthetases
    • Doolittle, R. F., and J. Handy. 1998. Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr. Opin. Genet. Dev. 8:630-636.
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 630-636
    • Doolittle, R.F.1    Handy, J.2
  • 12
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 13
    • 0035546129 scopus 로고    scopus 로고
    • The neutral theory in the genomic era
    • Fay, J. C., and C. I. Wu. 2001. The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11:642-646.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 642-646
    • Fay, J.C.1    Wu, C.I.2
  • 15
    • 0029901637 scopus 로고    scopus 로고
    • Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
    • Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:418-427.
    • (1996) Methods Enzymol. , vol.266 , pp. 418-427
    • Felsenstein, J.1
  • 16
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-106.
    • (1970) Syst. Zool. , vol.19 , pp. 99-106
    • Fitch, W.M.1
  • 17
    • 0036139471 scopus 로고    scopus 로고
    • Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation
    • Gamieldien, J., A. Ptitsyn, and W. Hide. 2002. Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation. Trends Genet. 18:5-8.
    • (2002) Trends Genet. , vol.18 , pp. 5-8
    • Gamieldien, J.1    Ptitsyn, A.2    Hide, W.3
  • 19
    • 0021715830 scopus 로고
    • The molecular clock may be an episodic clock
    • Gillespie, J. H. 1984. The molecular clock may be an episodic clock. Proc. Natl. Acad. Sci. USA 81:8009-8013.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 8009-8013
    • Gillespie, J.H.1
  • 21
    • 0033858110 scopus 로고    scopus 로고
    • From complete genomes to measures of substitution rate variability within and between proteins
    • Grishin, N. V., Y. I. Wolf, and E. V. Koonin. 2000. From complete genomes to measures of substitution rate variability within and between proteins. Genome Res. 10:991-1000.
    • (2000) Genome Res. , vol.10 , pp. 991-1000
    • Grishin, N.V.1    Wolf, Y.I.2    Koonin, E.V.3
  • 22
    • 0033859839 scopus 로고    scopus 로고
    • Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
    • Hansmann, S., and W. Martin. 2000. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50:1655-1663.
    • (2000) Int. J. Syst. Evol. Microbiol. , vol.50 , pp. 1655-1663
    • Hansmann, S.1    Martin, W.2
  • 23
    • 0028304908 scopus 로고
    • On global sequence alignment
    • Huang, X. 1994. On global sequence alignment. Comput. Appl. Biosci. 10:227-235.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 227-235
    • Huang, X.1
  • 24
    • 2942576138 scopus 로고    scopus 로고
    • Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
    • Iyer, L. M., E. V. Koonin, and L. Aravind. 2004. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335:73-88.
    • (2004) Gene , vol.335 , pp. 73-88
    • Iyer, L.M.1    Koonin, E.V.2    Aravind, L.3
  • 25
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes: The complexity hypothesis
    • Jain, R., M. C. Rivera, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801-3806.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 27
    • 0242606207 scopus 로고    scopus 로고
    • Horizontal gene transfer: The path to maturity
    • Koonin, E. V. 2003. Horizontal gene transfer: the path to maturity. Mol. Microbiol. 50:725-727.
    • (2003) Mol. Microbiol. , vol.50 , pp. 725-727
    • Koonin, E.V.1
  • 30
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: Quantification and classification
    • Koonin, E. V., K. S. Makarova, and L. Aravind. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55:709-742.
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 709-742
    • Koonin, E.V.1    Makarova, K.S.2    Aravind, L.3
  • 31
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski, L. B., and G. B. Golding. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:540-542.
    • (2001) J. Mol. Evol. , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 32
    • 0242490943 scopus 로고    scopus 로고
    • Lateral gene transfer: When will adolescence end?
    • Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
    • (2003) Mol. Microbiol. , vol.50 , pp. 739-749
    • Lawrence, J.G.1    Hendrickson, H.2
  • 33
    • 1342271382 scopus 로고    scopus 로고
    • From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria
    • Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol. 1:E19.
    • (2003) PLoS Biol. , vol.1
    • Lerat, E.1    Daubin, V.2    Moran, N.A.3
  • 34
    • 0035225012 scopus 로고    scopus 로고
    • Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    • RESEARCH 0033
    • Makarova, K. S., V. A. Ponomarev, and E. V. Koonin. 2001. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol. 2:RESEARCH 0033.
    • (2001) Genome Biol. , vol.2
    • Makarova, K.S.1    Ponomarev, V.A.2    Koonin, E.V.3
  • 35
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers, E. W., and W. Miller. 1988. Optimal alignments in linear space. Comput. Appl. Biosci. 4:11-17.
    • (1988) Comput. Appl. Biosci. , vol.4 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 37
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 38
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman, H., J. G. Lawrence, and E. A. Groisman. 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.A.3
  • 39
    • 0001654122 scopus 로고    scopus 로고
    • Development of neutral and nearly neutral theories
    • Ohta, T., and J. H. Gillespie. 1996. Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49:128-142.
    • (1996) Theor. Popul. Biol. , vol.49 , pp. 128-142
    • Ohta, T.1    Gillespie, J.H.2
  • 40
    • 0033057517 scopus 로고    scopus 로고
    • Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
    • Pouting, C. P., L. Aravind, J. Schultz, P. Bork, and E. V. Koonin. 1999. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289:729-745.
    • (1999) J. Mol. Biol. , vol.289 , pp. 729-745
    • Pouting, C.P.1    Aravind, L.2    Schultz, J.3    Bork, P.4    Koonin, E.V.5
  • 41
    • 0035943134 scopus 로고    scopus 로고
    • On surrogate methods for detecting lateral gene transfer
    • Ragan, M. A. 2001. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:187-191.
    • (2001) FEMS Microbiol. Lett. , vol.201 , pp. 187-191
    • Ragan, M.A.1
  • 42
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 43
    • 0035863767 scopus 로고    scopus 로고
    • A phylogenomic approach to microbial evolution
    • Sicheritz-Ponten, T., and S. G. Andersson. 2001. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 29:545-552.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 545-552
    • Sicheritz-Ponten, T.1    Andersson, S.G.2
  • 44
    • 0036889686 scopus 로고    scopus 로고
    • Orthology, paralogy and proposed classification for paralog subtypes
    • Sonnhammer, E. L., and E. V. Koonin. 2002. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18:619-620.
    • (2002) Trends Genet. , vol.18 , pp. 619-620
    • Sonnhammer, E.L.1    Koonin, E.V.2
  • 45
    • 0036017383 scopus 로고    scopus 로고
    • Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes
    • Syvanen, M. 2002. Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes. J. Mol. Evol. 55:85-91.
    • (2002) J. Mol. Evol. , vol.55 , pp. 85-91
    • Syvanen, M.1
  • 47
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 49
    • 0034053846 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
    • Woese, C. R., G. J. Olsen, M. Ibba, and D. Soll. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:202-236.
    • (2000) Microbiol. Mol. Biol. Rev. , vol.64 , pp. 202-236
    • Woese, C.R.1    Olsen, G.J.2    Ibba, M.3    Soll, D.4
  • 50
    • 0032830481 scopus 로고    scopus 로고
    • Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    • Wolf Y. I., L. Aravind, N. V. Grishin, and E. V. Koonin. 1999. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9:689-710.
    • (1999) Genome Res. , vol.9 , pp. 689-710
    • Wolf, Y.I.1    Aravind, L.2    Grishin, N.V.3    Koonin, E.V.4
  • 52
    • 0348044549 scopus 로고    scopus 로고
    • Genome trees constructed using five different approaches suggest new major bacterial clades
    • Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8.
    • (2001) BMC Evol. Biol. , vol.1 , pp. 8
    • Wolf, Y.I.1    Rogozin, I.B.2    Grishin, N.V.3    Tatusov, R.L.4    Koonin, E.V.5
  • 53
    • 0345874732 scopus 로고    scopus 로고
    • Coelomata and not ecdysozoa: Evidence from genome-wide phylogenetic analysis
    • Wolf, Y. I., I. B. Rogozin, and E. V. Koonin. 2004. Coelomata and not ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36.
    • (2004) Genome Res. , vol.14 , pp. 29-36
    • Wolf, Y.I.1    Rogozin, I.B.2    Koonin, E.V.3
  • 54
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 56
    • 0002331493 scopus 로고
    • Molecular evolution
    • M. Kasha and B. Pullman (ed.). Academic Press, New York, N.Y.
    • Zuckerkandl, E., and L. Pauling. 1962. Molecular evolution, p. 189-225. In M. Kasha and B. Pullman (ed.), Horizons in biochemistry. Academic Press, New York, N.Y.
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2
  • 57
    • 0013776758 scopus 로고
    • Molecules as documents of evolutionary history
    • Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-366.
    • (1965) J. Theor. Biol. , vol.8 , pp. 357-366
    • Zuckerkandl, E.1    Pauling, L.2


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