메뉴 건너뛰기




Volumn , Issue , 2010, Pages 37-60

Sequence-Based Analysis of Bacterial Population Structures

Author keywords

Genomic sequence alignment and types pairwise and multiple; Sequence based analysis, of bacterial population structure; Unweighted Pair Group Method (UPGMA) and bootstrapping phylogenetic tree construction

Indexed keywords


EID: 84870336564     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470600122.ch3     Document Type: Chapter
Times cited : (6)

References (93)
  • 1
    • 84959774562 scopus 로고
    • Consensus techniques and the comparison of taxonomic trees
    • Adams , E. N. (1972) Consensus techniques and the comparison of taxonomic trees . Systematic Zoology 21 , 390-397 .
    • (1972) Systematic Zoology , vol.21 , pp. 390-397
    • Adams, E.N.1
  • 2
    • 34047267637 scopus 로고
    • A canonical decomposition theory for metrics on a fi nite set
    • Bandelt , H. and Dress , A. (1992) A canonical decomposition theory for metrics on a fi nite set . Advances in Mathematics 92 , 47-105 .
    • (1992) Advances in Mathematics , vol.92 , pp. 47-105
    • Bandelt, H.1    Dress, A.2
  • 4
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K - 12
    • III
    • Blattner , F. , Plunkett , G. III , and Bloch , C. et al. (1997) The complete genome sequence of Escherichia coli K - 12 . Science 277 , 1453-1474 .
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.1    Plunkett, G.2    Bloch, C.3
  • 5
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • Bray , N. and Pachter , L. (2004) MAVID: Constrained ancestral alignment of multiple sequences . Genome Research 14 , 693-699 .
    • (2004) Genome Research , vol.14 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 6
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi - LAGAN: Effi cient tools for large - scale multiple alignment of genomic DNA
    • Brudno , M. , Do , C. , Cooper , G. et al. (2003) LAGAN and Multi - LAGAN: Effi cient tools for large - scale multiple alignment of genomic DNA . Genome Research 13 , 721-731 .
    • (2003) Genome Research , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.2    Cooper, G.3
  • 7
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor - net: An agglomerative method for the construction of phylogenetic networks
    • Bryant , D. and Moulton , V. (2004) Neighbor - net: An agglomerative method for the construction of phylogenetic networks . Molecular Biology and Evolution 21 , 255-265 .
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 8
    • 0000116740 scopus 로고
    • A method for deducing branching sequences in phylogeny
    • Camin , J. H. and Sokal , R. R. (1965) A method for deducing branching sequences in phylogeny . Evolution 19 , 311-326 .
    • (1965) Evolution , vol.19 , pp. 311-326
    • Camin, J.H.1    Sokal, R.R.2
  • 9
    • 0000303438 scopus 로고
    • The multiple sequence alignment problem in biology
    • Carrillo , H. and Lipman , D. (1988) The multiple sequence alignment problem in biology . SIAM Journal on Applied Mathematics 48 , 1073-1082 .
    • (1988) SIAM Journal on Applied Mathematics , vol.48 , pp. 1073-1082
    • Carrillo, H.1    Lipman, D.2
  • 11
    • 48249144818 scopus 로고    scopus 로고
    • Dynamics of genome rearrangement in bacterial populations
    • e1000128
    • Darling , A. , Mikl ó s , I. , and Ragan , M. (2008) Dynamics of genome rearrangement in bacterial populations . PLoS Genetics 4 , e1000128 .
    • (2008) PLoS Genetics , vol.4
    • Darling, A.1    Miklós, I.2    Ragan, M.3
  • 12
    • 36549060482 scopus 로고    scopus 로고
    • Analyzing patterns of microbial evolution using the mauve genome alignment system
    • Darling , A. , Treangen , T. , Messeguer , X. , and Perna , N. (2007) Analyzing patterns of microbial evolution using the mauve genome alignment system . Methods in Molecular Biology 396 , 135-152 .
    • (2007) Methods in Molecular Biology , vol.396 , pp. 135-152
    • Darling, A.1    Treangen, T.2    Messeguer, X.3    Perna, N.4
  • 13
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Darling , A. C. , Mau , B. , Blattner , F. R. , and Perna , N. T. (2004 ) Mauve: Multiple alignment of conserved genomic sequence with rearrangements . Genome Research 14 , 1394-1403 .
    • (2004) Genome Research , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 14
    • 38549157606 scopus 로고    scopus 로고
    • Computational analysis of genome evolution
    • University of Wisconsin.
    • Darling , A. E. (2006) Computational analysis of genome evolution . PhD thesis. University of Wisconsin.
    • (2006) PhD thesis
    • Darling, A.E.1
  • 16
    • 33846032295 scopus 로고    scopus 로고
    • A Bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
    • Didelot , X. , Achtman , M. , Parkhill , J. , Thomson , N. R. , and Falush , D. (2007) A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination? Genome Research 17 , 61-68 .
    • (2007) Genome Research , vol.17 , pp. 61-68
    • Didelot, X.1    Achtman, M.2    Parkhill, J.3    Thomson, N.R.4    Falush, D.5
  • 17
    • 59949084930 scopus 로고    scopus 로고
    • Inferring genomic fl ux in bacteria
    • Didelot , X. , Darling , A. , and Falush , D. (2009) Inferring genomic fl ux in bacteria . Genome Research 19 , 306-317 .
    • (2009) Genome Research , vol.19 , pp. 306-317
    • Didelot, X.1    Darling, A.2    Falush, D.3
  • 18
    • 34249027580 scopus 로고    scopus 로고
    • Inference of bacterial microevolution using multilocus sequence data
    • Didelot , X. and Falush , D. (2007) Inference of bacterial microevolution using multilocus sequence data . Genetics 175 , 1251-1266 .
    • (2007) Genetics , vol.175 , pp. 1251-1266
    • Didelot, X.1    Falush, D.2
  • 19
    • 77954143043 scopus 로고    scopus 로고
    • Bacterial recombination in vivo
    • (ed. M. Hensel and H. Schmidt)Cambridge University Press .
    • Didelot , X. and Falush , D. (2008) Bacterial recombination in vivo . In Horizontal Gene Transfer in the Evolution of Pathogenesis (ed. M. Hensel and H. Schmidt), pp. 23-48 . Cambridge University Press .
    • (2008) Horizontal Gene Transfer in the Evolution of Pathogenesis , pp. 23-48
    • Didelot, X.1    Falush, D.2
  • 20
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond , A. and Rambaut , A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees . BMC Evolutionary Biology 7 , 214 .
    • (2007) BMC Evolutionary Biology , vol.7 , pp. 214
    • Drummond, A.1    Rambaut, A.2
  • 21
    • 33344465800 scopus 로고    scopus 로고
    • Relaxed phylogenetics and dating with confi dence
    • Drummond , A. J. , Ho , S. Y. , Phillips , M. J. , and Rambaut , A. ( 2006) Relaxed phylogenetics and dating with confi dence . PLoS Biology 4 , 699-710 .
    • (2006) PLoS Biology , vol.4 , pp. 699-710
    • Drummond, A.J.1    Ho, S.Y.2    Phillips, M.J.3    Rambaut, A.4
  • 22
    • 0036021407 scopus 로고    scopus 로고
    • Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    • Drummond , A. J. , Nicholls , G. K. , Rodrigo , A. G. , and Solomon , W. (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data . Genetics 161 , 1307-1320 .
    • (2002) Genetics , vol.161 , pp. 1307-1320
    • Drummond, A.J.1    Nicholls, G.K.2    Rodrigo, A.G.3    Solomon, W.4
  • 23
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar , R. C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput . Nucleic Acids Research 32 , 1792-1797 .
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 25
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies
    • Falush , D. , Stephens , M. , and Pritchard , J. K. (2003a) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies . Genetics 164 , 1567-1587 .
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 26
    • 0037423837 scopus 로고    scopus 로고
    • Traces of human migrations in Helicobacter pylori populations
    • Falush , D. , Wirth , T. , Linz , B. et al. (2003b) Traces of human migrations in Helicobacter pylori populations . Science 299 , 1582-1585 .
    • (2003) Science , vol.299 , pp. 1582-1585
    • Falush, D.1    Wirth, T.2    Linz, B.3
  • 28
    • 0032733829 scopus 로고    scopus 로고
    • The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis
    • Feil , E. , Maiden , M. , Achtman , M. , and Spratt , B. (1999) The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis . Molecular Biology and Evolution 16 , 1496-1502 .
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 1496-1502
    • Feil, E.1    Maiden, M.2    Achtman, M.3    Spratt, B.4
  • 29
    • 0030456375 scopus 로고    scopus 로고
    • A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: Evidence for extensive interspecies recombination within adk
    • Feil , E. , Zhou , J. , Maynard Smith , J. , and Spratt , B. G. (1996) A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: Evidence for extensive interspecies recombination within adk . Journal of Molecular Evolution 43 , 631-640 .
    • (1996) Journal of Molecular Evolution , vol.43 , pp. 631-640
    • Feil, E.1    Zhou, J.2    Maynard Smith, J.3    Spratt, B.G.4
  • 31
    • 0035793056 scopus 로고    scopus 로고
    • Recombination within natural populations of pathogenic bacteria: Short - term empirical estimates and long - term phylogenetic consequences
    • Feil , E. J. , Holmes , E. C. , Enright , M. et al. (2001) Recombination within natural populations of pathogenic bacteria: Short - term empirical estimates and long - term phylogenetic consequences . Proceedings of the National Academy of Sciences of the United States of America 98 , 182-187 .
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , pp. 182-187
    • Feil, E.J.1    Holmes, E.C.2    Enright, M.3
  • 32
    • 0034128665 scopus 로고    scopus 로고
    • Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data
    • Feil , E. J. , Smith , J. M. , Enright , M. C. , and Spratt , B. G. ( 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
  • 33
    • 84959792503 scopus 로고
    • The number of evolutionary trees
    • Felsenstein , J. (1978a) The number of evolutionary trees . Systematic Zoology 27 , 27-33 .
    • (1978) Systematic Zoology , vol.27 , pp. 27-33
    • Felsenstein, J.1
  • 34
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein , J. (1978b) Cases in which parsimony or compatibility methods will be positively misleading . Systematic Zoology 27 , 401-410 .
    • (1978) Systematic Zoology , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 35
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein , J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach . Journal of Molecular Evolution 17 , 368-376 .
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 36
    • 0000461280 scopus 로고
    • Confi dence limits on phylogenies: An approach using the bootstrap
    • Felsenstein , J. (1985) Confi dence limits on phylogenies: An approach using the bootstrap . Evolution 39 , 783-791 .
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 37
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version 3.2)
    • Felsenstein , J. (1989) PHYLIP - Phylogeny Inference Package (Version 3.2) . Cladistics 5 , 164-166 .
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 38
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng , D. F. and Doolittle , R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees . Journal of Molecular Evolution 25 , 351-360 .
    • (1987) Journal of Molecular Evolution , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 39
    • 84959747425 scopus 로고
    • Toward defi ning the course of evolution: Minimum change for a specifi c tree topology
    • Fitch , W. (1971) Toward defi ning the course of evolution: Minimum change for a specifi c tree topology . Systematic Zoology 20 , 406-416 .
    • (1971) Systematic Zoology , vol.20 , pp. 406-416
    • Fitch, W.1
  • 40
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch , W. and Margoliash , E. (1967) Construction of phylogenetic trees . Science 155 , 279-284 .
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.1    Margoliash, E.2
  • 41
    • 0029653518 scopus 로고
    • Whole - genome random sequencing and assembly of Haemophilus infl uenzae Rd
    • Fleischmann , R. , Adams , M. , White , O. et al. (1995) Whole - genome random sequencing and assembly of Haemophilus infl uenzae Rd . Science 269 , 496-512 .
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.1    Adams, M.2    White, O.3
  • 42
    • 0030582739 scopus 로고    scopus 로고
    • Signifi cant improvement in accuracy of multiple protein sequence alignments by iterative refi nement as assessed by reference to structural alignments
    • Gotoh , O. (1996) Signifi cant improvement in accuracy of multiple protein sequence alignments by iterative refi nement as assessed by reference to structural alignments . Journal of Molecular Biology 264 , 823-838 .
    • (1996) Journal of Molecular Biology , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 43
    • 0028605344 scopus 로고
    • Clonal divergence in Escherichia coli as a result of recombination, not mutation
    • Guttman , D. S. and Dykhuizen , D. E. (1994) Clonal divergence in Escherichia coli as a result of recombination, not mutation . Science 266 , 1380-1383 .
    • (1994) Science , vol.266 , pp. 1380-1383
    • Guttman, D.S.1    Dykhuizen, D.E.2
  • 44
    • 0022376704 scopus 로고
    • Dating of the human - ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa , M. , Kishino , H. , and Yano , T. (1985) Dating of the human - ape splitting by a molecular clock of mitochondrial DNA . Journal of Molecular Evolution 22 , 160-174 .
    • (1985) Journal of Molecular Evolution , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 45
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings , W. K. (1970) Monte Carlo sampling methods using Markov chains and their applications . Biometrika 57 , 97-109 .
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 46
    • 0020286044 scopus 로고
    • Branch and bound algorithms to determine minimal evolutionary trees
    • Hendy , M. D. and Penny , D. (1982) Branch and bound algorithms to determine minimal evolutionary trees . Mathematical Biosciences 59 , 277-290 .
    • (1982) Mathematical Biosciences , vol.59 , pp. 277-290
    • Hendy, M.D.1    Penny, D.2
  • 48
    • 0024234855 scopus 로고
    • CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
    • Higgins , D. and Sharp , P. (1988) CLUSTAL: A package for performing multiple sequence alignment on a microcomputer . Gene 73 , 237-244 .
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.1    Sharp, P.2
  • 50
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck , J. P. and Ronquist , F. (2001) MrBayes: Bayesian inference of phylogenetic trees . Bioinformatics 17 , 754-755 .
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 51
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson , D. and Bryant , D. (2006) Application of phylogenetic networks in evolutionary studies . Molecular Biology and Evolution 23 , 254-267 .
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 254-267
    • Huson, D.1    Bryant, D.2
  • 52
    • 0031678692 scopus 로고    scopus 로고
    • SplitsTree: Analyzing and visualizing evolutionary data
    • Huson , D. H. (1998) SplitsTree: Analyzing and visualizing evolutionary data . Bioinformatics 14 , 68-73 .
    • (1998) Bioinformatics , vol.14-17 , pp. 68-73
    • Huson, D.H.1
  • 54
    • 14544305228 scopus 로고    scopus 로고
    • The infl uence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis
    • Jolley , K. A. , Wilson , D. J. , Kriz , P. , Mcvean , G. , and Maiden , M. C. J. (2005) The infl uence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis . Molecular Biology and Evolution 22 , 562-569 .
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 562-569
    • Jolley, K.A.1    Wilson, D.J.2    Kriz, P.3    Mcvean, G.4    Maiden, M.C.J.5
  • 56
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a fi nite population due to steady fl ux of mutations
    • Kimura , M. (1969) The number of heterozygous nucleotide sites maintained in a fi nite population due to steady fl ux of mutations . Genetics 61 , 893-903 .
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 57
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura , M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences . Journal of Molecular Evolution 16 , 111-120 .
    • (1980) Journal of Molecular Evolution , vol.16 , pp. 111-120
    • Kimura, M.1
  • 59
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner , M. and Felsenstein , J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates . Molecular Biology and Evolution 11 , 459-468 .
    • (1994) Molecular Biology and Evolution , vol.11 , pp. 459-468
    • Kuhner, M.1    Felsenstein, J.2
  • 60
    • 33644520519 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.2: A monitor of genome projects worldwide
    • Liolios , K. , Tavernarakis , N. , Hugenholtz , P. , and Kyrpides , N.C. (2006) The Genomes OnLine Database (GOLD) v.2: A monitor of genome projects worldwide . Nucleic Acids Research 34 , 332-334 .
    • (2006) Nucleic Acids Research , vol.34 , pp. 332-334
    • Liolios, K.1    Tavernarakis, N.2    Hugenholtz, P.3    Kyrpides, N.C.4
  • 61
    • 13144252236 scopus 로고    scopus 로고
    • Multilocus sequence typing: A portable approach to the identifi cation of clones within populations of pathogenic microorganisms
    • Maiden , M. C. J. , Bygraves , J. A. , Feil , E. et al. (1998) Multilocus sequence typing: A portable approach to the identifi cation of clones within populations of pathogenic microorganisms . Proceedings of the National Academy of Sciences of the United States of America 95 , 3140-3145 .
    • (1998) Proceedings of the National Academy of Sciences of the United States of America , vol.95 , pp. 3140-3145
    • Maiden, M.C.J.1    Bygraves, J.A.2    Feil, E.3
  • 62
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high - density picolitre reactors
    • Margulies , M. , Egholm , M. , Altman , W. et al. (2005) Genome sequencing in microfabricated high - density picolitre reactors . Nature 437 , 376-380 .
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.3
  • 63
    • 0031498410 scopus 로고    scopus 로고
    • Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo
    • Mau , B. and Newton , M. (1997) Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo . Journal of Computational and Graphical Statistics 6 , 122-131 .
    • (1997) Journal of Computational and Graphical Statistics , vol.6 , pp. 122-131
    • Mau, B.1    Newton, M.2
  • 64
    • 9644254192 scopus 로고    scopus 로고
    • Comparison of genome degradation in Paratyphi A and Typhi, human - restricted serovars of Salmonella enterica that cause typhoid
    • McClelland , M. , Sanderson , K. E. , Clifton , S. W. et al. (2004) Comparison of genome degradation in Paratyphi A and Typhi, human - restricted serovars of Salmonella enterica that cause typhoid . Nature Genetics 36 , 1268-1274 .
    • (2004) Nature Genetics , vol.36 , pp. 1268-1274
    • McClelland, M.1    Sanderson, K.E.2    Clifton, S.W.3
  • 66
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman , S. B. and Wunsch , C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins . Journal of Molecular Biology 48 , 443-453.
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 67
    • 0035950154 scopus 로고    scopus 로고
    • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
    • Parkhill , J. , Dougan , G. , James , K. D. et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 . Nature 413 , 848-852 .
    • (2001) Nature , vol.413 , pp. 848-852
    • Parkhill, J.1    Dougan, G.2    James, K.D.3
  • 68
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard , J. , Stephens , M. , and Donnelly , P. J. (2000) Inference of population structure using multilocus genotype data . Genetics 155 , 945-959 .
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.1    Stephens, M.2    Donnelly, P.J.3
  • 70
    • 5344230543 scopus 로고    scopus 로고
    • (September 1, 2008).
    • Rambaut , A. and Drummond , A. (2007) Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer (accessed September 1, 2008).
    • (2007) Tracer v1.4
    • Rambaut, A.1    Drummond, A.2
  • 72
    • 0023850178 scopus 로고
    • Primer - directed enzymatic amplifi cation of DNA with a thermostable DNA polymerase
    • Saiki , R. , Gelfand , D. , Stoffel , S. et al. (1988) Primer - directed enzymatic amplifi cation of DNA with a thermostable DNA polymerase . Science 239 , 487-491 .
    • (1988) Science , vol.239 , pp. 487-491
    • Saiki, R.1    Gelfand, D.2    Stoffel, S.3
  • 73
    • 0022372670 scopus 로고
    • Enzymatic amplifi cation of beta - globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia
    • Saiki , R. , Scharf , S. , Faloona , F. et al. (1985) Enzymatic amplifi cation of beta - globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia . Science 230 , 1350-1354 .
    • (1985) Science , vol.230 , pp. 1350-1354
    • Saiki, R.1    Scharf, S.2    Faloona, F.3
  • 74
    • 0023375195 scopus 로고
    • The neighbor - joining method: a new method for reconstructing phylogenetic trees
    • Saitou , N. and Nei , M. (1987) The neighbor - joining method: a new method for reconstructing phylogenetic trees . Molecular Biology and Evolution 4 , 406-425 .
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 75
    • 0034351397 scopus 로고    scopus 로고
    • Parametric phylogenetics?
    • Sanderson , M. J. and Kim , J. (2000) Parametric phylogenetics? Systematic Biology 49 , 817-829 .
    • (2000) Systematic Biology , vol.49 , pp. 817-829
    • Sanderson, M.J.1    Kim, J.2
  • 77
    • 0030046525 scopus 로고    scopus 로고
    • Allelic polymorphism and site - specifi c recombination in the opc locus of Neisseria meningitidis
    • Seiler , A. , Reinhardt , R. , Sarkari , J. , Caugant , D. A. , and Achtman , M. (1996) Allelic polymorphism and site - specifi c recombination in the opc locus of Neisseria meningitidis . Molecular Microbiolog 19 , 841-856 .
    • (1996) Molecular Microbiolog , vol.19 , pp. 841-856
    • Seiler, A.1    Reinhardt, R.2    Sarkari, J.3    Caugant, D.A.4    Achtman, M.5
  • 78
    • 42049090179 scopus 로고    scopus 로고
    • Convergence of Campylobacter species: Implications for bacterial evolution
    • Sheppard , S. , McCarthy , N. , Falush , D. , and Maiden , M. (2008) Convergence of Campylobacter species: Implications for bacterial evolution . Science 320 , 237-239 .
    • (2008) Science , vol.320 , pp. 237-239
    • Sheppard, S.1    McCarthy, N.2    Falush, D.3    Maiden, M.4
  • 79
    • 0019887799 scopus 로고
    • Identifi cation of common molecular subsequences
    • Smith , T. F. and Waterman , M. S. (1981) Identifi cation of common molecular subsequences . Journal of Molecular Biology 147 , 195-197 .
    • (1981) Journal of Molecular Biology , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 80
    • 0347532847 scopus 로고    scopus 로고
    • Applying the bootstrap in phylogeny reconstruction
    • Soltis , P. S. and Soltis , D. E. (2003) Applying the bootstrap in phylogeny reconstruction . Statistical Science 18 , 256-267 .
    • (2003) Statistical Science , vol.18 , pp. 256-267
    • Soltis, P.S.1    Soltis, D.E.2
  • 81
    • 33846827401 scopus 로고    scopus 로고
    • PAUP
    • (and Other Methods). Version 4 . Sinauer AssociatesSunderland, MA
    • Swofford , D. (2002) PAUP .Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4 . Sinauer Associates , Sunderland, MA .
    • (2002) Phylogenetic Analysis Using Parsimony
    • Swofford, D.1
  • 82
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
    • Tamura , K. , Dudley , J. , Nei , M. , and Kumar , S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 . Molecular Biology and Evolution 24 , 1596-1599 .
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 83
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position - specifi c gap penalties and weight matrix choice
    • Thompson , J. D. , Higgins , D. G. , and Gibson , T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position - specifi c gap penalties and weight matrix choice . Nucleic Acids Research 22 , 4673-4680 .
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 84
    • 0031149251 scopus 로고    scopus 로고
    • Links between maximum likelihood and maximum parsimony under a simple model of site substitution
    • Tuffley , C. and Steel , M. (1997) Links between maximum likelihood and maximum parsimony under a simple model of site substitution . Bulletin of Mathematical Biology 59 , 581-607 .
    • (1997) Bulletin of Mathematical Biology , vol.59 , pp. 581-607
    • Tuffley, C.1    Steel, M.2
  • 85
    • 0037380723 scopus 로고    scopus 로고
    • Comparative genomics: Genome - wide analysis in metazoan eukaryotes
    • Ureta - Vidal , A. , Ettwiller , L. , and Birney , E. (2003) Comparative genomics: Genome - wide analysis in metazoan eukaryotes . Nature Reviews. Genetics 4 , 251-262 .
    • (2003) Nature Reviews. Genetics , vol.4 , pp. 251-262
    • Ureta-Vidal, A.1    Ettwiller, L.2    Birney, E.3
  • 86
    • 58549084151 scopus 로고    scopus 로고
    • A comparison of homologous recombination rates in bacteria and archaea
    • Vos , M. and Didelot , X. (2008) A comparison of homologous recombination rates in bacteria and archaea . ISME Journal 3 , 199-208 .
    • (2008) ISME Journal , vol.3 , pp. 199-208
    • Vos, M.1    Didelot, X.2
  • 87
    • 0026443050 scopus 로고
    • Clonal and antigenic analysis of serogroup a Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People ' s Republic of China
    • Wang , J. F. , Caugant , D. A. , Li , X. et al. (1992) Clonal and antigenic analysis of serogroup a Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People ' s Republic of China . Infection and Immunity 60 , 5267-5282 .
    • (1992) Infection and Immunity , vol.60 , pp. 5267-5282
    • Wang, J.F.1    Caugant, D.A.2    Li, X.3
  • 88
    • 0027299595 scopus 로고
    • Antigenic and epidemiologic properties of the et - 37 complex of Neisseria meningitidis
    • Wang , J. F. , Caugant , D. A. , Morelli , G. , Koumar é , B. , and Achtman , M. (1993) Antigenic and epidemiologic properties of the et - 37 complex of Neisseria meningitidis . Journal of Infectious Diseases 167 , 1320-1329 .
    • (1993) Journal of Infectious Diseases , vol.167 , pp. 1320-1329
    • Wang, J.F.1    Caugant, D.A.2    Morelli, G.3    Koumaré, B.4    Achtman, M.5
  • 89
    • 0036137328 scopus 로고    scopus 로고
    • Sequence Type Analysis and Recombinational Tests (START)
    • Jolley , K. A. , Feil , E. J. , Chan , M. - S. , and Maiden , M. C. J. ( 2001) Sequence Type Analysis and Recombinational Tests (START) . Bioinformatics 17 , 1230-1231 .
    • Bioinformatics , pp. 1230-1231
    • Jolley, K.A.1    Feil, E.J.2    Chan, M.-S.3    Maiden, M.C.J.4
  • 90
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson , G. A. (1975) On the number of segregating sites in genetical models without recombination . Theoretical Population Biology 7 , 256-276 .
    • (1975) Theoretical Population Biology , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 91
    • 33745282930 scopus 로고    scopus 로고
    • Sex and virulence in Escherichia coli: An evolutionary perspective
    • Wirth , T. , Falush , D. , Lan , R. et al. (2006) Sex and virulence in Escherichia coli: An evolutionary perspective . Molecular Microbiology 60 , 1136-1151 .
    • (2006) Molecular Microbiology , vol.60 , pp. 1136-1151
    • Wirth, T.1    Falush, D.2    Lan, R.3
  • 92
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    • Yang , Z. (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood . Molecular Biology and Evolution 24 , 1586-1591 .
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 93
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • Yang , Z. and Rannala , B. (1997) Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method . Molecular Biology and Evolution 14 , 717-724 .
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.