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Volumn 364, Issue 1527, 2009, Pages 2209-2219

Gene and genome trees conflict at many levels

Author keywords

Conflict; Phylogeny; Prokaryotes

Indexed keywords

ADAPTATION; DATA SET; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENE TRANSFER; METABOLISM; PHYLOGENY; PROKARYOTE;

EID: 67651067964     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2009.0042     Document Type: Article
Times cited : (14)

References (59)
  • 1
    • 43849089834 scopus 로고    scopus 로고
    • Microbial diversity and the genetic nature of microbial species
    • doi:10.1038/nrmicro1872
    • Achtman, M. & Wagner, M. 2008 Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6, 431-440. (doi:10.1038/nrmicro1872)
    • (2008) Nat. Rev. Microbiol , vol.6 , pp. 431-440
    • Achtman, M.1    Wagner, M.2
  • 2
    • 0033515041 scopus 로고    scopus 로고
    • Asai, T., Zaporojets, D., Squires, C. & Squires, C. L. 1999 An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl Acad. Sci. USA 96, 19711976. (doi:10.1073/pnas.96.5.1971)
    • Asai, T., Zaporojets, D., Squires, C. & Squires, C. L. 1999 An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl Acad. Sci. USA 96, 19711976. (doi:10.1073/pnas.96.5.1971)
  • 3
    • 26444506791 scopus 로고    scopus 로고
    • Highways of gene sharing in prokaryotes
    • doi:10.1073/pnas.0504068102
    • Beiko, R. G., Harlow, T. J. & Ragan, M. A. 2005 Highways of gene sharing in prokaryotes. Proc. Natl Acad. Sci. USA 102, 14332-14337. (doi:10.1073/pnas.0504068102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 14332-14337
    • Beiko, R.G.1    Harlow, T.J.2    Ragan, M.A.3
  • 4
    • 0000257772 scopus 로고
    • Enterobacteriaceae
    • eds N. R. Krieg & J. G. Holt, pp, Baltimore, MD: Williams and Wilkins
    • Brenner, D. J. 1984 Enterobacteriaceae. In Bergey's manual of systematic bacteriology, vol. 1 (eds N. R. Krieg & J. G. Holt), pp. 408-420. Baltimore, MD: Williams and Wilkins.
    • (1984) Bergey's manual of systematic bacteriology , vol.1 , pp. 408-420
    • Brenner, D.J.1
  • 6
    • 54449093613 scopus 로고    scopus 로고
    • in Neisseria meningitidis. Proc. Natl Acad. Sci. USA 105, 15082-15087. (doi:10.1073/pnas.0712019105)
    • in Neisseria meningitidis. Proc. Natl Acad. Sci. USA 105, 15082-15087. (doi:10.1073/pnas.0712019105)
  • 7
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • doi:10.1126/science.1123061
    • Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. 2006 Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287. (doi:10.1126/science.1123061)
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    von Mering, C.3    Creevey, C.J.4    Snel, B.5    Bork, P.6
  • 8
    • 3342926241 scopus 로고    scopus 로고
    • Multilocus sequence typing what is resolved?
    • doi:10.1016/j.tim.2004. 06.003
    • Cooper, J. E. & Feil, E. J. 2004 Multilocus sequence typing what is resolved? Trends Microbiol. 12, 373-377. (doi:10.1016/j.tim.2004. 06.003)
    • (2004) Trends Microbiol , vol.12 , pp. 373-377
    • Cooper, J.E.1    Feil, E.J.2
  • 9
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • doi:10.1093/bioinfor- matics/bti020
    • Creevey, C. J. & McInerney, J. O. 2005 Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21, 390-392. (doi:10.1093/bioinfor- matics/bti020)
    • (2005) Bioinformatics , vol.21 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 11
    • 33750810896 scopus 로고    scopus 로고
    • The tree of one percent
    • doi:10.1186/gb-2006-7-10-118
    • Dagan, T. & Martin, W. 2006 The tree of one percent. Genome Biol. 7, 118. (doi:10.1186/gb-2006-7-10-118)
    • (2006) Genome Biol , vol.7 , pp. 118
    • Dagan, T.1    Martin, W.2
  • 12
    • 33846476262 scopus 로고    scopus 로고
    • Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokar- yote evolution
    • doi:10.1073/pnas.0606318104
    • Dagan, T. & Martin, W. 2007 Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokar- yote evolution. Proc. Natl Acad. Sci. USA 104, 870-875. (doi:10.1073/pnas.0606318104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 870-875
    • Dagan, T.1    Martin, W.2
  • 13
    • 48249151749 scopus 로고    scopus 로고
    • Modular networks and cumulative impact of lateral transfer in pro- karyote genome evolution
    • doi:10.1073/pnas.0800679105
    • Dagan, T., Artzy-Randrup, Y. & Martin, W. 2008 Modular networks and cumulative impact of lateral transfer in pro- karyote genome evolution. Proc. Natl Acad. Sci. USA 105, 10 039-10 044. (doi:10.1073/pnas.0800679105)
    • (2008) Proc. Natl Acad. Sci. USA , vol.105
    • Dagan, T.1    Artzy-Randrup, Y.2    Martin, W.3
  • 14
    • 0036198891 scopus 로고    scopus 로고
    • Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: A model molecule for molecular systematic studies
    • Dauga, C. 2002 Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52, 531-547.
    • (2002) Int. J. Syst. Evol. Microbiol , vol.52 , pp. 531-547
    • Dauga, C.1
  • 15
    • 0033401933 scopus 로고    scopus 로고
    • Lateral genomics
    • doi:10.1016/S0962-8924(99)01664-5
    • Doolittle, W. F. 1999 Lateral genomics. Trends Cell Biol. 9, M5-M8. (doi:10.1016/S0962-8924(99)01664-5)
    • (1999) Trends Cell Biol , vol.9
    • Doolittle, W.F.1
  • 16
    • 33847790997 scopus 로고    scopus 로고
    • Pattern pluralism and the Tree of Life hypothesis
    • doi:10.1073/pnas.0610699104
    • Doolittle, W. F. & Bapteste, E. 2007 Pattern pluralism and the Tree of Life hypothesis. Proc. Natl Acad. Sci. USA 104, 2043-2049. (doi:10.1073/pnas.0610699104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 2043-2049
    • Doolittle, W.F.1    Bapteste, E.2
  • 17
    • 33845890829 scopus 로고    scopus 로고
    • Genomics and the bacterial species problem
    • doi:10.1186/ gb-2006-7-9-116
    • Doolittle, W. F. & Papke, R. T. 2006 Genomics and the bacterial species problem. Genome Biol. 7, 116. (doi:10.1186/ gb-2006-7-9-116)
    • (2006) Genome Biol , vol.7 , pp. 116
    • Doolittle, W.F.1    Papke, R.T.2
  • 18
    • 0042386134 scopus 로고    scopus 로고
    • The evolutionary history ofShigella and enteroin- vasive Escherichia coli revised
    • doi:10.1007/s00239- 003-2460-3
    • Escobar-Paramo, P., Giudicelli, C., Parsot, C. & Denamur, E. 2003 The evolutionary history ofShigella and enteroin- vasive Escherichia coli revised. J. Mol. Evol. 57, 140-148. (doi:10.1007/s00239- 003-2460-3)
    • (2003) J. Mol. Evol , vol.57 , pp. 140-148
    • Escobar-Paramo, P.1    Giudicelli, C.2    Parsot, C.3    Denamur, E.4
  • 19
    • 0035909914 scopus 로고    scopus 로고
    • Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age
    • doi:10.1073/pnas.251396098
    • Falush, D., Kraft, C., Taylor, N. S., Correa, P., Fox, J. G., Achtman, M. & Suerbaum, S. 2001 Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl Acad. Sci. USA 98, 15056-15061. (doi:10.1073/pnas.251396098)
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 15056-15061
    • Falush, D.1    Kraft, C.2    Taylor, N.S.3    Correa, P.4    Fox, J.G.5    Achtman, M.6    Suerbaum, S.7
  • 20
    • 85020839619 scopus 로고    scopus 로고
    • Felsenstein, J. 1993 PHYLIP 3.6 edn. Distributed by Author.
    • Felsenstein, J. 1993 PHYLIP 3.6 edn. Distributed by Author.
  • 21
    • 28944434614 scopus 로고    scopus 로고
    • Genome phylogenies indicate a meaningful alpha- proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales
    • doi:10.1093/molbev/msj009
    • Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. 2006 Genome phylogenies indicate a meaningful alpha- proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23, 74-85. (doi:10.1093/molbev/msj009)
    • (2006) Mol. Biol. Evol , vol.23 , pp. 74-85
    • Fitzpatrick, D.A.1    Creevey, C.J.2    McInerney, J.O.3
  • 22
    • 23944437942 scopus 로고    scopus 로고
    • Gevers, D. et al. 2005 Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3, 733-739. (doi:10.1038/ nrmicro1236) Guo, Y., Zheng, W., Rong, X. & Huang, Y. 2008 A multilo- cus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomy- cete systematics. Int. J. Syst. Evol. Microbiol. 58, 149-159. (doi:10.1099/ijs.0.65224-0)
    • Gevers, D. et al. 2005 Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3, 733-739. (doi:10.1038/ nrmicro1236) Guo, Y., Zheng, W., Rong, X. & Huang, Y. 2008 A multilo- cus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomy- cete systematics. Int. J. Syst. Evol. Microbiol. 58, 149-159. (doi:10.1099/ijs.0.65224-0)
  • 23
    • 33645816587 scopus 로고    scopus 로고
    • Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    • doi:10.1186/ 1471-2148-6-29
    • Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & McLnerney, J. O. 2006 Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6, 29. (doi:10.1186/ 1471-2148-6-29)
    • (2006) BMC Evol. Biol , vol.6 , pp. 29
    • Keane, T.M.1    Creevey, C.J.2    Pentony, M.M.3    Naughton, T.J.4    McLnerney, J.O.5
  • 24
    • 34547583680 scopus 로고    scopus 로고
    • MultiPhyl: A high-throughput phylogenomics webserver using distributed computing
    • doi:10.1093/nar/gkm359
    • Keane, T. M., Naughton, T. J. & Mclnerney, J. O. 2007 MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Res. 35, W33 -W37. (doi:10.1093/nar/gkm359)
    • (2007) Nucleic Acids Res , vol.35
    • Keane, T.M.1    Naughton, T.J.2    Mclnerney, J.O.3
  • 25
    • 0036792524 scopus 로고    scopus 로고
    • Salmonella typhi, the causative agent of typhoid fever, is approximately 50, 000 years old
    • doi: 10.1016/S1567-1348(02)00089-8
    • Kidgell, C., Reichard, U., Wain, J., Linz, B., Torpdahl, M., Dougan, G. & Achtman, M. 2002 Salmonella typhi, the causative agent of typhoid fever, is approximately 50, 000 years old. Infect. Genet. Evol. 2, 39-45. (doi: 10.1016/S1567-1348(02)00089-8)
    • (2002) Infect. Genet. Evol , vol.2 , pp. 39-45
    • Kidgell, C.1    Reichard, U.2    Wain, J.3    Linz, B.4    Torpdahl, M.5    Dougan, G.6    Achtman, M.7
  • 27
    • 0034833128 scopus 로고    scopus 로고
    • Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli
    • doi:10.1128/IAI.69.10.6303-6309. 2001
    • Lan, R., Lumb, B., Ryan, D. & Reeves, P. R. 2001 Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli. Infect. Immun. 69, 6303-6309. (doi:10.1128/IAI.69.10.6303-6309. 2001)
    • (2001) Infect. Immun , vol.69 , pp. 6303-6309
    • Lan, R.1    Lumb, B.2    Ryan, D.3    Reeves, P.R.4
  • 28
    • 0036598066 scopus 로고    scopus 로고
    • Gene transfer in bacteria: Speciation without species?
    • doi:10.1006/tpbi.2002. 1587
    • Lawrence, J. G. 2002 Gene transfer in bacteria: speciation without species? Theor. Popul. Biol. 61, 449-460. (doi:10.1006/tpbi.2002. 1587)
    • (2002) Theor. Popul. Biol , vol.61 , pp. 449-460
    • Lawrence, J.G.1
  • 29
    • 0034109516 scopus 로고    scopus 로고
    • Molecular analysis of Shigella sonnei isolated from three well-documented outbreaks in school children
    • Lee, T. M., Chang, L. L., Chang, C. Y., Wang, J. C., Pan, T. M., Wang, T. K. & Chang, S. F. 2000 Molecular analysis of Shigella sonnei isolated from three well-documented outbreaks in school children. J. Med. Microbiol. 49, 355-360.
    • (2000) J. Med. Microbiol , vol.49 , pp. 355-360
    • Lee, T.M.1    Chang, L.L.2    Chang, C.Y.3    Wang, J.C.4    Pan, T.M.5    Wang, T.K.6    Chang, S.F.7
  • 30
    • 0031350056 scopus 로고    scopus 로고
    • NEXUS: An extensible file format for systematic information
    • doi:10.2307/2413497
    • Maddison, D. R., Swofford, D. L. & Maddison, W. P. 1997 NEXUS: an extensible file format for systematic information. Syst. Biol. 46, 590-621. (doi:10.2307/2413497)
    • (1997) Syst. Biol , vol.46 , pp. 590-621
    • Maddison, D.R.1    Swofford, D.L.2    Maddison, W.P.3
  • 31
    • 16944365566 scopus 로고    scopus 로고
    • An international outbreak of Salmonella infections caused by alfalfa sprouts grown from contaminated seeds
    • doi:10.1086/513985
    • Mahon, B. E. et al. 1997 An international outbreak of Salmonella infections caused by alfalfa sprouts grown from contaminated seeds. J. Infect. Dis. 175, 876 -882. (doi:10.1086/513985)
    • (1997) J. Infect. Dis , vol.175 , pp. 876-882
    • Mahon, B.E.1
  • 32
    • 36749104267 scopus 로고    scopus 로고
    • Genetics. Paradigmforlife
    • doi:10.1126/science.1151657
    • McInerney, J. O. & Pisani, D. 2007 Genetics. Paradigmforlife. Science 318, 1390-1391. (doi:10.1126/science.1151657)
    • (2007) Science , vol.318 , pp. 1390-1391
    • McInerney, J.O.1    Pisani, D.2
  • 33
    • 43049090907 scopus 로고    scopus 로고
    • The pro- karyotic tree of life: Past, present... and future?
    • doi:10.1016/j.tree.2008.01. 008
    • McInerney, J. O., Cotton, J. A. & Pisani, D. 2008 The pro- karyotic tree of life: past, present... and future? Trends Ecol. Evol. 23, 276-281. (doi:10.1016/j.tree.2008.01. 008)
    • (2008) Trends Ecol. Evol , vol.23 , pp. 276-281
    • McInerney, J.O.1    Cotton, J.A.2    Pisani, D.3
  • 34
    • 18244380086 scopus 로고    scopus 로고
    • Examining bacterial species under the specter of gene transfer and exchange
    • Ochman, H., Lerat, E. & Daubin, V. 2005 Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl Acad. Sci. USA 102(Suppl. 1), 6595-6599.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.SUPPL. 1 , pp. 6595-6599
    • Ochman, H.1    Lerat, E.2    Daubin, V.3
  • 35
    • 0014546327 scopus 로고
    • Chromosomal location of ribosomal protein cistrons determined by intergeneric bacterial mating
    • O'Neil, D. M., Baron, L. S. & Sypherd, P. S. 1969 Chromosomal location of ribosomal protein cistrons determined by intergeneric bacterial mating. J. Bacteriol. 99, 242-247.
    • (1969) J. Bacteriol , vol.99 , pp. 242-247
    • O'Neil, D.M.1    Baron, L.S.2    Sypherd, P.S.3
  • 37
    • 26244448900 scopus 로고    scopus 로고
    • Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase beta-subunit
    • doi:10.1099/ijs.0.63539-0
    • Paradis, S. et al. 2005 Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase beta-subunit. Int. J. Syst. Evol. Microbiol. 55, 2013-2025. (doi:10.1099/ijs.0.63539-0)
    • (2005) Int. J. Syst. Evol. Microbiol , vol.55 , pp. 2013-2025
    • Paradis, S.1
  • 38
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • doi:10.1093/molbev/msh137
    • Phillips, M. J., Delsuc, F. & Penny, D. 2004 Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21, 1455-1458. (doi:10.1093/molbev/msh137)
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 39
    • 34547751897 scopus 로고    scopus 로고
    • Supertrees disentangle the chimerical origin of eukaryotic genomes
    • doi:10.1093/molbev/ msm095
    • Pisani, D., Cotton, J. A. & McInerney, J. O. 2007 Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol. Biol. Evol. 24, 1752-1760. (doi:10.1093/molbev/ msm095)
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1752-1760
    • Pisani, D.1    Cotton, J.A.2    McInerney, J.O.3
  • 40
    • 0034641731 scopus 로고    scopus 로고
    • Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
    • doi:10.1073/pnas.180094797
    • Pupo, G. M., Lan, R. & Reeves, P. R. 2000 Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl Acad. Sci. USA 97, 10 567-10 572. (doi:10.1073/pnas.180094797)
    • (2000) Proc. Natl Acad. Sci. USA , vol.97
    • Pupo, G.M.1    Lan, R.2    Reeves, P.R.3
  • 41
    • 0141502465 scopus 로고    scopus 로고
    • 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: Extension of the dataset and proposal of a new lineage within the nitrosomonads
    • doi: 10.1099/ijs.0.02638-0
    • Purkhold, U., Wagner, M., Timmermann, G., Pommerening-Roser, A. & Koops, H. P. 2003 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads.Int. J. Syst. Evol. Microbiol. 53, 1485 -1494. (doi: 10.1099/ijs.0.02638-0)
    • (2003) Int. J. Syst. Evol. Microbiol , vol.53 , pp. 1485-1494
    • Purkhold, U.1    Wagner, M.2    Timmermann, G.3    Pommerening-Roser, A.4    Koops, H.P.5
  • 42
    • 0019424782 scopus 로고
    • Comparison of phyloge-netic trees
    • Robinson, D. & Foulds, L. 1981 Comparison of phyloge-netic trees. Biosciences 53, 131 -147.
    • (1981) Biosciences , vol.53 , pp. 131-147
    • Robinson, D.1    Foulds, L.2
  • 43
    • 85020811925 scopus 로고    scopus 로고
    • Rodriguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F. & Philippe, H. 2007 Detecting
    • Rodriguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F. & Philippe, H. 2007 Detecting
  • 44
    • 33847656285 scopus 로고    scopus 로고
    • and overcoming systematic errors in genome-scalephylogenies. Syst. Biol. 56, 389 -399. (doi:10.1080/ 10635150701397643)
    • and overcoming systematic errors in genome-scalephylogenies. Syst. Biol. 56, 389 -399. (doi:10.1080/ 10635150701397643)
  • 45
    • 0242365676 scopus 로고    scopus 로고
    • Rokas, A., Williams, B. L., King, N. & Carroll, S. B. 2003 Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798 -804.(doi:10.1038/nature02053)
    • Rokas, A., Williams, B. L., King, N. & Carroll, S. B. 2003 Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798 -804.(doi:10.1038/nature02053)
  • 46
    • 34248188251 scopus 로고    scopus 로고
    • SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics
    • Roure, B., Rodriguez-Ezpeleta, N. & Philippe, H. 2007 SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7(Suppl. 1), S2.
    • (2007) BMC Evol. Biol , vol.7 , Issue.SUPPL. 1
    • Roure, B.1    Rodriguez-Ezpeleta, N.2    Philippe, H.3
  • 47
    • 0038158155 scopus 로고    scopus 로고
    • Obtaining maximal concatenated phylo- genetic data sets from large sequence databases
    • doi:10.1093/molbev/msg115
    • Sanderson, M. J., Driskell, A. C., Ree, R. H., Eulenstein, O. & Langley, S. 2003 Obtaining maximal concatenated phylo- genetic data sets from large sequence databases. Mol. Biol. Evol. 20, 1036-1042. (doi:10.1093/molbev/msg115)
    • (2003) Mol. Biol. Evol , vol.20 , pp. 1036-1042
    • Sanderson, M.J.1    Driskell, A.C.2    Ree, R.H.3    Eulenstein, O.4    Langley, S.5
  • 48
    • 0019389567 scopus 로고
    • Shigella sonnei plasmids: Evidence that a large plasmid is necessary for virulence
    • Sansonetti, P. J., Kopecko, D. J. & Formal, S. B. 1981 Shigella sonnei plasmids: evidence that a large plasmid is necessary for virulence. Infect. Immun. 34, 75 -83.
    • (1981) Infect. Immun , vol.34 , pp. 75-83
    • Sansonetti, P.J.1    Kopecko, D.J.2    Formal, S.B.3
  • 49
    • 55249091610 scopus 로고    scopus 로고
    • PhySIC-IST: Cleaning source trees to infer more informative supertrees
    • doi:10.1186/1471-2105-9-413
    • Scornavacca, C., Berry, V., Lefort, V., Douzery, E. J. & Ranwez, V. 2008 PhySIC-IST: cleaning source trees to infer more informative supertrees. BMC Bioinform. 9, 413. (doi:10.1186/1471-2105-9-413)
    • (2008) BMC Bioinform , vol.9 , pp. 413
    • Scornavacca, C.1    Berry, V.2    Lefort, V.3    Douzery, E.J.4    Ranwez, V.5
  • 50
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • doi:10.1093/bioinfor- matics/17.12.1246
    • Shimodaira, H. & Hasegawa, M. 2001 CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247. (doi:10.1093/bioinfor- matics/17.12.1246)
    • (2001) Bioinformatics , vol.17 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 51
    • 36249021315 scopus 로고    scopus 로고
    • Genome-wide experimental determination of barriers to horizontal gene transfer
    • doi:10.1126/science. 1147112
    • Sorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Bork, P. & Rubin, E. M. 2007 Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449-1452. (doi:10.1126/science. 1147112)
    • (2007) Science , vol.318 , pp. 1449-1452
    • Sorek, R.1    Zhu, Y.2    Creevey, C.J.3    Francino, M.P.4    Bork, P.5    Rubin, E.M.6
  • 52
    • 33751258603 scopus 로고    scopus 로고
    • The bacterial species dilemma and the genomic-phylogenetic species concept
    • doi:10.1098/rstb.2006.1914
    • Staley, J. T. 2006 The bacterial species dilemma and the genomic-phylogenetic species concept. Phil. Trans. R. Soc. B 361, 1899-1909. (doi:10.1098/rstb.2006.1914)
    • (2006) Phil. Trans. R. Soc. B , vol.361 , pp. 1899-1909
    • Staley, J.T.1
  • 53
    • 0021802770 scopus 로고
    • An outbreak of Yersinia enterocolitica infections caused by contaminated tofu (soybean curd)
    • Tacket, C. O., Ballard, J., Harris, N., Allard, J., Nolan, C., Quan, T. & Cohen, M. L. 1985 An outbreak of Yersinia enterocolitica infections caused by contaminated tofu (soybean curd). Am. J. Epidemiol. 121, 705 -711.
    • (1985) Am. J. Epidemiol , vol.121 , pp. 705-711
    • Tacket, C.O.1    Ballard, J.2    Harris, N.3    Allard, J.4    Nolan, C.5    Quan, T.6    Cohen, M.L.7
  • 54
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phyloge- nies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • doi:10.1080/ 10635150701472164
    • Talavera, G. & Castresana, J. 2007 Improvement of phyloge- nies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577. (doi:10.1080/ 10635150701472164)
    • (2007) Syst. Biol , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 56
    • 54049108449 scopus 로고    scopus 로고
    • Multiple sequencealignment using ClustalW and ClustalX
    • Chapter 2: Unit 2.3
    • Thompson, J. D., Gibson, T. J. & Higgins, D. G. 2002 Multiple sequencealignment using ClustalW and ClustalX. Curr. Protoc. Bioinform. , Chapter 2: Unit 2.3.
    • (2002) Curr. Protoc. Bioinform
    • Thompson, J.D.1    Gibson, T.J.2    Higgins, D.G.3
  • 57
    • 85136378162 scopus 로고    scopus 로고
    • Varma, J. K. et al. 2003 An outbreak of Escherichia coli O157 infection following exposure to a contaminated building. JAMA 290, 2709-2712.(doi:10.1001/jama.290.20.2709)
    • Varma, J. K. et al. 2003 An outbreak of Escherichia coli O157 infection following exposure to a contaminated building. JAMA 290, 2709-2712.(doi:10.1001/jama.290.20.2709)
  • 58
    • 55649087852 scopus 로고    scopus 로고
    • Inferring evolutionary trees with PAUP
    • Chapter 6, Unit 6.4. Hoboken, NJ: John Wiley & Son
    • Wilgenbusch J. C. & Swofford, D. 2003 Inferring evolutionary trees with PAUP. Curr. Protoc. Bioinform. , Chapter 6, Unit 6.4. Hoboken, NJ: John Wiley & Son.
    • (2003) Curr. Protoc. Bioinform
    • Wilgenbusch, J.C.1    Swofford, D.2
  • 59
    • 33845903592 scopus 로고    scopus 로고
    • Revisiting the molecular evolutionary history of Shigella spp
    • doi:10.1007/s00239-006-0052-8
    • Yang, J., Nie, H., Chen, L., Zhang, X., Yang, F., Xu, X., Zhu, Y., Yu, J. & Jin, Q. 2007 Revisiting the molecular evolutionary history of Shigella spp. J. Mol. Evol. 64, 71 -79. (doi:10.1007/s00239-006-0052-8)
    • (2007) J. Mol. Evol , vol.64 , pp. 71-79
    • Yang, J.1    Nie, H.2    Chen, L.3    Zhang, X.4    Yang, F.5    Xu, X.6    Zhu, Y.7    Yu, J.8    Jin, Q.9


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