메뉴 건너뛰기




Volumn 856, Issue , 2012, Pages 53-79

Genome-wide comparative analysis of phylogenetic trees: The prokaryotic forest of life

Author keywords

Forest of life; Map of quartets; Phylogenomic methods; Tree comparison; Tree of life

Indexed keywords

ALGORITHM; ARCHAEON; ARTICLE; BACTERIUM; COMPARATIVE STUDY; GENETICS; GENOMICS; HORIZONTAL GENE TRANSFER; METHODOLOGY; PHYLOGENY;

EID: 84860121370     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-585-5_3     Document Type: Article
Times cited : (11)

References (80)
  • 2
    • 38549137819 scopus 로고    scopus 로고
    • PhylomeDB: A database for genome-wide collections of gene phylogenies
    • Huerta-Cepas, J., Bueno, A., Dopazo, J., and Gabaldon, T. (2008) PhylomeDB: A database for genome-wide collections of gene phylogenies. Nucleic Acids Res 36, D491-496.
    • (2008) Nucleic. Acids Res. , vol.36
    • Huerta-Cepas, J.1    Bueno, A.2    Dopazo, J.3    Gabaldon, T.4
  • 3
    • 4944233611 scopus 로고    scopus 로고
    • Phylo-Genie: Automated phylome generation and analysis
    • Frickey, T., and Lupas, A. N. (2004) Phylo-Genie: Automated phylome generation and analysis. Nucleic Acids Res 32, 5231-5238.
    • (2004) Nucleic. Acids Res. , vol.32 , pp. 5231-5238
    • Frickey, T.1    Lupas, A.N.2
  • 5
    • 68149093715 scopus 로고    scopus 로고
    • Search for a Tree of Life in the thicket of the phylogenetic forest
    • Puigbo, P., Wolf, Y. I., and Koonin, E. V. (2009) Search for a Tree of Life in the thicket of the phylogenetic forest. J Biol 8, 59.
    • (2009) J. Biol. , vol.8 , pp. 59
    • Puigbo, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 8
    • 36448969030 scopus 로고    scopus 로고
    • Topological variation in single-gene phylogenetic trees
    • Castresana, J. (2007) Topological variation in single-gene phylogenetic trees. Genome Biol 8, 216.
    • (2007) Genome Biol. , vol.8 , pp. 216
    • Castresana, J.1
  • 9
    • 54149095437 scopus 로고    scopus 로고
    • Estimation of phylogenetic inconsistencies in the three domains of life
    • Soria-Carrasco, V., and Castresana, J. (2008) Estimation of phylogenetic inconsistencies in the three domains of life. Mol Biol Evol 25, 2319-2329.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2319-2329
    • Soria-Carrasco, V.1    Castresana, J.2
  • 10
    • 84857229990 scopus 로고    scopus 로고
    • The tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome
    • Marcet-Houben, M., and Gabaldon, T. (2009) The tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome. PLoS ONE 4, e4357.
    • (2009) PLoS ONE , vol.4
    • Marcet-Houben, M.1    Gabaldon, T.2
  • 11
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D. F., and Foulds, L. R. (1981) Comparison of phylogenetic trees. Math Biosci 53, 131-147.
    • (1981) Math Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 12
    • 34547844062 scopus 로고    scopus 로고
    • TOPD/FMTS: A new software to compare phylogenetic trees
    • Puigbo, P., Garcia-Vallve, S., and McInerney, J. O. (2007) TOPD/FMTS: A new software to compare phylogenetic trees. Bioinformatics 23, 1556-1558.
    • (2007) Bioinformatics , vol.23 , pp. 1556-1558
    • Puigbo, P.1    Garcia-Vallve, S.2    McInerney, J.O.3
  • 13
    • 12044252586 scopus 로고
    • Distribution of tree comparison metrics -some new results
    • Steel, M. A., and Penny, D. (1993) Distribution of tree comparison metrics -some new results. Systematic Biol 42, 126-141.
    • (1993) Systematic Biol. , vol.42 , pp. 126-141
    • Steel, M.A.1    Penny, D.2
  • 16
    • 84959752542 scopus 로고
    • Comparison of undirected phylogenetic trees based on subtree of four evolutionary units
    • Estabrook, G. F., McMorris, F. R., and Meachan, A. (1985) Comparison of undirected phylogenetic trees based on subtree of four evolutionary units. Syst Zool 34, 193-200.
    • (1985) Syst. Zool , vol.34 , pp. 193-200
    • Estabrook, G.F.1    McMorris, F.R.2    Meachan, A.3
  • 18
    • 0018117949 scopus 로고
    • On the similarity of dendrograms
    • Waterman, M. S., and Steel, M. (1978) On the similarity of dendrograms. J Theor Biol 73, 789-800.
    • (1978) J. Theor. Biol. , vol.73 , pp. 789-800
    • Waterman, M.S.1    Steel, M.2
  • 19
    • 33645568886 scopus 로고    scopus 로고
    • Phylogenetic identification of lateral genetic transfer events
    • Beiko, R. G., and Hamilton, N. (2006) Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol 6, 15.
    • (2006) BMC Evol. Biol , vol.6 , pp. 15
    • Beiko, R.G.1    Hamilton, N.2
  • 22
    • 30344473638 scopus 로고    scopus 로고
    • A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
    • Nye, T. M., Lio, P., and Gilks, W. R. (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22, 117-119.
    • (2006) Bioinformatics , vol.22 , pp. 117-119
    • Nye, T.M.1    Lio, P.2    Gilks, W.R.3
  • 23
    • 36549003111 scopus 로고    scopus 로고
    • A congruence index for testing topological similarity between trees
    • De Vienne, D. M., Giraud, T., and Martin, O. C. (2007) A congruence index for testing topological similarity between trees. Bioinformatics 23, 3119-3124.
    • (2007) Bioinformatics , vol.23 , pp. 3119-3124
    • De Vienne, D.M.1    Giraud, T.2    Martin, O.C.3
  • 24
    • 0037036630 scopus 로고    scopus 로고
    • Going nuclear: Gene family evolution and vertebrate phylogeny reconciled
    • Cotton, J. A., and Page, R. D. (2002) Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc Biol Sci 269, 1555-1561.
    • (2002) Proc. Biol. Sci. , vol.269 , pp. 1555-1561
    • Cotton, J.A.1    Page, R.D.2
  • 25
    • 36448956752 scopus 로고    scopus 로고
    • The K tree score: Quantification of differences in the relative branch length and topology of phylogenetic trees
    • Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007) The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23, 2954-2956.
    • (2007) Bioinformatics , vol.23 , pp. 2954-2956
    • Soria-Carrasco, V.1    Talavera, G.2    Igea, J.3    Castresana, J.4
  • 26
    • 79961206352 scopus 로고    scopus 로고
    • TreeKO: A duplication-aware algorithm for the comparison of phylogenetic trees
    • Marcet-Houben, M., and Gabaldon, T. (2011) TreeKO: A duplication-aware algorithm for the comparison of phylogenetic trees. Nucleic Acids Res 39, e66.
    • (2011) Nucleic. Acids Res. , vol.39
    • Marcet-Houben, M.1    Gabaldon, T.2
  • 27
    • 77957728668 scopus 로고    scopus 로고
    • The phylogenetic forest and the quest for the elusive tree of life
    • Koonin, E. V., Wolf, Y. I., and Puigbo, P. (2009) The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harb Symp Quant Biol 74, 205-213.
    • (2009) Cold Spring Harb. Symp. Quant. Biol. , vol.74 , pp. 205-213
    • Koonin, E.V.1    Wolf, Y.I.2    Puigbo, P.3
  • 28
    • 0002331493 scopus 로고
    • Horizons in Biochemistry. Edited by Kasha M, B. P. New York Academic Press;
    • Zuckerkandl, E., and Pauling, L. (1962) Molecular evolution. In: Horizons in Biochemistry. Edited by Kasha M, B. P. New York: Academic Press; 189-225.
    • (1962) Molecular Evolution , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2
  • 29
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese, C. R. (1987) Bacterial evolution. Microbiol Rev 51, 221-271.
    • (1987) Microbiol. Rev , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 31
    • 0034132468 scopus 로고    scopus 로고
    • Uprooting the tree of life
    • Doolittle, W. F. (2000) Uprooting the tree of life. Sci Am 282, 90-95.
    • (2000) Sci. Am. , vol.282 , pp. 90-95
    • Doolittle, W.F.1
  • 32
    • 33847790997 scopus 로고    scopus 로고
    • Pattern pluralism and the tree of life hypothesis
    • Doolittle, W. F., and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A 104, 2043-2049.
    • (2007) Proc. Natl. Acad. Sci. U S A , vol.104 , pp. 2043-2049
    • Doolittle, W.F.1    Bapteste, E.2
  • 34
    • 23044437168 scopus 로고    scopus 로고
    • What tangled web: Barriers to rampant horizontal gene transfer
    • Kurland, C. G. (2005) What tangled web: barriers to rampant horizontal gene transfer. Bioessays 27, 741-747.
    • (2005) Bioessays , vol.27 , pp. 741-747
    • Kurland, C.G.1
  • 35
    • 0033533618 scopus 로고    scopus 로고
    • Thermotoga heats up lateral gene transfer
    • Logsdon, J. M., and Faguy, D. M. (1999) Thermotoga heats up lateral gene transfer. Curr Biol 9, R747-751.
    • (1999) Curr. Biol. , vol.9
    • Logsdon, J.M.1    Faguy, D.M.2
  • 36
    • 0037383272 scopus 로고    scopus 로고
    • Much ado about bacteria-to-vertebrate lateral gene transfer
    • Genereux, D. P., and Logsdon, J.M., Jr. (2003) Much ado about bacteria-to-vertebrate lateral gene transfer. Trends Genet 19, 191-195.
    • (2003) Trends Genet , vol.19 , pp. 191-195
    • Genereux, D.P.1    Logsdon Jr., J.M.2
  • 37
    • 22244450083 scopus 로고    scopus 로고
    • The net of life: Reconstructing the microbial phylogenetic network
    • Kunin, V., Goldovsky, L., Darzentas, N., and Ouzounis, C. A. (2005) The net of life: reconstructing the microbial phylogenetic network. Genome Res 15, 954-959.
    • (2005) Genome Res. , vol.15 , pp. 954-959
    • Kunin, V.1    Goldovsky, L.2    Darzentas, N.3    Ouzounis, C.A.4
  • 38
    • 0042027842 scopus 로고    scopus 로고
    • Phylogenetics and the cohesion of bacterial genomes
    • Daubin, V., Moran, N. A., and Ochman, H. (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    Ochman, H.3
  • 39
    • 1342271382 scopus 로고    scopus 로고
    • From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria
    • Lerat, E., Daubin, V., and Moran, N. A. (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
  • 40
    • 0034053846 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
    • Woese, C. R., Olsen, G. J., Ibba, M., and Soll, D. (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
  • 41
    • 0033231209 scopus 로고    scopus 로고
    • Whole genome-based phylogenetic analysis of free-living microorganisms
    • Fitz-Gibbon, S. T., and House, C. H. (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27, 4218-4222.
    • (1999) Nucleic. Acids Res. , vol.27 , pp. 4218-4222
    • Fitz-Gibbon, S.T.1    House, C.H.2
  • 43
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • Eisen, J. A., and Fraser, C. M. (2003) Phylogenomics: intersection of evolution and genomics. Science 300, 1706-1707.
    • (2003) Science , vol.300 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 44
    • 0035827328 scopus 로고    scopus 로고
    • Microbial genes in the human genome: Lateral transfer or gene loss?
    • Salzberg, S. L., White, O., Peterson, J., and Eisen, J. A. (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292, 1903-1906.
    • (2001) Science , vol.292 , pp. 1903-1906
    • Salzberg, S.L.1    White, O.2    Peterson, J.3    Eisen, J.A.4
  • 45
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier, N. (2007) A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol 56, 633-642.
    • (2007) Syst. Biol. , vol.56 , pp. 633-642
    • Galtier, N.1
  • 48
    • 34248396432 scopus 로고    scopus 로고
    • Global extent of horizontal gene transfer
    • Choi, I. G., and Kim, S. H. (2007) Global extent of horizontal gene transfer. Proc Natl Acad Sci U S A 104, 4489-4494.
    • (2007) Proc. Natl. Acad. Sci. U S A , vol.104 , pp. 4489-4494
    • Choi, I.G.1    Kim, S.H.2
  • 50
    • 67651008667 scopus 로고    scopus 로고
    • Getting a better picture of microbial evolution en route to a network of genomes
    • Dagan, T., and Martin, W. (2009) Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci 364, 2187-2196.
    • (2009) Philos. Trans. R Soc. Lond. B Biol. Sci , vol.364 , pp. 2187-2196
    • Dagan, T.1    Martin, W.2
  • 53
    • 79952835117 scopus 로고    scopus 로고
    • Harvesting evolutionary signals in a forest of prokaryotic gene trees
    • Schliep, K., Lopez, P., Lapointe, F. J., and Bapteste, E. (2011) Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol 28, 1393-1405.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 1393-1405
    • Schliep, K.1    Lopez, P.2    Lapointe, F.J.3    Bapteste, E.4
  • 54
    • 58149231047 scopus 로고    scopus 로고
    • The impact of reticulate evolution on genome phylogeny
    • Beiko, R. G., Doolittle, W. F., and Charlebois, R. L. (2008) The impact of reticulate evolution on genome phylogeny. Syst Biol 57, 844-856.
    • (2008) Syst. Biol. , vol.57 , pp. 844-856
    • Beiko, R.G.1    Doolittle, W.F.2    Charlebois, R.L.3
  • 55
    • 66049089612 scopus 로고    scopus 로고
    • On the origin of prokaryotic species
    • Doolittle, W. F., and Zhaxybayeva, O. (2009) On the origin of prokaryotic species. Genome Res 19, 744-756.
    • (2009) Genome. Res. , vol.19 , pp. 744-756
    • Doolittle, W.F.1    Zhaxybayeva, O.2
  • 56
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • Gogarten, J. P., and Townsend, J. P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3, 679-687.
    • (2005) Nat. Rev. Microbiol , vol.3 , pp. 679-687
    • Gogarten, J.P.1    Townsend, J.P.2
  • 58
    • 79952201675 scopus 로고    scopus 로고
    • The tree and net components of prokaryote evolution
    • Puigbo, P., Wolf, Y. I., and Koonin, E. V. (2010) The tree and net components of prokaryote evolution. Genome Biol Evol 2, 745-756.
    • (2010) Genome. Biol. Evol. , vol.2 , pp. 745-756
    • Puigbo, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 61
    • 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 Res 32, 1792-1797.
    • (2004) Nucleic. Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 62
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 63
    • 34547583680 scopus 로고    scopus 로고
    • MultiPhyl: A high-throughput phylogenomics webserver using distributed computing
    • Keane, T. M., Naughton, T. J., and McInerney, J. O. (2007) MultiPhyl: A high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Res 35, W33-37.
    • (2007) Nucleic. Acids Res. , vol.35
    • Keane, T.M.1    Naughton, T.J.2    McInerney, J.O.3
  • 64
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • Creevey, C. J., and McInerney, J. O. (2005) Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21, 390-392.
    • (2005) Bioinformatics , vol.21 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 65
    • 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
  • 67
    • 0000071395 scopus 로고
    • Some distance properties of latent root and vector methods used in multivariate analysis
    • Gower, J. C. (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53, 325-328.
    • (1966) Biometrika , vol.53 , pp. 325-328
    • Gower, J.C.1
  • 69
    • 22844442543 scopus 로고    scopus 로고
    • Analysis and visualization of tree space
    • Hillis, D. M., Heath, T. A., and St John, K. (2005) Analysis and visualization of tree space. Syst Biol 54, 471-482.
    • (2005) Syst. Biol. , vol.54 , pp. 471-482
    • Hillis, D.M.1    Heath, T.A.2    St John, K.3
  • 70
    • 0037314097 scopus 로고    scopus 로고
    • Matrix2png: A utility for visualizing matrix data
    • Pavlidis, P., and Noble, W. S. (2003) Matrix2png: A utility for visualizing matrix data. Bioinformatics 19, 295-296.
    • (2003) Bioinformatics , vol.19 , pp. 295-296
    • Pavlidis, P.1    Noble, W.S.2
  • 71
    • 57149085868 scopus 로고    scopus 로고
    • Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world
    • Koonin, E. V., and Wolf, Y. I. (2008) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36, 6688-6719.
    • (2008) Nucleic. Acids Res. , vol.36 , pp. 6688-6719
    • Koonin, E.V.1    Wolf, Y.I.2
  • 72
    • 26444580130 scopus 로고    scopus 로고
    • The cobweb of life revealed by genome-scale Estimates of horizontal gene transfer
    • Ge, F., Wang, L. S., and Kim, J. (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3, e316.
    • (2005) PLoS Biol. , vol.3
    • Ge, F.1    Wang, L.S.2    Kim, J.3
  • 73
    • 0036137155 scopus 로고    scopus 로고
    • Eubacterial phylogeny based on translational apparatus proteins
    • Brochier, C., Bapteste, E., Moreira, D., and Philippe, H. (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
  • 77
    • 39149118031 scopus 로고    scopus 로고
    • Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota
    • Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6, 245-252.
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 245-252
    • Brochier-Armanet, C.1    Boussau, B.2    Gribaldo, S.3    Forterre, P.4
  • 79
    • 0032830481 scopus 로고    scopus 로고
    • Evolution of aminoacyltrna synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    • Wolf, Y. I., Aravind, L., Grishin, N. V., and Koonin, E. V. (1999) Evolution of aminoacyltRNA 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
  • 80
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics, minimal gene-sets and the last universal common ancestor
    • Koonin, E. V. (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Rev Microbiol 1, 127-136.
    • (2003) Nature. Rev. Microbiol. , vol.1 , pp. 127-136
    • Koonin, E.V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.