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Volumn 25, Issue 11, 2008, Pages 2319-2329

Estimation of phylogenetic inconsistencies in the three domains of life

Author keywords

Archaea; Eukaryotes; Lateral gene transfer; Orthology; Phylogenetic methodology; Proteobacteria

Indexed keywords

PROTEOME;

EID: 54149095437     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn176     Document Type: Article
Times cited : (17)

References (52)
  • 2
    • 21144441817 scopus 로고    scopus 로고
    • Lateral gene transfer in eukaryotes
    • Andersson JO. 2005. Lateral gene transfer in eukaryotes. Cell Mol Life Sci. 62:1182-1197.
    • (2005) Cell Mol Life Sci , vol.62 , pp. 1182-1197
    • Andersson, J.O.1
  • 4
    • 33645568886 scopus 로고    scopus 로고
    • Phylogenetic identification of lateral genetic transfer events
    • Beiko RG, 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
  • 9
    • 33749572917 scopus 로고    scopus 로고
    • Exploring the relationship between sequence similarity and accurate phylogenetic trees
    • Cantarel BL, Morrison HG, Pearson W. 2006. Exploring the relationship between sequence similarity and accurate phylogenetic trees. Mol Biol Evol. 23:2090-2100.
    • (2006) Mol Biol Evol , vol.23 , pp. 2090-2100
    • Cantarel, B.L.1    Morrison, H.G.2    Pearson, W.3
  • 10
    • 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
  • 11
    • 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
  • 12
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen F, Mackey AJ, Vermunt JK, Roos DS. 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE. 2:e383.
    • (2007) PLoS ONE , vol.2
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 14
    • 0035222174 scopus 로고    scopus 로고
    • Nucleotide substitutions and the evolution of duplicate genes
    • Conery JS, Lynch M. 2001. Nucleotide substitutions and the evolution of duplicate genes. Pac Symp Biocomput. 6:167-178.
    • (2001) Pac Symp Biocomput , vol.6 , pp. 167-178
    • Conery, J.S.1    Lynch, M.2
  • 15
    • 0036061865 scopus 로고    scopus 로고
    • A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
    • Daubin V, Gouy M, Perriere G. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12:1080-1090.
    • (2002) Genome Res , vol.12 , pp. 1080-1090
    • Daubin, V.1    Gouy, M.2    Perriere, G.3
  • 16
    • 0034894278 scopus 로고    scopus 로고
    • PAL: An object-oriented programming library for molecular evolution and phylogenetics
    • Drummond A, Strimmer K. 2001. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics. 17:662-663.
    • (2001) Bioinformatics , vol.17 , pp. 662-663
    • Drummond, A.1    Strimmer, K.2
  • 17
    • 42149157760 scopus 로고    scopus 로고
    • Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
    • Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452:745-749.
  • 18
    • 26444580130 scopus 로고    scopus 로고
    • The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    • Ge F, Wang LS, 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
  • 19
    • 0033752775 scopus 로고    scopus 로고
    • About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal
    • Glansdorff N. 2000. About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol Microbiol. 38:177-185.
    • (2000) Mol Microbiol , vol.38 , pp. 177-185
    • Glansdorff, N.1
  • 21
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 22
    • 13444251422 scopus 로고    scopus 로고
    • Hubbard T, Andrews D, Caccamo M, et al. (52 co-authors). 2005. Ensembl 2005. Nucleic Acids Res. 33:D447-D453.
    • Hubbard T, Andrews D, Caccamo M, et al. (52 co-authors). 2005. Ensembl 2005. Nucleic Acids Res. 33:D447-D453.
  • 24
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 25
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 27
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: Quantification and classification
    • Koonin EV, Makarova KS, Aravind L. 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
  • 28
    • 22244450083 scopus 로고    scopus 로고
    • The net of life: Reconstructing the microbial phylogenetic network
    • Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. 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
  • 29
    • 23044437168 scopus 로고    scopus 로고
    • What tangled web: Barriers to rampant horizontal gene transfer
    • Kurland CG. 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
  • 31
    • 21844434913 scopus 로고    scopus 로고
    • Evolutionary origins of genomic repertoires in bacteria
    • Lerat E, Daubin V, Ochman H, Moran NA. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:e130.
    • (2005) PLoS Biol , vol.3
    • Lerat, E.1    Daubin, V.2    Ochman, H.3    Moran, N.A.4
  • 32
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • Lynch M, Conery JS. 2003. The origins of genome complexity. Science. 302:1401-1404.
    • (2003) Science , vol.302 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 33
    • 43049090907 scopus 로고    scopus 로고
    • The prokaryotic tree of life: Past, present. . . and future?
    • McInerney JO, Cotton JA, Pisani D. 2008. The prokaryotic tree of life: past, present. . . and future? Trends Ecol Evol. 23:276-281.
    • (2008) Trends Ecol Evol , vol.23 , pp. 276-281
    • McInerney, J.O.1    Cotton, J.A.2    Pisani, D.3
  • 34
    • 2942622384 scopus 로고    scopus 로고
    • Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
    • Mirkin BG, Fenner TI, Galperin MY, Koonin EV. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol. 3:2.
    • (2003) BMC Evol Biol , vol.3 , pp. 2
    • Mirkin, B.G.1    Fenner, T.I.2    Galperin, M.Y.3    Koonin, E.V.4
  • 35
    • 0031737821 scopus 로고    scopus 로고
    • How good are deep phylogenetic trees?
    • Philippe H, Laurent J. 1998. How good are deep phylogenetic trees? Curr Opin Genet Dev. 8:616-623.
    • (1998) Curr Opin Genet Dev , vol.8 , pp. 616-623
    • Philippe, H.1    Laurent, J.2
  • 36
    • 0036773016 scopus 로고    scopus 로고
    • GENIE: Estimating demographic history from molecular phylogenies
    • Pybus OG, Rambaut A. 2002. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics. 18:1404-1405.
    • (2002) Bioinformatics , vol.18 , pp. 1404-1405
    • Pybus, O.G.1    Rambaut, A.2
  • 37
    • 30344471824 scopus 로고    scopus 로고
    • Do different surrogate methods detect lateral genetic transfer events of different relative ages?
    • Ragan MA, Harlow TJ, Beiko RG. 2006. Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol. 14:4-8.
    • (2006) Trends Microbiol , vol.14 , pp. 4-8
    • Ragan, M.A.1    Harlow, T.J.2    Beiko, R.G.3
  • 38
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DF, Foulds LR. 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
  • 39
    • 29344441657 scopus 로고    scopus 로고
    • Animal evolution and the molecular signature of radiations compressed in time
    • Rokas A, Kruger D, Carroll SB. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science. 310:1933-1938.
    • (2005) Science , vol.310 , pp. 1933-1938
    • Rokas, A.1    Kruger, D.2    Carroll, S.B.3
  • 40
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 41
    • 0030773749 scopus 로고    scopus 로고
    • A nonparametric approach to estimating divergence times in the absence of rate constancy
    • Sanderson MJ. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol. 14:1218-1231.
    • (1997) Mol Biol Evol , vol.14 , pp. 1218-1231
    • Sanderson, M.J.1
  • 42
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • Sanderson MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 19:101-109.
    • (2002) Mol Biol Evol , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 43
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492-508.
    • (2002) Syst Biol , vol.51 , pp. 492-508
    • Shimodaira, H.1
  • 44
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 17:1246-1247.
    • (2001) Bioinformatics , vol.17 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 45
    • 27144493223 scopus 로고    scopus 로고
    • Genome trees and the nature of genome evolution
    • Snel B, Huynen MA, Dutilh BE. 2005. Genome trees and the nature of genome evolution. Annu Rev Microbiol. 59:191-209.
    • (2005) Annu Rev Microbiol , vol.59 , pp. 191-209
    • Snel, B.1    Huynen, M.A.2    Dutilh, B.E.3
  • 46
    • 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, 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
  • 48
    • 18644368714 scopus 로고    scopus 로고
    • Stajich JE, Block D, Boulez K, et al. (21 co-authors). 2002. The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12:1611-1618.
    • Stajich JE, Block D, Boulez K, et al. (21 co-authors). 2002. The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12:1611-1618.
  • 49
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye J, Evers D, Meyer F. 1998. Rose: generating sequence families. Bioinformatics. 14:157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 50
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • Strimmer K, von Haeseler A. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol. 13:964-969.
    • (1996) Mol Biol Evol , vol.13 , pp. 964-969
    • Strimmer, K.1    von Haeseler, A.2
  • 51
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577.
    • (2007) Syst Biol , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 52
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2


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