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Volumn 54, Issue 5, 2005, Pages 743-757

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics

Author keywords

Distant outgroup; Eukaryotic tree; Long branch attraction; Microsporidia; Multigene data sets; Nucleomorph; Rooting; Species sampling; Systematic biases

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; EPIDEMIOLOGY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PROTOZOON; SAMPLE SIZE; STATISTICAL MODEL;

EID: 27744524191     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150500234609     Document Type: Article
Times cited : (198)

References (109)
  • 1
    • 0030207565 scopus 로고    scopus 로고
    • Instability of quartet analyses of molecular sequence data by the maximum likelihood method: The Cetacea/Artiodactyla relationships
    • Adachi, J., and M. Hasegawa. 1996a. Instability of quartet analyses of molecular sequence data by the maximum likelihood method: The Cetacea/Artiodactyla relationships. Mol. Phylogenet. Evol. 6:72-76.
    • (1996) Mol. Phylogenet. Evol. , vol.6 , pp. 72-76
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 0002367729 scopus 로고    scopus 로고
    • MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
    • Adachi, J., and M. Hasegawa. 1996b. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
    • (1996) Comput. Sci. Monogr. , vol.28 , pp. 1-150
    • Adachi, J.1    Hasegawa, M.2
  • 4
    • 0000501656 scopus 로고
    • Information theory and an extension of the maximum likelihood principle
    • (B. N. Petrov and F. Csaki, eds.). Akademia Kiado, Budapest
    • Akaike, H. 1973. Information theory and an extension of the maximum likelihood principle. Pages 267-281 in Proceedings 2nd International Symposium on Information Theory (B. N. Petrov and F. Csaki, eds.). Akademia Kiado, Budapest.
    • (1973) Proceedings 2nd International Symposium on Information Theory , pp. 267-281
    • Akaike, H.1
  • 5
    • 4444220955 scopus 로고    scopus 로고
    • Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
    • Anderson, F. E., and D. L. Swofford. 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 33:440-451.
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 440-451
    • Anderson, F.E.1    Swofford, D.L.2
  • 6
    • 0034602344 scopus 로고    scopus 로고
    • A kingdom-level phylogeny of eukaryotes based on combined protein data
    • Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
    • (2000) Science , vol.290 , pp. 972-977
    • Baldauf, S.L.1    Roger, A.J.2    Wenk-Siefert, I.3    Doolittle, W.F.4
  • 9
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
    • Brinkmann, H., and H. Philippe. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:817-825.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 817-825
    • Brinkmann, H.1    Philippe, H.2
  • 10
    • 0037118037 scopus 로고    scopus 로고
    • Phylogeny: A non-hyperthermophilic ancestor for bacteria
    • Brochier, C., and H. Philippe. 2002. Phylogeny: A non-hyperthermophilic ancestor for bacteria. Nature 417:244.
    • (2002) Nature , vol.417 , pp. 244
    • Brochier, C.1    Philippe, H.2
  • 11
    • 0033921801 scopus 로고    scopus 로고
    • The power of relative rates tests depends on the data
    • Bromham, L., D. Penny, A. Rambaut, and M. D. Hendy. 2000. The power of relative rates tests depends on the data. J. Mol. Evol. 50:296-301.
    • (2000) J. Mol. Evol. , vol.50 , pp. 296-301
    • Bromham, L.1    Penny, D.2    Rambaut, A.3    Hendy, M.D.4
  • 12
    • 0037444274 scopus 로고    scopus 로고
    • Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences
    • Bullerwell, C. E., L. Forget, and B. F. Lang. 2003. Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic. Acids Res. 31:1614-1623.
    • (2003) Nucleic. Acids Res. , vol.31 , pp. 1614-1623
    • Bullerwell, C.E.1    Forget, L.2    Lang, B.F.3
  • 13
    • 10644238478 scopus 로고    scopus 로고
    • Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life
    • Burleigh, J. G., and S. Mathews. 2004. Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life. Am. J. Bot. 91:1599-1613.
    • (2004) Am. J. Bot. , vol.91 , pp. 1599-1613
    • Burleigh, J.G.1    Mathews, S.2
  • 15
    • 0037359055 scopus 로고    scopus 로고
    • Systematics of primary osmotrophic euglenids: A molecular approach to the phylogeny of Distigma and Astasia (Euglenozoa)
    • Busse, I., and A. Preisfeld. 2003. Systematics of primary osmotrophic euglenids: A molecular approach to the phylogeny of Distigma and Astasia (Euglenozoa). Int. J. Syst. Evol. Microbiol. 53:617-624.
    • (2003) Int. J. Syst. Evol. Microbiol. , vol.53 , pp. 617-624
    • Busse, I.1    Preisfeld, A.2
  • 16
    • 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
  • 17
    • 0034177573 scopus 로고    scopus 로고
    • Membrane heredity and early chloroplast evolution
    • Cavalier-Smith, T. 2000. Membrane heredity and early chloroplast evolution. Trends Plant. Sci. 5:174-182.
    • (2000) Trends Plant. Sci. , vol.5 , pp. 174-182
    • Cavalier-Smith, T.1
  • 18
    • 0036269480 scopus 로고    scopus 로고
    • Analyses of RNA Polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang
    • Dacks, J. B., A. Marinets, W. Doolittle, T. Cavalier-Smith, and J. M. Logsdon, Jr. 2002. Analyses of RNA Polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang. Mol. Biol. Evol. 19:830-840.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 830-840
    • Dacks, J.B.1    Marinets, A.2    Doolittle, W.3    Cavalier-Smith, T.4    Logsdon Jr., J.M.5
  • 20
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the Tree of Life: Methods, advances, and challenges
    • Delsuc, F., H. Brinkmann, and H. Philippe. 2005. Phylogenomics and the reconstruction of the Tree of Life: Methods, advances, and challenges. Nat. Rev. Genet. 6:361-375.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 22
    • 7444237566 scopus 로고    scopus 로고
    • The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
    • USA
    • Douzery, E. J., E. A. Snell, E. Bapteste, F. Delsuc, and H. Philippe. 2004. The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc. Natl. Acad. Sci. USA 101:15386-15391.
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , pp. 15386-15391
    • Douzery, E.J.1    Snell, E.A.2    Bapteste, E.3    Delsuc, F.4    Philippe, H.5
  • 24
    • 0035103466 scopus 로고    scopus 로고
    • Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids
    • Fast, N. M., J. C. Kissinger, D. S. Roos, and P. J. Keeling. 2001. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 18:418-426.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 418-426
    • Fast, N.M.1    Kissinger, J.C.2    Roos, D.S.3    Keeling, P.J.4
  • 25
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 26
    • 0003991673 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland, Massachusetts
    • Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
    • (2004) Inferring Phylogenies
    • Felsenstein, J.1
  • 27
    • 0033214077 scopus 로고    scopus 로고
    • Where is the root of the universal tree of life?
    • Forterre, P., and H. Philippe. 1999. Where is the root of the universal tree of life? BioEssays 21:871-879.
    • (1999) BioEssays , vol.21 , pp. 871-879
    • Forterre, P.1    Philippe, H.2
  • 28
    • 0033004743 scopus 로고    scopus 로고
    • Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
    • Foster, P. G., and D. A. Hickey. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290.
    • (1999) J. Mol. Evol. , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 29
    • 0035029534 scopus 로고    scopus 로고
    • Maximum-likelihood phylogenetic analysis under a covarion-like model
    • Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866-873.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 866-873
    • Galtier, N.1
  • 30
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel, O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 31
    • 0030844640 scopus 로고    scopus 로고
    • Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae
    • Germot, A., H. Philippe, and H. Le Guyader. 1997. Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol. Biochem. Parasitol. 87:159-168.
    • (1997) Mol. Biochem. Parasitol. , vol.87 , pp. 159-168
    • Germot, A.1    Philippe, H.2    Le Guyader, H.3
  • 32
    • 0019485803 scopus 로고
    • The chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae
    • Gibbs, S. P. 1981. The chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae. Ann NY Acad. Sci. 361:193-208.
    • (1981) Ann. NY Acad. Sci. , vol.361 , pp. 193-208
    • Gibbs, S.P.1
  • 33
    • 0030670413 scopus 로고    scopus 로고
    • PSeq-Gen: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
    • Grassly, N. C., J. Adachi, and A. Rambaut. 1997. PSeq-Gen: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:559-560.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 559-560
    • Grassly, N.C.1    Adachi, J.2    Rambaut, A.3
  • 34
    • 0028350365 scopus 로고
    • Molecular evidence for the inclusion of cetaceans within the order Artiodactyla
    • Graur, D., and D. G. Higgins. 1994. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Mol. Biol. Evol. 11:357-364.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 357-364
    • Graur, D.1    Higgins, D.G.2
  • 35
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 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
  • 36
    • 3843141789 scopus 로고    scopus 로고
    • Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree
    • Hampl, V., I. Cepicka, J. Flegr, J. Tachezy, and J. Kulda. 2004. Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree. Mol. Phylogenet. Evol. 32:711-723.
    • (2004) Mol. Phylogenet. Evol. , vol.32 , pp. 711-723
    • Hampl, V.1    Cepicka, I.2    Flegr, J.3    Tachezy, J.4    Kulda, J.5
  • 37
    • 0027565033 scopus 로고
    • Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny
    • Hasegawa, M., and M. Fujiwara. 1993. Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phylogenet. Evol. 2:1-5.
    • (1993) Mol. Phylogenet. Evol. , vol.2 , pp. 1-5
    • Hasegawa, M.1    Fujiwara, M.2
  • 38
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy, M., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
    • (1989) Syst. Zool. , vol.38 , pp. 297-309
    • Hendy, M.1    Penny, D.2
  • 39
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference?
    • Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
    • (2003) Syst. Biol. , vol.52 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.D.2    McGuire, J.A.3    Zwickl, D.J.4
  • 40
    • 0031084114 scopus 로고    scopus 로고
    • Is the Felsenstein zone a fly trap?
    • Huelsenbeck, J. P. 1997. Is the Felsenstein zone a fly trap? Syst. Biol. 46:69-74.
    • (1997) Syst. Biol. , vol.46 , pp. 69-74
    • Huelsenbeck, J.P.1
  • 41
    • 0032148641 scopus 로고    scopus 로고
    • Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
    • Huelsenbeck, J. P. 1998. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
    • (1998) Syst. Biol. , vol.47 , pp. 519-537
    • Huelsenbeck, J.P.1
  • 42
    • 0036097894 scopus 로고    scopus 로고
    • Testing a covariotide model of DNA substitution
    • Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 698-707
    • Huelsenbeck, J.P.1
  • 43
    • 3042601821 scopus 로고    scopus 로고
    • Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 α phylogenies
    • Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 α phylogenies. Mol. Biol. Evol. 21:1340-1349.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1340-1349
    • Inagaki, Y.1    Susko, E.2    Fast, N.M.3    Roger, A.J.4
  • 44
    • 0034120954 scopus 로고    scopus 로고
    • Molecular phylogenetics of the Chytridiomycota support the utility of ultrastructural data in chytrid systematics
    • James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota support the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78:336-350.
    • (2000) Can. J. Bot. , vol.78 , pp. 336-350
    • James, T.Y.1    Porter, D.2    Leander, C.A.3    Vilgalys, R.4    Longcore, J.E.5
  • 45
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D. T., W. R. Taylor, and J. M. Thornton. 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
  • 47
    • 0037384263 scopus 로고    scopus 로고
    • Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia
    • Keeling, P. J. 2003. Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol. 38:298-309.
    • (2003) Fungal Genet. Biol. , vol.38 , pp. 298-309
    • Keeling, P.J.1
  • 48
    • 0036406924 scopus 로고    scopus 로고
    • Microsporidia: Biology and evolution of highly reduced intracellular parasites
    • Keeling, P. J., and N. M. Fast. 2002. Microsporidia: Biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol. 56:93-116.
    • (2002) Annu. Rev. Microbiol. , vol.56 , pp. 93-116
    • Keeling, P.J.1    Fast, N.M.2
  • 49
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • Kim, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
    • (1996) Syst. Biol. , vol.45 , pp. 363-374
    • Kim, J.1
  • 50
    • 0037962406 scopus 로고    scopus 로고
    • Evolution of key cell signaling and adhesion protein families predates animal origins
    • King, N., C. T. Hittinger, and S. B. Carroll. 2003. Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301:361-336.
    • (2003) Science , vol.301 , pp. 361-1336
    • King, N.1    Hittinger, C.T.2    Carroll, S.B.3
  • 51
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts
    • Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
    • (1990) J. Mol. Evol. , vol.31 , pp. 151-160
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 52
    • 7244221755 scopus 로고    scopus 로고
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    • Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
    • (2004) Nature , vol.431 , pp. 980-984
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 53
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner, M. K., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 54
    • 0028203243 scopus 로고
    • Was the nucleus the first endosymbiont?
    • USA
    • Lake, J. A., and M. C. Rivera. 1994. Was the nucleus the first endosymbiont? Proc. Natl. Acad. Sci. USA 91:2880-2881.
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 2880-2881
    • Lake, J.A.1    Rivera, M.C.2
  • 56
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot, N., and H. Philippe. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21:1095-1109.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 58
    • 1342271382 scopus 로고    scopus 로고
    • From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria
    • Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria. PLoS Biol. 1:E19.
    • (2003) PLoS Biol. , vol.1
    • Lerat, E.1    Daubin, V.2    Moran, N.A.3
  • 59
    • 0029935637 scopus 로고    scopus 로고
    • Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
    • USA
    • Lockhart, P. J., A. W. Larkum, M. Steel, P. J. Waddell, and D. Penny. 1996. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:1930-1934.
    • (1996) Proc. Natl. Acad. Sci. , vol.93 , pp. 1930-1934
    • Lockhart, P.J.1    Larkum, A.W.2    Steel, M.3    Waddell, P.J.4    Penny, D.5
  • 60
    • 0345299175 scopus 로고    scopus 로고
    • Metabolic symbiosis at the origin of eukaryotes
    • Lopez-Garcia, P., and D. Moreira. 1999. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem. Sci. 24:88-93.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 88-93
    • Lopez-Garcia, P.1    Moreira, D.2
  • 62
    • 2642689666 scopus 로고    scopus 로고
    • The hydrogen hypothesis for the first eukaryote
    • Martin, W., and M. Müller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
    • (1998) Nature , vol.392 , pp. 37-41
    • Martin, W.1    Müller, M.2
  • 64
    • 0037381973 scopus 로고    scopus 로고
    • The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids
    • Nozaki, H., M. Matsuzaki, M. Takahara, O. Misumi, H. Kuroiwa, M. Hasegawa, I. T. Shin, Y. Kohara, N. Ogasawara, and T. Kuroiwa. 2003. The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J. Mol. Evol. 56:485-497.
    • (2003) J. Mol. Evol. , vol.56 , pp. 485-497
    • Nozaki, H.1    Matsuzaki, M.2    Takahara, M.3    Misumi, O.4    Kuroiwa, H.5    Hasegawa, M.6    Shin, I.T.7    Kohara, Y.8    Ogasawara, N.9    Kuroiwa, T.10
  • 65
    • 4243140058 scopus 로고    scopus 로고
    • A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    • Pagel, M., and A. Meade. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53:571-581.
    • (2004) Syst. Biol. , vol.53 , pp. 571-581
    • Pagel, M.1    Meade, A.2
  • 66
    • 17744379783 scopus 로고    scopus 로고
    • The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa
    • Philip, G. K., C. J. Creevey, and J. O. McInerney. 2005. The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol. Biol. Evol. 22:1175-1184.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1175-1184
    • Philip, G.K.1    Creevey, C.J.2    McInerney, J.O.3
  • 67
    • 0031301965 scopus 로고    scopus 로고
    • Rodent monophyly: Pitfalls of molecular phylogenies
    • Philippe, H. 1997. Rodent monophyly: Pitfalls of molecular phylogenies. J. Mol. Evol. 45:712-715.
    • (1997) J. Mol. Evol. , vol.45 , pp. 712-715
    • Philippe, H.1
  • 68
    • 0000909802 scopus 로고
    • The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships
    • Philippe, H., and E. Douzery. 1994. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. J. Mamm. Evol. 2:133-152.
    • (1994) J. Mamm. Evol. , vol.2 , pp. 133-152
    • Philippe, H.1    Douzery, E.2
  • 69
    • 0034019771 scopus 로고    scopus 로고
    • Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
    • Philippe, H., and A. Germot. 2000. Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-834.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 830-834
    • Philippe, H.1    Germot, A.2
  • 71
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protostomia
    • Philippe, H., N. Lartillot, and H. Brinkmann. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protostomia. Mol. Biol. Evol. 22:1246-1253.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 72
    • 0031737821 scopus 로고    scopus 로고
    • How good are deep phylogenetic trees?
    • Philippe, H., and J. Laurent. 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
  • 75
    • 0028176239 scopus 로고
    • Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record
    • Philippe, H., U. Sörhannus, A. Baroin, R. Perasso, F. Gasse, and A. Adoutte. 1994. Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record. J. Evol. Biol. 7:247-265.
    • (1994) J. Evol. Biol. , vol.7 , pp. 247-265
    • Philippe, H.1    Sörhannus, U.2    Baroin, A.3    Perasso, R.4    Gasse, F.5    Adoutte, A.6
  • 76
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips, M. J., F. Delsuc, and D. Penny. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455-1458.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 77
    • 12444313041 scopus 로고    scopus 로고
    • Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda
    • Pisani, D. 2004. Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda. Syst. Biol. 53:978-989.
    • (2004) Syst. Biol. , vol.53 , pp. 978-989
    • Pisani, D.1
  • 78
    • 0038487279 scopus 로고    scopus 로고
    • Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods
    • Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol. 52:423-428.
    • (2003) Syst. Biol. , vol.52 , pp. 423-428
    • Poe, S.1
  • 79
    • 0033214195 scopus 로고    scopus 로고
    • Early evolution: Prokaryotes, the new kids on the block
    • Poole, A., D. Jeffares, and D. Penny. 1999. Early evolution: Prokaryotes, the new kids on the block. Bioessays 21:880-889.
    • (1999) Bioessays , vol.21 , pp. 880-889
    • Poole, A.1    Jeffares, D.2    Penny, D.3
  • 81
    • 0034889910 scopus 로고    scopus 로고
    • Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya
    • Qiu, Y. L., J. Lee, B. A. Whitlock, F. Bernasconi-Quadroni, and O. Dombrovska. 2001. Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya. Mol Biol Evol 18:1745-1753.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1745-1753
    • Qiu, Y.L.1    Lee, J.2    Whitlock, B.A.3    Bernasconi-Quadroni, F.4    Dombrovska, O.5
  • 83
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 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
  • 84
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 85
    • 0037291976 scopus 로고    scopus 로고
    • Taxon sampling, bioinformatics, and phylogenomics
    • Rosenberg, M. S., and S. Kumar. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-124.
    • (2003) Syst. Biol. , vol.52 , pp. 119-124
    • Rosenberg, M.S.1    Kumar, S.2
  • 86
    • 0035527401 scopus 로고    scopus 로고
    • Complexity of the likelihood surface for a large DNA dataset
    • Salter, L. A. 2001. Complexity of the likelihood surface for a large DNA dataset. Syst Biol 50:970-978.
    • (2001) Syst. Biol. , vol.50 , pp. 970-978
    • Salter, L.A.1
  • 87
    • 0034069504 scopus 로고    scopus 로고
    • Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
    • Sanderson, M. J., M. F. Wojciechowski, J. Hu, T. S. Khan, and S. G. Brady. 2000. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Mol. Biol. Evol. 17:782-797.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 782-797
    • Sanderson, M.J.1    Wojciechowski, M.F.2    Hu, J.3    Khan, T.S.4    Brady, S.G.5
  • 88
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 89
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 90
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira, H., and M. Hasegawa. 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
  • 92
    • 0033604619 scopus 로고    scopus 로고
    • Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
    • Soltis, P. S., D. E. Soltis, and M. W. Chase. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-404.
    • (1999) Nature , vol.402 , pp. 402-404
    • Soltis, P.S.1    Soltis, D.E.2    Chase, M.W.3
  • 93
    • 0037025197 scopus 로고    scopus 로고
    • Rooting the eukaryote tree by using a derived gene fusion
    • Stechmann, A., and T. Cavalier-Smith. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91.
    • (2002) Science , vol.297 , pp. 89-91
    • Stechmann, A.1    Cavalier-Smith, T.2
  • 94
    • 0032871269 scopus 로고    scopus 로고
    • Long-branch attraction and the rDNA model of early eukaryotic evolution
    • Stiller, J., and B. Hall. 1999. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol. 16:1270-1279.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1270-1279
    • Stiller, J.1    Hall, B.2
  • 95
    • 0035527373 scopus 로고    scopus 로고
    • Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
    • Sullivan, J., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
    • (2001) Syst. Biol. , vol.50 , pp. 723-729
    • Sullivan, J.1    Swofford, D.L.2
  • 97
    • 0035527406 scopus 로고    scopus 로고
    • Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
    • Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
    • (2001) Syst. Biol. , vol.50 , pp. 525-539
    • Swofford, D.L.1    Waddell, P.J.2    Huelsenbeck, J.P.3    Foster, P.G.4    Lewis, P.O.5    Rogers, J.S.6
  • 98
    • 0027478431 scopus 로고
    • Anaerobic fungi and their cellulolytic and xylanolytic enzymes
    • Teunissen, M. J., and H. J. Op den Camp. 1993. Anaerobic fungi and their cellulolytic and xylanolytic enzymes. Antonie Van Leeuwenhoek 63:63-76.
    • (1993) Antonie Van Leeuwenhoek , vol.63 , pp. 63-76
    • Teunissen, M.J.1    Op Den Camp, H.J.2
  • 99
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan, S., and N. Goldman. 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
  • 100
    • 0032225748 scopus 로고    scopus 로고
    • Does adding characters with missing data increase or decrease phylogenetic accuracy?
    • Wiens, J. J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640.
    • (1998) Syst. Biol. , vol.47 , pp. 625-640
    • Wiens, J.J.1
  • 101
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens, J. J. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 102
    • 30344464074 scopus 로고    scopus 로고
    • Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?
    • Wiens, J. J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. 731-742.
    • (2005) Syst. Biol. , pp. 731-742
    • Wiens, J.J.1
  • 103
    • 0345874732 scopus 로고    scopus 로고
    • Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis
    • Wolf, Y. I., I. B. Rogozin, and E. V. Koonin. 2004. Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome. Res. 14:29-36.
    • (2004) Genome. Res. , vol.14 , pp. 29-36
    • Wolf, Y.I.1    Rogozin, I.B.2    Koonin, E.V.3
  • 104
    • 0026731453 scopus 로고
    • Cloning and expression of multiple cellulase cDNAs from the anaerobic rumen fungus Neoccillimastix patriciarum in Escherichia coli
    • Xue, G. P., C. G. Orpin, K. S. Gobius, J. H. Aylward, and G. D. Simpson. 1992. Cloning and expression of multiple cellulase cDNAs from the anaerobic rumen fungus Neoccillimastix patriciarum in Escherichia coli. J. Gen. Microbiol. 138:1413-1420.
    • (1992) J. Gen. Microbiol. , vol.138 , pp. 1413-1420
    • Xue, G.P.1    Orpin, C.G.2    Gobius, K.S.3    Aylward, J.H.4    Simpson, G.D.5
  • 105
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 106
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang, Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 107
    • 0030638573 scopus 로고    scopus 로고
    • How often do wrong models produce better phylogenies?
    • Yang, Z. 1997a. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 144:105-108.
    • (1997) Mol. Biol. Evol. , vol.144 , pp. 105-108
    • Yang, Z.1
  • 108
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997b. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1


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