메뉴 건너뛰기




Volumn 21, Issue 9, 2004, Pages 1740-1752

Phylogenomics of eukaryotes: Impact of missing data on large alignments

Author keywords

Choanoflagellata; Missing data; Molecular phylogeny; Multi gene analysis

Indexed keywords

COMPLEMENTARY DNA; MITOCHONDRIAL DNA; RIBOSOME RNA;

EID: 4143122089     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh182     Document Type: Article
Times cited : (342)

References (105)
  • 1
    • 0002367729 scopus 로고    scopus 로고
    • MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
    • Adachi, J., and M. Hasegawa. 1996. 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
    • Petrov, and Csaki, eds. Akademia Kiado, Budapest
    • Akaike, H. 1973, Information theory and an extension of the maximum likelihood principle. Pp, 267-281 in Petrov, and Csaki, eds. Proceedings of the 2nd International Symposium on Information Theory. Akademia Kiado, Budapest.
    • (1973) Proceedings of the 2nd International Symposium on Information Theory , pp. 267-281
    • Akaike, H.1
  • 5
    • 0035527497 scopus 로고    scopus 로고
    • The phylogenetic trunk: Maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda)
    • Anderson, J. S. 2001. The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda). Syst. Biol. 50:170-193.
    • (2001) Syst. Biol. , vol.50 , pp. 170-193
    • Anderson, J.S.1
  • 6
    • 0036125091 scopus 로고    scopus 로고
    • The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2
    • Arisue, N., T. Hashimot, J. A. Lee, D. V. Moore, P. Gordon, C. W. Sensen, T. Gaasterland, M. Hasegawa, and M. Muller. 2002a, The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. J Eukaryot. Microbiol. 49:1-10.
    • (2002) J Eukaryot. Microbiol. , vol.49 , pp. 1-10
    • Arisue, N.1    Hashimot, T.2    Lee, J.A.3    Moore, D.V.4    Gordon, P.5    Sensen, C.W.6    Gaasterland, T.7    Hasegawa, M.8    Muller, M.9
  • 8
    • 0027138675 scopus 로고
    • Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins
    • Baldauf, S. L., and J. D. Palmer. 1993. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90:11558-11562.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 11558-11562
    • Baldauf, S.L.1    Palmer, J.D.2
  • 9
    • 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
  • 13
    • 0036700155 scopus 로고    scopus 로고
    • Examining Basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling, and sequence length
    • Braun, E. L., and R. T. Kimball, 2002. Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. Syst. Biol, 51:614-625.
    • (2002) Syst. Biol. , vol.51 , pp. 614-625
    • Braun, E.L.1    Kimball, R.T.2
  • 14
    • 0345016261 scopus 로고    scopus 로고
    • The evolution of multicellularity and early animal genomes
    • Brooke, N. M., and P. W. Holland. 2003. The evolution of multicellularity and early animal genomes. Curr. Opin. Genet. Dev, 13:599-603.
    • (2003) Curr. Opin. Genet. Dev. , vol.13 , pp. 599-603
    • Brooke, N.M.1    Holland, P.W.2
  • 15
    • 0031928773 scopus 로고    scopus 로고
    • New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences
    • Budin, K., and H. Philippe. 1998. New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences. Mol. Biol. Evol, 15:943-956.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 943-956
    • Budin, K.1    Philippe, H.2
  • 17
    • 0030442691 scopus 로고    scopus 로고
    • Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote
    • Cavalier-Smith, T., and E. E. Chao. 1996. Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote. J. Mol. Evol. 43:551-562.
    • (1996) J. Mol. Evol. , vol.43 , pp. 551-562
    • Cavalier-Smith, T.1    Chao, E.E.2
  • 18
    • 0037403365 scopus 로고    scopus 로고
    • Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution
    • Cavalier-Smith, T., and E. E. Chao. 2003. Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution. J. Mol. Evol. 56:540-563.
    • (2003) J. Mol. Evol. , vol.56 , pp. 540-563
    • Cavalier-Smith, T.1    Chao, E.E.2
  • 19
    • 0034710927 scopus 로고    scopus 로고
    • Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase
    • Chihade, J. W., J. R. Brown, P. R. Schimmel, and L. Ribas De Pouplana. 2000. Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 97:12153-12157.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12153-12157
    • Chihade, J.W.1    Brown, J.R.2    Schimmel, P.R.3    Ribas De Pouplana, L.4
  • 20
    • 0034712855 scopus 로고    scopus 로고
    • The Cambrian "explosion": Slow-fuse or megatonnage?
    • Conway Morris, S. 2000. The Cambrian "explosion": slow-fuse or megatonnage? Proc. Natl. Acad. Sci. USA 97:4426-4429.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 4426-4429
    • Conway Morris, S.1
  • 21
    • 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. Ford 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    Ford Doolittle, W.3    Cavalier-Smith, T.4    Logsdon Jr., J.M.5
  • 22
    • 0036061865 scopus 로고    scopus 로고
    • A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
    • Daubin, V., M. Gouy, and G. Perriere. 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
  • 23
    • 0141685723 scopus 로고    scopus 로고
    • Comment on "Hexapod origins: Monophyletic or paraphyletic?"
    • Delsuc, F., M. J. Phillips, and D. Penny, 2003. Comment on "Hexapod origins: monophyletic or paraphyletic?" Science 301:1482.
    • (2003) Science , vol.301 , pp. 1482
    • Delsuc, F.1    Phillips, M.J.2    Penny, D.3
  • 25
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 26
    • 0024743516 scopus 로고
    • Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library
    • Dynes, J. L., and R. A. Firtel. 1989. Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library. Proc. Natl. Acad, Sci. USA 86:7966-7970.
    • (1989) Proc. Natl. Acad, Sci. USA , vol.86 , pp. 7966-7970
    • Dynes, J.L.1    Firtel, R.A.2
  • 28
    • 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
  • 29
    • 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
  • 30
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 40:783-791.
    • (1985) Evolution , vol.40 , pp. 783-791
    • Felsenstein, J.1
  • 31
    • 0003437299 scopus 로고    scopus 로고
    • Distributed by the author, Department of Genetics, University of Washington, Seattle
    • Felsenstein, J. 2001. PHYLIP (Phylogene Inference Package). Distributed by the author, Department of Genetics, University of Washington, Seattle.
    • (2001) PHYLIP (Phylogene Inference Package)
    • Felsenstein, J.1
  • 32
    • 0037464589 scopus 로고    scopus 로고
    • The genome sequence of the filamentous fungus Neurospora crassa
    • Galagan, J. E., S. E. Calvo, K. A. Borkovich, et al. (74 coauthors). 2003, The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868.
    • (2003) Nature , vol.422 , pp. 859-868
    • Galagan, J.E.1    Calvo, S.E.2    Borkovich, K.A.3
  • 33
    • 0003136612 scopus 로고    scopus 로고
    • Taxonomic revision of Carusia (Reptilia: Squamata) from the late cretaceous of the Gobi Desert and phylogenetic relationships of anguimorphan lizards
    • Gao, K., and M. A. Norell. 1998, Taxonomic revision of Carusia (Reptilia: Squamata) from the late cretaceous of the Gobi Desert and phylogenetic relationships of anguimorphan lizards. Am. Mus. Novit. 3230:1-51.
    • (1998) Am. Mus. Novit. , vol.3230 , pp. 1-51
    • Gao, K.1    Norell, M.A.2
  • 34
    • 0033104491 scopus 로고    scopus 로고
    • Critical analysis of eukaryotic phylogeny: A case study based on the HSP70 family
    • Germot, A., and H. Philippe. 1999. Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family. J. Eukaryot. Microbiol. 46:116-124.
    • (1999) J. Eukaryot. Microbiol. , vol.46 , pp. 116-124
    • Germot, A.1    Philippe, H.2
  • 35
    • 0036380787 scopus 로고    scopus 로고
    • Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?
    • Giribet, G. 2002. Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Mol. Phylogenet. Evol. 24:345-357.
    • (2002) Mol. Phylogenet. Evol. , vol.24 , pp. 345-357
    • Giribet, G.1
  • 36
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
    • (1998) Syst. Biol. , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 37
    • 0036221747 scopus 로고    scopus 로고
    • Efficient biased estimation of evolutionary distances when substitution rates vary across sites
    • Guindon, S., and O. Gascuel. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol. 19:534-543.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 534-543
    • Guindon, S.1    Gascuel, O.2
  • 38
    • 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
  • 39
    • 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
  • 40
    • 0034350372 scopus 로고    scopus 로고
    • Early evolution of the bilateria
    • Hausdorf, B. 2000. Early evolution of the bilateria. Syst. Biol. 49:130-142.
    • (2000) Syst. Biol. , vol.49 , pp. 130-142
    • Hausdorf, B.1
  • 41
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 42
    • 0033582323 scopus 로고    scopus 로고
    • Microsporidia are related to fungi: Evidence from the largest subunit of RNA polymerase II and other proteins
    • Hirt, R. P., J. M. Logsdon, Jr., B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci. USA 96:580-585.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 580-585
    • Hirt, R.P.1    Logsdon Jr., J.M.2    Healy, B.3    Dorey, M.W.4    Doolittle, W.F.5    Embley, T.M.6
  • 43
    • 84960586331 scopus 로고
    • When are fossils better than extant taxa in phylogenetic analysis?
    • Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Syst. Zool. 40:458-469.
    • (1991) Syst. Zool. , vol.40 , pp. 458-469
    • Huelsenbeck, J.P.1
  • 44
    • 0442323217 scopus 로고    scopus 로고
    • Differential loss of ancestral gene families as a source of genomic divergence in animals
    • Hugues, A. L., and R. Friedman. 2004. Differential loss of ancestral gene families as a source of genomic divergence in animals. Proc. R. Soc. Lond. B (Suppl.) 271:S107-S109.
    • (2004) Proc. R. Soc. Lond. B (Suppl.) , vol.271
    • Hugues, A.L.1    Friedman, R.2
  • 45
    • 0000679786 scopus 로고
    • Note on the infusoria flagellata and the spongiae ciliatae
    • James-Clark, H. 1866. Note on the infusoria flagellata and the spongiae ciliatae. Am. J. Sci. 1:113-114.
    • (1866) Am. J. Sci. , vol.1 , pp. 113-114
    • James-Clark, H.1
  • 46
    • 0036554650 scopus 로고    scopus 로고
    • Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions
    • Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Syst. Biol. 51:369-381.
    • (2002) Syst. Biol. , vol.51 , pp. 369-381
    • Kearney, M.1
  • 47
    • 0035909922 scopus 로고    scopus 로고
    • A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution
    • King, N., and S. B. Carroll. 2001. A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution. Proc. Natl. Acad. Sci. USA 98:15032-15037.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 15032-15037
    • King, N.1    Carroll, S.B.2
  • 48
    • 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 301:361-363.
    • (2003) Science , vol.301 , pp. 361-363
    • King, N.1    Hittinger, C.T.2    Carroll, S.B.3
  • 49
    • 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
  • 50
    • 0026613365 scopus 로고
    • The early evolution of eukaryotes: A geological perspective
    • Knoll, A. H. 1992. The early evolution of eukaryotes: a geological perspective. Science 256:622-627.
    • (1992) Science , vol.256 , pp. 622-627
    • Knoll, A.H.1
  • 51
    • 0036499057 scopus 로고    scopus 로고
    • SHOT: A web server for the construction of genome phylogenies
    • Korbel, J. O., B. Snel, M. A. Huynen, and P. Bork. 2002. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18:158-162.
    • (2002) Trends Genet. , vol.18 , pp. 158-162
    • Korbel, J.O.1    Snel, B.2    Huynen, M.A.3    Bork, P.4
  • 52
    • 0000533828 scopus 로고
    • Phylogeny of extant hexapods
    • I. D. Naumann, and CSIRO, eds. Cornell University Press, Ithaca, NY
    • Kristensen, N. P. 1991. Phylogeny of extant hexapods. Pp. 125-140 in I. D. Naumann, and CSIRO, eds. Insects of Australia. Cornell University Press, Ithaca, NY.
    • (1991) Insects of Australia , pp. 125-140
    • Kristensen, N.P.1
  • 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
  • 56
    • 0028723230 scopus 로고
    • How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences
    • Lecointre, G., H. Philippe, H. L. V. Le, and H. Le Guyader. 1994. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Mol. Phylogenet. Evol. 3:292-309.
    • (1994) Mol. Phylogenet. Evol. , vol.3 , pp. 292-309
    • Lecointre, G.1    Philippe, H.2    Le, H.L.V.3    Le Guyader, H.4
  • 57
    • 0035964296 scopus 로고    scopus 로고
    • Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited
    • Loytynoja, A., and M. C. Milinkovitch. 2001. Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited. Proc. Natl. Acad. Sci. USA 98:10202-10207.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10202-10207
    • Loytynoja, A.1    Milinkovitch, M.C.2
  • 58
    • 0036184428 scopus 로고    scopus 로고
    • Testing the new animal phylogeny: First use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes
    • Mallatt, J., and C. J. Winchell. 2002. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol. Biol. Evol. 19:289-301.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 289-301
    • Mallatt, J.1    Winchell, C.J.2
  • 59
    • 0035844972 scopus 로고    scopus 로고
    • The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: Its rRNA predicted secondary structure and phylogenetic implication
    • Milyutina, I. A., V. V. Aleshin, K. A. Mikrjukov, O. S. Kedrova, and N. B. Petrov. 2001. The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication. Gene 272:131-139.
    • (2001) Gene , vol.272 , pp. 131-139
    • Milyutina, I.A.1    Aleshin, V.V.2    Mikrjukov, K.A.3    Kedrova, O.S.4    Petrov, N.B.5
  • 60
    • 0034350422 scopus 로고    scopus 로고
    • More taxa or more characters revisited: Combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)
    • Mitchell, A., C. Mitter, and J. C. Regier. 2000. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49:202-224.
    • (2000) Syst. Biol. , vol.49 , pp. 202-224
    • Mitchell, A.1    Mitter, C.2    Regier, J.C.3
  • 61
    • 0034604170 scopus 로고    scopus 로고
    • The origin of red algae: Implications for the evolution of chloroplasts
    • Moreira, D., H. Le Guyader, and H. Philippe. 2000. The origin of red algae: implications for the evolution of chloroplasts. Nature 405:69-72.
    • (2000) Nature , vol.405 , pp. 69-72
    • Moreira, D.1    Le Guyader, H.2    Philippe, H.3
  • 62
    • 0031877893 scopus 로고    scopus 로고
    • Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes
    • Mushegian, A. R., J. R. Garey, J. Martin, and L. X. Liu. 1998. Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res. 8:590-598.
    • (1998) Genome Res. , vol.8 , pp. 590-598
    • Mushegian, A.R.1    Garey, J.R.2    Martin, J.3    Liu, L.X.4
  • 63
    • 0028000346 scopus 로고
    • Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species
    • Nikoh, N., N. Hayase, N. Iwabe, K. Kuma, and T. Miyata. 1994. Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species. Mol. Biol. Evol. 11:762-768.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 762-768
    • Nikoh, N.1    Hayase, N.2    Iwabe, N.3    Kuma, K.4    Miyata, T.5
  • 64
    • 0034106726 scopus 로고    scopus 로고
    • Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
    • Ota, R., P. J. Waddell, M. Hasegawa, H. Shimodaira, and H. Kishino. 2000. Appropriate Likelihood Ratio Tests and Marginal Distributions for Evolutionary Tree Models with Constraints on Parameters. Mol Biol Evol 17:798-803.
    • (2000) Mol Biol Evol. , vol.17 , pp. 798-803
    • Ota, R.1    Waddell, P.J.2    Hasegawa, M.3    Shimodaira, H.4    Kishino, H.5
  • 65
    • 0033936591 scopus 로고    scopus 로고
    • Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny
    • Page, R. D. 2000. Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol. 14:89-106.
    • (2000) Mol. Phylogenet. Evol. , vol.14 , pp. 89-106
    • Page, R.D.1
  • 66
    • 0027614253 scopus 로고
    • Systematics of holometabolous insect orders based on 18S ribosomal RNA
    • Pashley, D. P., B. A. McPheron, and E. A. Zimmer. 1993. Systematics of holometabolous insect orders based on 18S ribosomal RNA. Mol. Phylogenet. Evol. 2:132-142.
    • (1993) Mol. Phylogenet. Evol. , vol.2 , pp. 132-142
    • Pashley, D.P.1    McPheron, B.A.2    Zimmer, E.A.3
  • 67
    • 0027494836 scopus 로고
    • MUST, a computer package of management utilities for sequences and trees
    • Philippe, H. 1993. MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res. 21:5264-5272.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 5264-5272
    • Philippe, H.1
  • 68
    • 0002214837 scopus 로고    scopus 로고
    • The molecular phylogeny of Eukaryota: Solid facts and uncertainties
    • G. Coombs, K. Vickerman, M. Sleigh, and A. Warren, eds. Kluwer, Dordrecht
    • Philippe, H., and A. Adoutte. 1998. The molecular phylogeny of Eukaryota: solid facts and uncertainties. Pp. 25-56 in G. Coombs, K. Vickerman, M. Sleigh, and A. Warren, eds. Evolutionary relationships among Protozoa. Kluwer, Dordrecht.
    • (1998) Evolutionary Relationships among Protozoa , pp. 25-56
    • Philippe, H.1    Adoutte, A.2
  • 69
    • 0028578194 scopus 로고
    • Can the cambrian explosion be inferred through molecular phylogeny?
    • Philippe, H., A. Chenuil, and A. Adoutte. 1994. Can the cambrian explosion be inferred through molecular phylogeny? Development 120:S15-S25.
    • (1994) Development , vol.120
    • Philippe, H.1    Chenuil, A.2    Adoutte, A.3
  • 70
    • 0032874259 scopus 로고    scopus 로고
    • The rooting of the universal tree of life is not reliable
    • Philippe, H., and P. Forterre. 1999. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49:509-523.
    • (1999) J. Mol. Evol. , vol.49 , pp. 509-523
    • Philippe, H.1    Forterre, P.2
  • 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
  • 74
    • 0033602474 scopus 로고    scopus 로고
    • Taxon sampling revisited
    • Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
    • (1999) Nature , vol.398 , pp. 299-300
    • Poe, S.1    Swofford, D.L.2
  • 75
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
    • (2002) Syst. Biol. , vol.51 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    McGuire, J.A.3    Hillis, D.M.4
  • 76
    • 0036900111 scopus 로고    scopus 로고
    • Combining multiple data sets in a likelihood analysis: Which models are the best?
    • Pupko, T., D. Huchon, Y. Cao, N. Okada, and M. Hasegawa. 2002. Combining Multiple Data Sets in a Likelihood Analysis: Which Models are the Best? Mol. Biol. Evol. 19:2294-2307.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2294-2307
    • Pupko, T.1    Huchon, D.2    Cao, Y.3    Okada, N.4    Hasegawa, M.5
  • 77
    • 0345149777 scopus 로고    scopus 로고
    • Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor lalpha of Ichthyophonus irregularis
    • Ragan, M. A., C. A. Murphy, and T. G. Rand. 2003. Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor lalpha of Ichthyophonus irregularis. Mol. Phylogenet. Evol. 29:550-562.
    • (2003) Mol. Phylogenet. Evol. , vol.29 , pp. 550-562
    • Ragan, M.A.1    Murphy, C.A.2    Rand, T.G.3
  • 78
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 79
    • 0032225752 scopus 로고    scopus 로고
    • Taxon sampling and the accuracy of large phylogenies
    • Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
    • (1998) Syst. Biol. , vol.47 , pp. 702-710
    • Rannala, B.1    Huelsenbeck, J.P.2    Yang, Z.3    Nielsen, R.4
  • 80
    • 0033039592 scopus 로고    scopus 로고
    • An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes
    • Roger, A. J., O. Sandblom, W. F. Doolittle, and H. Philippe. 1999. An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. Mol. Biol. Evol. 16:218-233.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 218-233
    • Roger, A.J.1    Sandblom, O.2    Doolittle, W.F.3    Philippe, H.4
  • 81
    • 0033230110 scopus 로고    scopus 로고
    • Intron insertion as a phylogenetic character: The engrailed homeobox of Strepsiptera does not indicate affinity with Diptera
    • Rokas, A., J. Kathirithamby, and P. W. Holland. 1999. Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect. Mol. Biol. 8:527-530.
    • (1999) Insect. Mol. Biol. , vol.8 , pp. 527-530
    • Rokas, A.1    Kathirithamby, J.2    Holland, P.W.3
  • 83
    • 0035845536 scopus 로고    scopus 로고
    • Incomplete taxon sampling is not a problem for phylogenetic inference
    • Rosenberg, M. S., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98:10751-10756.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10751-10756
    • Rosenberg, M.S.1    Kumar, S.2
  • 84
    • 0037143719 scopus 로고    scopus 로고
    • A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians
    • Ruiz-Trillo, I., J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguna, and M. Riutort. 2002. A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc. Natl. Acad. Sci. USA 99:11246-11251.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11246-11251
    • Ruiz-Trillo, I.1    Paps, J.2    Loukota, M.3    Ribera, C.4    Jondelius, U.5    Baguna, J.6    Riutort, M.7
  • 85
    • 0038158155 scopus 로고    scopus 로고
    • Obtaining maximal concatenated phylogenetic 'data sets from large sequence databases
    • Sanderson, M. J., A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley. 2003. Obtaining maximal concatenated phylogenetic 'data sets from large sequence databases. Mol. Biol. Evol. 20:1036-1042.
    • (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
  • 86
    • 0037136554 scopus 로고    scopus 로고
    • Eukaryotic evolution: Early origin of canonical introns
    • Simpson, A. G., E. K. MacQuarrie, and A. J. Roger. 2002. Eukaryotic evolution: early origin of canonical introns. Nature 419:270.
    • (2002) Nature , vol.419 , pp. 270
    • Simpson, A.G.1    MacQuarrie, E.K.2    Roger, A.J.3
  • 87
    • 0037108318 scopus 로고    scopus 로고
    • Eukaryotic evolution: Getting to the root of the problem
    • Simpson, A. G., and A. J. Roger. 2002. Eukaryotic evolution: getting to the root of the problem. Curr. Biol. 12:R691-693.
    • (2002) Curr. Biol. , vol.12
    • Simpson, A.G.1    Roger, A.J.2
  • 88
    • 0035954250 scopus 로고    scopus 로고
    • Hsp70 sequences indicate that choanoflagellates are closely related to animals
    • Snell, E. A., R. F. Furlong, and P. W. Holland. 2001. Hsp70 sequences indicate that choanoflagellates are closely related to animals. Curr. Biol. 11:967-970.
    • (2001) Curr. Biol. , vol.11 , pp. 967-970
    • Snell, E.A.1    Furlong, R.F.2    Holland, P.W.3
  • 89
    • 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
  • 90
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer, K., and A. von Haeseler. 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
  • 92
    • 0033854992 scopus 로고    scopus 로고
    • Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
    • Takahashi, K., and M. Nei. 2000. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17:1251-1258.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1251-1258
    • Takahashi, K.1    Nei, M.2
  • 93
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 94
    • 0034538854 scopus 로고    scopus 로고
    • An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances
    • Van de Peer, Y., S. L. Baldauf, W. F. Doolittle, and A. Meyer. 2000. An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J. Mol. Evol. 51:565-576.
    • (2000) J. Mol. Evol. , vol.51 , pp. 565-576
    • Van De Peer, Y.1    Baldauf, S.L.2    Doolittle, W.F.3    Meyer, A.4
  • 95
    • 0031750407 scopus 로고    scopus 로고
    • Phylogenetic relationships of fungi, plantae, and animalia inferred from homologous comparison of ribosomal proteins
    • Veuthey, A. L., and G. Bittar. 1998. Phylogenetic relationships of fungi, plantae, and animalia inferred from homologous comparison of ribosomal proteins. J. Mol. Evol. 47:81-92.
    • (1998) J. Mol. Evol. , vol.47 , pp. 81-92
    • Veuthey, A.L.1    Bittar, G.2
  • 96
    • 0027241482 scopus 로고
    • Monophyletic origins of the metazoa: An evolutionary link with fungi
    • Wainright, P. O., G. Hinkle, M. L. Sogin, and S. K. Stickel. 1993. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 260:340-342.
    • (1993) Science , vol.260 , pp. 340-342
    • Wainright, P.O.1    Hinkle, G.2    Sogin, M.L.3    Stickel, S.K.4
  • 97
    • 84989446394 scopus 로고
    • Nucleic acid sequence phylogeny and random outgroups
    • Wheeler, W. 1990. Nucleic acid sequence phylogeny and random outgroups. Cladistics 6:363-367.
    • (1990) Cladistics , vol.6 , pp. 363-367
    • Wheeler, W.1
  • 98
    • 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
  • 99
    • 0029466830 scopus 로고
    • Combining data sets with different numbers of taxa for phylogenetic analysis
    • Wiens, J. J., and T. W. Reeder. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.
    • (1995) Syst. Biol. , vol.44 , pp. 548-558
    • Wiens, J.J.1    Reeder, T.W.2
  • 100
    • 84972952095 scopus 로고
    • Missing data and rhynchosaur phylogeny
    • Wilkinson, M., and M. J. Benton. 1995. Missing data and rhynchosaur phylogeny. Hist. Biol. 10:137-150.
    • (1995) Hist. Biol. , vol.10 , pp. 137-150
    • Wilkinson, M.1    Benton, M.J.2
  • 101
    • 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
  • 102
    • 0030638573 scopus 로고    scopus 로고
    • How often do wrong models produce better phylogenies?
    • Yang, Z. 1997. 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
  • 103
    • 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
  • 104
    • 0033933640 scopus 로고    scopus 로고
    • Estimation of primate speciation dates using local molecular clocks
    • Yoder, A. D., and Z. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1081-1090
    • Yoder, A.D.1    Yang, Z.2
  • 105
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
    • (2002) Syst. Biol. , vol.51 , pp. 588-598
    • Zwickl, D.J.1    Hillis, D.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.