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Volumn 425, Issue 6960, 2003, Pages 798-804

Genome-scale approaches to resolving incongruence in molecular phylogenies

Author keywords

[No Author keywords available]

Indexed keywords

PROBABILITY; TOPOLOGY; YEAST;

EID: 0242365676     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02053     Document Type: Article
Times cited : (1212)

References (50)
  • 1
    • 0034602344 scopus 로고    scopus 로고
    • A kingdom-level phylogeny of eukaryotes based on combined protein data
    • Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977 (2000).
    • (2000) Science , vol.290 , pp. 972-977
    • Baldauf, S.L.1    Roger, A.J.2    Wenk-Siefert, I.3    Doolittle, W.F.4
  • 3
    • 0031010579 scopus 로고    scopus 로고
    • Evidence for a clade of nematodes, arthropods and other moulting animals
    • Aguinaido, A. M. A. et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-493 (1997).
    • (1997) Nature , vol.387 , pp. 489-493
    • Aguinaido, A.M.A.1
  • 4
    • 0033603541 scopus 로고    scopus 로고
    • Early animal evolution: Emerging views from comparative biology and geology
    • Knoll, A. H. & Carroll, S. B. Early animal evolution: emerging views from comparative biology and geology. Science 284, 2129-2137 (1999).
    • (1999) Science , vol.284 , pp. 2129-2137
    • Knoll, A.H.1    Carroll, S.B.2
  • 5
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 (1997).
    • (1997) Science , vol.276 , pp. 734-740
    • Pace, N.R.1
  • 6
    • 0036804525 scopus 로고    scopus 로고
    • Phylogeny of the Oriental Drosophila melanogaster species group: A multilocus reconstruction
    • Kopp, A. & True, J. R. Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction. Syst. Biol. 51, 786-805 (2002).
    • (2002) Syst. Biol. , vol.51 , pp. 786-805
    • Kopp, A.1    True, J.R.2
  • 7
    • 0030311441 scopus 로고    scopus 로고
    • Testing for phylogenctic conflict among molecular data sets in the tribe Triticeae (Gramineae)
    • Mason-Gamer, R. J. & Kellogg, E. A. Testing for phylogenctic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45, 522-543 (1996).
    • (1996) Syst. Biol. , vol.45 , pp. 522-543
    • Mason-Gamer, R.J.1    Kellogg, E.A.2
  • 8
    • 0035855865 scopus 로고    scopus 로고
    • Arthropod phylogeny based on eight molecular loci and morphology
    • Giribet, G., Edgecombe, G. D. & Wheeler, W. C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161 (2001).
    • (2001) Nature , vol.413 , pp. 157-161
    • Giribet, G.1    Edgecombe, G.D.2    Wheeler, W.C.3
  • 9
    • 0035855871 scopus 로고    scopus 로고
    • Mitochondrial protein phylogeny joins myriapods with chelicerates
    • Hwang, U. W., Friedrich, M., Tautz, D., Park, C. J. & Kim, W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413, 154-157 (2001).
    • (2001) Nature , vol.413 , pp. 154-157
    • Hwang, U.W.1    Friedrich, M.2    Tautz, D.3    Park, C.J.4    Kim, W.5
  • 10
    • 0042313795 scopus 로고    scopus 로고
    • Conflicting phylogenetic signals at the base of the metazoan tree
    • Rokas, A., King, N., Finnerty, J. & Carroll, S. B. Conflicting phylogenetic signals at the base of the metazoan tree. Evol. Dev. 5, 346-359 (2003).
    • (2003) Evol. Dev. , vol.5 , pp. 346-359
    • Rokas, A.1    King, N.2    Finnerty, J.3    Carroll, S.B.4
  • 11
    • 0035964296 scopus 로고    scopus 로고
    • Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited
    • Loytynoja, A. & Milinkovitch, M. C. Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited. Proc. Natl Acad. Sci. USA 98, 10202-10207 (2001).
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10202-10207
    • Loytynoja, A.1    Milinkovitch, M.C.2
  • 12
    • 0027138675 scopus 로고
    • Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins
    • Baldauf, S. L. & Palmer, J. D. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl Acad. Sci. USA 90, 11558-11562 (1993).
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 11558-11562
    • Baldauf, S.L.1    Palmer, J.D.2
  • 13
    • 0000162362 scopus 로고    scopus 로고
    • (eds Soltis, D. E., Soltis, P. S. & Doyle, J. J.) 265-296 (Kluwer, Boston, Massachusetts)
    • Wendel, J. F. & Doyle, J. J. in Molecular Systematics of Plants II: DNA Sequencing (eds Soltis, D. E., Soltis, P. S. & Doyle, J. J.) 265-296 (Kluwer, Boston, Massachusetts, 1998).
    • (1998) Molecular Systematics of Plants DNA Sequencing
    • Wendel, J.F.1    Doyle J.J. II2
  • 14
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • Huelsenbeck, J. P. Performance of phylogenetic methods in simulation. Syst. Biol. 44, 17-48 (1995).
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 15
    • 0028578194 scopus 로고
    • Can the cambrian explosion be inferred through molecular phylogeny?
    • Philippe, H., Chenuil, A. & Adoutte, A. Can the cambrian explosion be inferred through molecular phylogeny? Development (Suppl.) 15-25 (1994).
    • (1994) Development , Issue.SUPPL. , pp. 15-25
    • Philippe, H.1    Chenuil, A.2    Adoutte, A.3
  • 16
    • 0029096506 scopus 로고
    • Sampling properties of DNA sequence data in phylogenetic analysis
    • Cummings, M. P., Otto, S. P. & Wakeley, J. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12, 814-822 (1995).
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 814-822
    • Cummings, M.P.1    Otto, S.P.2    Wakeley, J.3
  • 17
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal, A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47, 9-17 (1998).
    • (1998) Syst. Biol. , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 18
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • Yang, Z., Goldman, N. & Friday, A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11, 316-324 (1994).
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 19
    • 0036699004 scopus 로고    scopus 로고
    • Perils of paralogy: Using HSP70 genes for inferring organismal phylogenies
    • Martin, A. P. & Burg, T. M. Perils of paralogy: using HSP70 genes for inferring organismal phylogenies. Syst. Biol. 51, 570-587 (2002).
    • (2002) Syst. Biol. , vol.51 , pp. 570-587
    • Martin, A.P.1    Burg, T.M.2
  • 20
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison, W. P. Gene trees in species trees. Syst. Biol. 46, 523-536 (1997).
    • (1997) Syst. Biol. , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 21
    • 0034031477 scopus 로고    scopus 로고
    • DNA archives and our nearest relative: The trichotomy problem revisited
    • Satta, Y., Klein, J. & Takahata, N. DNA archives and our nearest relative: the trichotomy problem revisited. Mol. Phylog. Evol. 14, 259-275 (2000).
    • (2000) Mol. Phylog. Evol. , vol.14 , pp. 259-275
    • Satta, Y.1    Klein, J.2    Takahata, N.3
  • 22
    • 0030497796 scopus 로고    scopus 로고
    • Molecular marker incongruence in plant hybrid zones and in phylogenetic trees
    • Rieseberg, L. H., Whitton, J. & Linder, C. R. Molecular marker incongruence in plant hybrid zones and in phylogenetic trees. Acta Bot. Neerland. 45, 243-262 (1996).
    • (1996) Acta Bot. Neerland. , vol.45 , pp. 243-262
    • Rieseberg, L.H.1    Whitton, J.2    Linder, C.R.3
  • 25
    • 0039466725 scopus 로고    scopus 로고
    • Combining data with different distributions of among-site rate variation
    • Sullivan, J. Combining data with different distributions of among-site rate variation. Syst. Biol. 45, 375-380 (1996).
    • (1996) Syst. Biol. , vol.45 , pp. 375-380
    • Sullivan, J.1
  • 26
    • 0030816742 scopus 로고    scopus 로고
    • Can three incongruence tests predict when data should be combined?
    • Cunningham, C. W. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14, 733-740 (1997).
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 733-740
    • Cunningham, C.W.1
  • 27
    • 0033604619 scopus 로고    scopus 로고
    • Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
    • Soltis, P. S., Soltis, D. E. & Chase, M. W. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402, 402-404 (1999).
    • (1999) Nature , vol.402 , pp. 402-404
    • Soltis, P.S.1    Soltis, D.E.2    Chase, M.W.3
  • 28
    • 0035252080 scopus 로고    scopus 로고
    • Molecular phylogenetics and the origins of placental mammals
    • Murphy, W. J. et al. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618 (2001).
    • (2001) Nature , vol.409 , pp. 614-618
    • Murphy, W.J.1
  • 29
    • 0034604170 scopus 로고    scopus 로고
    • The origin of red algae and the evolution of chloroplasts
    • Moreira, D., Le Guyader, H. & Philippe, H. The origin of red algae and the evolution of chloroplasts. Nature 405, 69-72 (2000).
    • (2000) Nature , vol.405 , pp. 69-72
    • Moreira, D.1    Le Guyader, H.2    Philippe, H.3
  • 30
    • 0032028997 scopus 로고    scopus 로고
    • Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
    • Naylor, G. J. P. & Brown, W. M. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47, 61-76 (1998).
    • (1998) Syst. Biol. , vol.47 , pp. 61-76
    • Naylor, G.J.P.1    Brown, W.M.2
  • 31
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D. M. Inferring complex phylogenies. Nature 383, 130-131 (1996).
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 32
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 33
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau, A. et al. Life with 6000 genes. Science 274, 546 (1996) 563-567.
    • (1996) Science , vol.546 , pp. 563-567
    • Goffeau, A.1
  • 34
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 (2003).
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1
  • 35
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713 (1997).
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 36
    • 0037047141 scopus 로고    scopus 로고
    • Gene order evolution and paleopolyploidy in hemiascomycete yeasts
    • Wong, S., Butler, G. & Wolfe, K. H. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl Acad. Sci. USA 99, 9272-9277 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 9272-9277
    • Wong, S.1    Butler, G.2    Wolfe, K.H.3
  • 37
    • 0037456380 scopus 로고    scopus 로고
    • Yeast genome duplication was followed by asynchronous differentiation of duplicated genes
    • Langkjaer, R. B., Cliften, P. F., Johnston, M. & Piskur, J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421, 848-852 (2003).
    • (2003) Nature , vol.421 , pp. 848-852
    • Langkjaer, R.B.1    Cliften, P.F.2    Johnston, M.3    Piskur, J.4
  • 39
    • 0037022379 scopus 로고    scopus 로고
    • The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
    • Bapteste, E. et al. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl Acad. Sci. USA 99, 1414-1419 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1414-1419
    • Bapteste, E.1
  • 40
    • 0034681511 scopus 로고    scopus 로고
    • Evidence for a high frequency of simultaneous double-nucleotide substitutions
    • Averof, M., Rokas, A., Wolfe, K. H. & Sharp, P. M. Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287, 1285-1286 (2000).
    • (2000) Science , vol.287 , pp. 1285-1286
    • Averof, M.1    Rokas, A.2    Wolfe, K.H.3    Sharp, P.M.4
  • 41
    • 0036926048 scopus 로고    scopus 로고
    • Troubleshooting molecular phylogenetic analyses
    • Sanderson, M. J. & Shaffer, H. B. Troubleshooting molecular phylogenetic analyses. Annu. Rev. Ecol. Syst. 33, 49-72 (2002).
    • (2002) Annu. Rev. Ecol. Syst. , vol.33 , pp. 49-72
    • Sanderson, M.J.1    Shaffer, H.B.2
  • 42
    • 0037540048 scopus 로고    scopus 로고
    • Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses
    • Kurtzman, C. P. & Robnett, C. J. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res. 3, 417-432 (2003).
    • (2003) FEMS Yeast Res. , vol.3 , pp. 417-432
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 43
    • 0036134757 scopus 로고    scopus 로고
    • Heterotachy, an important process of protein evolution
    • Lopez, P., Casane, D. & Philippe, H. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19, 1-7 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1-7
    • Lopez, P.1    Casane, D.2    Philippe, H.3
  • 44
    • 0033814080 scopus 로고    scopus 로고
    • Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae
    • Naumov, G. I., James, S. A., Naumowa, E. S., Louis, E. J. & Roberts, I. N. Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int. J. Syst. Evol. Microbiol. 50, 1931-1942 (2000).
    • (2000) Int. J. Syst. Evol. Microbiol. , vol.50 , pp. 1931-1942
    • Naumov, G.I.1    James, S.A.2    Naumowa, E.S.3    Louis, E.J.4    Roberts, I.N.5
  • 45
    • 0037819441 scopus 로고    scopus 로고
    • Widespread horizontal transfer of mitochondrial genes in flowering plants
    • Bergthorsson, U., Adams, K. L., Thomason, B. & Palmer, J. D. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424, 197-201 (2003).
    • (2003) Nature , vol.424 , pp. 197-201
    • Bergthorsson, U.1    Adams, K.L.2    Thomason, B.3    Palmer, J.D.4
  • 47
    • 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., Higgins, D. G. & Gibson, T. J. 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).
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 48
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98tNT
    • Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98tNT. Nucleic Acids Symp. Ser. 41, 95-98 (1999).
    • (1999) Nucleic Acids Symp. Ser. , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 50
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada, D. & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998).
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2


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