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Volumn 22, Issue 10, 2005, Pages 1948-1963

Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone

Author keywords

Angiosperm phylogeny; Parametric bootstrap; Phylogenomics

Indexed keywords

DNA;

EID: 24744449757     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi191     Document Type: Article
Times cited : (239)

References (99)
  • 1
    • 16344379182 scopus 로고    scopus 로고
    • Covarion structure in plastid genome evolution: A new statistical test
    • Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22:914-924.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 914-924
    • Ané, C.1    Burleigh, J.G.2    McMahon, M.M.3    Sanderson, M.J.4
  • 2
    • 11144263232 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes
    • Asano, T., T. Tsudzuki, S. Takahashi, H. Shimada, and K. Kadowaki. 2004. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res. 11:93-99.
    • (2004) DNA Res. , vol.11 , pp. 93-99
    • Asano, T.1    Tsudzuki, T.2    Takahashi, S.3    Shimada, H.4    Kadowaki, K.5
  • 4
    • 0345581665 scopus 로고    scopus 로고
    • The major clades of MADS-box genes and their role in the development and evolution of flowering plants
    • Becker, A., and G. Theissen. 2003. The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol. Phylogenet. Evol. 29:464-489.
    • (2003) Mol. Phylogenet. Evol. , vol.29 , pp. 464-489
    • Becker, A.1    Theissen, G.2
  • 5
    • 0037594762 scopus 로고    scopus 로고
    • Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms
    • Borsch, T., K. W. Hilu, D. Quandt, V. Wilde, C. Neinhuis, and W. Barthlott. 2003. Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol. 16:558-576.
    • (2003) J. Evol. Biol. , vol.16 , pp. 558-576
    • Borsch, T.1    Hilu, K.W.2    Quandt, D.3    Wilde, V.4    Neinhuis, C.5    Barthlott, W.6
  • 6
    • 10644220870 scopus 로고    scopus 로고
    • Monocot relationships: An overview
    • Chase, M. W. 2004. Monocot relationships: an overview. Am. J. Bot. 91:1645-1655.
    • (2004) Am. J. Bot. , vol.91 , pp. 1645-1655
    • Chase, M.W.1
  • 7
    • 2442517979 scopus 로고    scopus 로고
    • Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes
    • Chaw, S. M., C. C. Chang, H. L. Chen, and W. H. Li. 2004. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol. Evol. 58:424-441.
    • (2004) J. Mol. Evol. , vol.58 , pp. 424-441
    • Chaw, S.M.1    Chang, C.C.2    Chen, H.L.3    Li, W.H.4
  • 8
    • 5444264964 scopus 로고    scopus 로고
    • Chloroplast DNA rearrangements in Campanulaceae: Phylogenetic utility of highly rearranged genomes
    • Cosner, M. E., L. A. Raubeson, and R. K. Jansen. 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol. Biol. 4:27.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 27
    • Cosner, M.E.1    Raubeson, L.A.2    Jansen, R.K.3
  • 9
    • 0028973842 scopus 로고
    • The origin and early diversification of angiosperms
    • Crane, P. R., E. M. Friis, and K. R. Pederson. 1995. The origin and early diversification of angiosperms. Nature 374:27-33.
    • (1995) Nature , vol.374 , pp. 27-33
    • Crane, P.R.1    Friis, E.M.2    Pederson, K.R.3
  • 10
    • 0003418143 scopus 로고
    • Letter to J. D. Hooker
    • F. Darwin and A.C. Seward, eds. John Murray, London
    • Darwin, C. 1903. Letter to J. D. Hooker. In F. Darwin and A.C. Seward, eds. More letters of Charles Darwin, Vol. 2. John Murray, London.
    • (1903) More Letters of Charles Darwin , vol.2
    • Darwin, C.1
  • 12
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 13
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 14
    • 0030888864 scopus 로고    scopus 로고
    • Correlated rates of synonymous site evolution across plant genomes
    • Eyre-Walker, A., and B. S. Gaut. 1997. Correlated rates of synonymous site evolution across plant genomes. Mol. Biol. Evol. 14:455-460.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 455-460
    • Eyre-Walker, A.1    Gaut, B.S.2
  • 15
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 16
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • _. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
  • 17
    • 0003437299 scopus 로고    scopus 로고
    • Distributed by the author, Department of Genome Sciences, University of Washington, Seattle
    • _. 2004. PHYLIP (phylogeny inference package). Version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle.
    • (2004) PHYLIP (Phylogeny Inference Package). Version 3.6
  • 18
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
    • (1998) Genome Res. , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 19
    • 0030052344 scopus 로고    scopus 로고
    • Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms
    • Goremykin, V., V. Bobrova, J. Pahnke, A. Troitsky, A. Antonov, and W. Martin. 1996. Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms. Mol. Biol. Evol. 13:383-396.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 383-396
    • Goremykin, V.1    Bobrova, V.2    Pahnke, J.3    Troitsky, A.4    Antonov, A.5    Martin, W.6
  • 20
    • 0041834716 scopus 로고    scopus 로고
    • Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm
    • Goremykin, V. V., K. I. Hirsch-Ernst, S. Wolfl, and F. H. Hellwig. 2003. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20:1499-1505.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1499-1505
    • Goremykin, V.V.1    Hirsch-Ernst, K.I.2    Wolfl, S.3    Hellwig, F.H.4
  • 21
    • 3042683994 scopus 로고    scopus 로고
    • The chloroplast genome of Nymphaea alba: Whole-genome analyses and the problem of identifying the most basal angiosperm
    • _. 2004. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol. Biol. Evol. 21:1445-1454.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1445-1454
  • 22
    • 0033666273 scopus 로고    scopus 로고
    • Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms
    • Graham, S. W., and R. G. Olmstead. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87:1712-1730.
    • (2000) Am. J. Bot. , vol.87 , pp. 1712-1730
    • Graham, S.W.1    Olmstead, R.G.2
  • 23
    • 0033679542 scopus 로고    scopus 로고
    • Microstructural changes in noncoding chloroplast DNA: Interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference
    • Graham, S. W., P. A. Reeves, A. C. E. Burns, and R. G. Olmstead. 2000. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int. J. Plant Sci. 161:S83-S96.
    • (2000) Int. J. Plant Sci. , vol.161
    • Graham, S.W.1    Reeves, P.A.2    Burns, A.C.E.3    Olmstead, R.G.4
  • 24
    • 1642554676 scopus 로고    scopus 로고
    • Reading the entrails of chickens: Molecular timescales of evolution and the illusion of precision
    • Graur, D., and W. Martin. 2004. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20:80-86.
    • (2004) Trends Genet. , vol.20 , pp. 80-86
    • Graur, D.1    Martin, W.2
  • 25
    • 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
  • 26
    • 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
  • 27
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 28
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy, M. D., 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.D.1    Penny, D.2
  • 29
    • 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
  • 30
    • 0347723872 scopus 로고    scopus 로고
    • Angiosperm phylogeny based on matK sequence information
    • Hilu, K. W., T. Borsch, K. Muller et al. (16 co-authors). 2003. Angiosperm phylogeny based on matK sequence information. Am. J. Bot. 90:1758-1776.
    • (2003) Am. J. Bot. , vol.90 , pp. 1758-1776
    • Hilu, K.W.1    Borsch, T.2    Muller, K.3
  • 31
    • 0024674380 scopus 로고
    • The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
    • Hiratsuka, J., H. Shimada, R. Whittier et al. (16 co-authors). 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217:185-194.
    • (1989) Mol. Gen. Genet. , vol.217 , pp. 185-194
    • Hiratsuka, J.1    Shimada, H.2    Whittier, R.3
  • 32
    • 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
  • 33
    • 0033804270 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes
    • Hupfer, H., M. Swiatek, S. Hornung, R. G. Herrmann, R. M. Maier, W. L. Chiu, and B. Sears. 2000. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes. Mol. Gen. Genet. 263:581-585.
    • (2000) Mol. Gen. Genet. , vol.263 , pp. 581-585
    • Hupfer, H.1    Swiatek, M.2    Hornung, S.3    Herrmann, R.G.4    Maier, R.M.5    Chiu, W.L.6    Sears, B.7
  • 34
    • 19944424442 scopus 로고    scopus 로고
    • Methods for obtaining and analyzing whole chloroplast genome sequences
    • Jansen, R. K., L. A. Raubeson, J. L. Boore et al. (15 co-authors). 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol. 395:348-384.
    • (2005) Methods Enzymol. , vol.395 , pp. 348-384
    • Jansen, R.K.1    Raubeson, L.A.2    Boore, J.L.3
  • 35
    • 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
  • 36
    • 18944364299 scopus 로고    scopus 로고
    • A survey of tricolpate (eudicot) phylogenetic relationships
    • Judd, W. S., and R. G. Olmstead. 2004. A survey of tricolpate (eudicot) phylogenetic relationships. Am. J. Bot. 91:1627-1644.
    • (2004) Am. J. Bot. , vol.91 , pp. 1627-1644
    • Judd, W.S.1    Olmstead, R.G.2
  • 37
    • 0034739889 scopus 로고    scopus 로고
    • Complete structure of the chloroplast genome of a legume, Lotus japonicus
    • Kato, T., T. Kaneko, S. Sato, Y. Nakamura, and S. Tabata. 2000. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7:323-330.
    • (2000) DNA Res. , vol.7 , pp. 323-330
    • Kato, T.1    Kaneko, T.2    Sato, S.3    Nakamura, Y.4    Tabata, S.5
  • 38
    • 0035103949 scopus 로고    scopus 로고
    • Evolutionary history of the grasses
    • Kellogg, E. 2000. Evolutionary history of the grasses. Plant Physiol. 125:1198-1205.
    • (2000) Plant Physiol. , vol.125 , pp. 1198-1205
    • Kellogg, E.1
  • 39
    • 11144284040 scopus 로고    scopus 로고
    • Complete chloroplast genome sequence from korea ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
    • Kim, K.-J., and H.-L. Lee. 2004. Complete chloroplast genome sequence from korea ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11:247-261.
    • (2004) DNA Res. , vol.11 , pp. 247-261
    • Kim, K.-J.1    Lee, H.-L.2
  • 40
    • 15944381065 scopus 로고    scopus 로고
    • Phylogeny and diversification of B-function MADS-box genes in angiosperms: Evolutionary and functional implications of a 260-million-year-old duplication
    • Kim, S., M.-J. Yoo, V. A. Albert, J. S. Farris, P. S. Soltis, and D. E. Soltis. 2004. Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am. J. Bot. 91:2102-2118.
    • (2004) Am. J. Bot. , vol.91 , pp. 2102-2118
    • Kim, S.1    Yoo, M.-J.2    Albert, V.A.3    Farris, J.S.4    Soltis, P.S.5    Soltis, D.E.6
  • 41
    • 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
  • 42
    • 1642305995 scopus 로고    scopus 로고
    • Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms
    • Kramer, E. M., M. A. Jaramillo, and V. S. Di Stilio. 2004. Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics 166:1011-1023.
    • (2004) Genetics , vol.166 , pp. 1011-1023
    • Kramer, E.M.1    Jaramillo, M.A.2    Di Stilio, V.S.3
  • 43
    • 0037440006 scopus 로고    scopus 로고
    • The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: Insight into the earliest land plants
    • Kugita, M., A. Kaneko, Y. Yamamoto, Y. Takeya, T. Matsumoto, and K. Yoshinaga. 2003a. The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Res. 31:716-721.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 716-721
    • Kugita, M.1    Kaneko, A.2    Yamamoto, Y.3    Takeya, Y.4    Matsumoto, T.5    Yoshinaga, K.6
  • 44
    • 0037736768 scopus 로고    scopus 로고
    • RNA editing in hornwort chloroplasts makes more than half the genes functional
    • Kugita, M., Y. Yamamoto, T. Fujikawa, T. Matsumoto, and K. Yoshinaga. 2003b. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31:2417-2423.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2417-2423
    • Kugita, M.1    Yamamoto, Y.2    Fujikawa, T.3    Matsumoto, T.4    Yoshinaga, K.5
  • 45
    • 0028181246 scopus 로고
    • Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances
    • Lake, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA 91:1455-1459.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 1455-1459
    • Lake, J.A.1
  • 46
    • 0242381269 scopus 로고    scopus 로고
    • Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: Implications for the evolution of floral development
    • Litt, A., and V. F. Irish. 2003. Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165:821-833.
    • (2003) Genetics , vol.165 , pp. 821-833
    • Litt, A.1    Irish, V.F.2
  • 48
    • 18144425198 scopus 로고    scopus 로고
    • The place of Amborella within the radiation of angiosperms
    • Lockhart, P. J., and D. Penny. 2005. The place of Amborella within the radiation of angiosperms. Trends Plant Sci. 10:201-202.
    • (2005) Trends Plant Sci. , vol.10 , pp. 201-202
    • Lockhart, P.J.1    Penny, D.2
  • 49
    • 0031852105 scopus 로고    scopus 로고
    • A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
    • Lockhart, P. J., M. A. Steel, A. C. Barbrook, D. H. Huson, M. A. Charleston, and C. J. Howe. 1998. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15:1183-1188.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1183-1188
    • Lockhart, P.J.1    Steel, M.A.2    Barbrook, A.C.3    Huson, D.H.4    Charleston, M.A.5    Howe, C.J.6
  • 50
    • 0028361182 scopus 로고
    • Recovering evolutionary trees under a more realistic model of sequence evolution
    • Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 51
    • 0036134757 scopus 로고    scopus 로고
    • Heterotachy, an important process of protein evolution
    • Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:1-7.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1-7
    • Lopez, P.1    Casane, D.2    Philippe, H.3
  • 52
    • 0030000952 scopus 로고    scopus 로고
    • Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal
    • Lyons-Weiler, J., G. A. Hoelzer, and R. J. Tausch. 1996. Relative apparent synapomorphy analysis (RASA). I: the statistical measurement of phylogenetic signal. Mol. Biol. Evol. 13:749-757.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 749-757
    • Lyons-Weiler, J.1    Hoelzer, G.A.2    Tausch, R.J.3
  • 53
    • 0029160870 scopus 로고
    • Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing
    • Maier, R. M., K. Neckermann, G. L. Igloi, and H. Kossel. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251:614-628.
    • (1995) J. Mol. Biol. , vol.251 , pp. 614-628
    • Maier, R.M.1    Neckermann, K.2    Igloi, G.L.3    Kossel, H.4
  • 54
    • 18144368560 scopus 로고    scopus 로고
    • Chloroplast genome phylogenetics: Why we need independent approaches to plant molecular evolution
    • Martin, W., O. Deusch, N. Stawski, N. Grunheit, and V. Goremykin. 2005. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci. 10:203-209.
    • (2005) Trends Plant Sci. , vol.10 , pp. 203-209
    • Martin, W.1    Deusch, O.2    Stawski, N.3    Grunheit, N.4    Goremykin, V.5
  • 55
    • 0033615479 scopus 로고    scopus 로고
    • The root of angiosperm phylogeny inferred from duplicate phytochrome genes
    • Mathews, S., and M. J. Donoghue. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286:947-950.
    • (1999) Science , vol.286 , pp. 947-950
    • Mathews, S.1    Donoghue, M.J.2
  • 56
    • 0033693754 scopus 로고    scopus 로고
    • Basal angiosperm phylogeny inferred from duplicate phytochromes A and C
    • _. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. J. Plant Sci. 161:S41-S41.
    • (2000) Int. J. Plant Sci. , vol.161
  • 57
    • 0034560807 scopus 로고    scopus 로고
    • Chinese spring wheat (Triticum aestivum L.) chloroplast genome: Complete sequence and contig clones
    • Ogihara, Y., K. Isono, T. Kojimal et al. (18 co-authors). 2000. Chinese spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Plant Molec. Biol. Rep. 18:243-253.
    • (2000) Plant Molec. Biol. Rep. , vol.18 , pp. 243-253
    • Ogihara, Y.1    Isono, K.2    Kojimal, T.3
  • 58
    • 17644438923 scopus 로고
    • Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification
    • Ohyama, K., H. Fukuzawa, T. Kohchi et al. 1988. Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification. J. Mol. Biol. 203:281-298.
    • (1988) J. Mol. Biol. , vol.203 , pp. 281-298
    • Ohyama, K.1    Fukuzawa, H.2    Kohchi, T.3
  • 59
    • 0033576614 scopus 로고    scopus 로고
    • Multigene analyses identify the three earliest lineages of extant flowering plants
    • Parkinson, C. L., K. L. Adams, and J. D. Palmer. 1999. Multigene analyses identify the three earliest lineages of extant flowering plants. Curr. Biol. 9:1485-1488.
    • (1999) Curr. Biol. , vol.9 , pp. 1485-1488
    • Parkinson, C.L.1    Adams, K.L.2    Palmer, J.D.3
  • 60
    • 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
  • 61
    • 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
  • 62
    • 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
  • 63
    • 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
  • 65
    • 0033677575 scopus 로고    scopus 로고
    • Phylogeny of basal angiosperms: Analyses of five genes from three genomes
    • _. 2000. Phylogeny of basal angiosperms: analyses of five genes from three genomes. Int. J. Plant Sci. 161:S3-S27.
    • (2000) Int. J. Plant Sci. , vol.161
  • 66
    • 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
  • 67
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas, A., and P. W. Holland. 2000 Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15:454-459.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 454-459
    • Rokas, A.1    Holland, P.W.2
  • 68
    • 0037314098 scopus 로고    scopus 로고
    • r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson, M. J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 70
    • 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. M. 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.M.3    Khan, T.S.4    Brady, S.G.5
  • 71
    • 0033615372 scopus 로고    scopus 로고
    • Complete structure of the chloroplast genome of Arabidopsis thaliana
    • Sato, S., Y. Nakamura, T. Kaneko, E. Asamizu, and S. Tabata. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6:283-290.
    • (1999) DNA Res. , vol.6 , pp. 283-290
    • Sato, S.1    Nakamura, Y.2    Kaneko, T.3    Asamizu, E.4    Tabata, S.5
  • 72
    • 0035082732 scopus 로고    scopus 로고
    • The plastid chromosome of spinach (Spinacia oleracea): Complete nucleotide sequence and gene organization
    • Schmitz-Linneweber, C., R. M. Maier, J. P. Alcaraz, A. Cottet, R. G. Herrmann, and R. Mache. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45:307-315.
    • (2001) Plant Mol. Biol. , vol.45 , pp. 307-315
    • Schmitz-Linneweber, C.1    Maier, R.M.2    Alcaraz, J.P.3    Cottet, A.4    Herrmann, R.G.5    Mache, R.6
  • 73
    • 0036726451 scopus 로고    scopus 로고
    • The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: The role of RNA editing in generating divergence in the process of plant speciation
    • Schmitz-Linneweber, C., R. Regel, T. G. Du, H. Hupfer, R. G. Herrmann, and R. M. Maier. 2002. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol. Biol. Evol. 19:1602-1612.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1602-1612
    • Schmitz-Linneweber, C.1    Regel, R.2    Du, T.G.3    Hupfer, H.4    Herrmann, R.G.5    Maier, R.M.6
  • 75
    • 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
  • 76
    • 84968989005 scopus 로고
    • The complete nucleotide sequence of tobacco chloroplast genome: Its gene organization and expression
    • Shinozaki, K., M. Ohme, M. Tanaka et al. (23 co-authors). 1986. The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049.
    • (1986) EMBO J. , vol.5 , pp. 2043-2049
    • Shinozaki, K.1    Ohme, M.2    Tanaka, M.3
  • 77
    • 1642546638 scopus 로고    scopus 로고
    • Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: A case study using mitogenomic data from 100 higher teleost fishes
    • Simmons, M. P., and M. Miya. 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. Mol. Phylogenet. Evol. 31:351-362.
    • (2004) Mol. Phylogenet. Evol. , vol.31 , pp. 351-362
    • Simmons, M.P.1    Miya, M.2
  • 78
    • 15944419700 scopus 로고    scopus 로고
    • Evolution of the flower
    • R. Henry, ed. CABI, Wallingford, Oxfordshire
    • Soltis, D. E., V. A. Albert, S. Kim et al. (11 co-authors). 2004a. Evolution of the flower. In R. Henry, ed. Diversity and evolution of plants. CABI, Wallingford, Oxfordshire.
    • (2004) Diversity and Evolution of Plants
    • Soltis, D.E.1    Albert, V.A.2    Kim, S.3
  • 79
    • 4644350604 scopus 로고    scopus 로고
    • Genome-scale data, angiosperm relationships, and "ending incongruence": A cautionary tale in phylogenetics
    • Soltis, D. E., V. A. Albert, V. Savolainen et al. (11 co-authors). 2004b. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 9:477-483.
    • (2004) Trends Plant Sci. , vol.9 , pp. 477-483
    • Soltis, D.E.1    Albert, V.A.2    Savolainen, V.3
  • 80
    • 4644250777 scopus 로고    scopus 로고
    • Amborella not a "basal angiosperm"? Not so fast
    • Soltis, D. E., and P. S. Soltis. 2004. Amborella not a "basal angiosperm"? Not so fast. Am. J. Bot. 91:997-1001.
    • (2004) Am. J. Bot. , vol.91 , pp. 997-1001
    • Soltis, D.E.1    Soltis, P.S.2
  • 81
    • 10644288251 scopus 로고    scopus 로고
    • The origin and diversification of angiosperms
    • Soltis, P. S., and D. E. Soltis. 2004. The origin and diversification of angiosperms. Am. J. Bot. 91:1614-1626.
    • (2004) Am. J. Bot. , vol.91 , pp. 1614-1626
    • Soltis, P.S.1    Soltis, D.E.2
  • 82
    • 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
  • 83
    • 17744400517 scopus 로고    scopus 로고
    • Likelihood, parsimony, and heterogeneous evolution
    • Spencer, M., E. Susko, and A. J. Roger. 2005. Likelihood, parsimony, and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1161-1164
    • Spencer, M.1    Susko, E.2    Roger, A.J.3
  • 84
    • 43949153645 scopus 로고
    • Recovering a tree from the leaf colorations it generates under a Markov model
    • Steel, M. A. 1994. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7:19-23.
    • (1994) Appl. Math. Lett. , vol.7 , pp. 19-23
    • Steel, M.A.1
  • 85
    • 10644253746 scopus 로고    scopus 로고
    • Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
    • Stefanović, S., D. W. Rice, and J. D. Palmer. 2004. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol. 4:35.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 35
    • Stefanović, S.1    Rice, D.W.2    Palmer, J.D.3
  • 86
    • 1542405308 scopus 로고    scopus 로고
    • Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms
    • Stellari, G. M., M. A. Jaramillo, and E. M. Kramer. 2004. Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol. Biol. Evol. 21:506-519.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 506-519
    • Stellari, G.M.1    Jaramillo, M.A.2    Kramer, E.M.3
  • 87
    • 0344875209 scopus 로고    scopus 로고
    • Complete chloroplast DNA sequence of the moss Physcomitrella patens: Evidence for the loss and relocation of rpoA from the chloroplast to the nucleus
    • Sugiura, C., Y. Kobayashi, S. Aoki, C. Sugita, and M. Sugita. 2003. Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res. 31:5324-5331.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5324-5331
    • Sugiura, C.1    Kobayashi, Y.2    Aoki, S.3    Sugita, C.4    Sugita, M.5
  • 89
    • 1342288009 scopus 로고    scopus 로고
    • LDDist: A Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
    • Thollesson, M. 2004. LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics 20:416-418.
    • (2004) Bioinformatics , vol.20 , pp. 416-418
    • Thollesson, M.1
  • 90
    • 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
  • 91
    • 0038229553 scopus 로고    scopus 로고
    • A complete nucleotide sequence of the plastid genome from a fern, Psilotum nudum
    • Wakasuki, T., A. Nishikawa, K. Yamada and M. Sugiura. 1998. A complete nucleotide sequence of the plastid genome from a fern, Psilotum nudum. Endocyt. Cell Res., 13 (Suppl.):147.
    • (1998) Endocyt. Cell Res. , vol.13 , Issue.SUPPL. , pp. 147
    • Wakasuki, T.1    Nishikawa, A.2    Yamada, K.3    Sugiura, M.4
  • 92
    • 0028043489 scopus 로고
    • Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii
    • Wakasugi, T., J. Tsudzuki, S. Ito, K. Nakashima, T. Tsudzuki, and M. Sugiura. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA 91:9794-9798.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 9794-9798
    • Wakasugi, T.1    Tsudzuki, J.2    Ito, S.3    Nakashima, K.4    Tsudzuki, T.5    Sugiura, M.6
  • 93
    • 0037203866 scopus 로고    scopus 로고
    • Identification of diploid endosperm in an early angiosperm lineage
    • Williams, J. H., and W. E. Friedman. 2002. Identification of diploid endosperm in an early angiosperm lineage. Nature 415:522-526.
    • (2002) Nature , vol.415 , pp. 522-526
    • Williams, J.H.1    Friedman, W.E.2
  • 94
    • 0037572306 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L.
    • Wolf, P. G., C. A. Rowe, R. B. Sinclair, and M. Hasebe. 2003. Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res. 10:59-65.
    • (2003) DNA Res. , vol.10 , pp. 59-65
    • Wolf, P.G.1    Rowe, C.A.2    Sinclair, R.B.3    Hasebe, M.4
  • 95
    • 10244240599 scopus 로고    scopus 로고
    • Automatic annotation of organellar genomes with DOGMA
    • Wyman, S. K., R. K. Jansen, and J. L. Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255.
    • (2004) Bioinformatics , vol.20 , pp. 3252-3255
    • Wyman, S.K.1    Jansen, R.K.2    Boore, J.L.3
  • 96
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 99
    • 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


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