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Volumn 29, Issue 2, 2003, Pages 350-359

Inference of higher-order relationships in the cycads from a large chloroplast data set

Author keywords

Encephalartos; NADH dehydrogenase genes; Photosystem II genes; Ribosomal protein genes; Seed plant phylogeny

Indexed keywords

BOWENIA; CERATOZAMIA; CYCADACEAE; CYCADOPSIDA; CYCAS; DIOON; ENCEPHALARTOS; GINKGO BILOBA; SPERMATOPHYTA; STANGERIA; STANGERIACEAE; ZAMIA; ZAMIACEAE;

EID: 0842291765     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00131-3     Document Type: Article
Times cited : (77)

References (60)
  • 1
    • 0023359361 scopus 로고
    • Asynchronous distance between homologous DNA sequences
    • Barry, D., Hartigan, J.A., 1987. Asynchronous distance between homologous DNA sequences. Biometrics 43, 261-276.
    • (1987) Biometrics , vol.43 , pp. 261-276
    • Barry, D.1    Hartigan, J.A.2
  • 2
    • 0141914305 scopus 로고    scopus 로고
    • Molecular systematic studies in cycads: Evidence from trnL intron and ITS2 rDNA sequences
    • in press
    • Bogler, D.J., Francisco-Ortega, J., in press. Molecular systematic studies in cycads: evidence from trnL intron and ITS2 rDNA sequences. Mem. New York Bot. Gard.
    • Mem. New York Bot. Gard.
    • Bogler, D.J.1    Francisco-Ortega, J.2
  • 3
    • 0030208147 scopus 로고    scopus 로고
    • Phylogenetic inferences from chloroplast chlB gene sequences of Nephrolepis exaltata (Filicopsida), Ephedra altissima (Gnetopsida), and diverse land plants
    • Boivin, R., Richard, M., Beauseigle, D., Bousquet, J., Bellemare, G., 1996. Phylogenetic inferences from chloroplast chlB gene sequences of Nephrolepis exaltata (Filicopsida), Ephedra altissima (Gnetopsida), and diverse land plants. Mol. Phylogenet. Evol. 6, 19-29.
    • (1996) Mol. Phylogenet. Evol. , vol.6 , pp. 19-29
    • Boivin, R.1    Richard, M.2    Beauseigle, D.3    Bousquet, J.4    Bellemare, G.5
  • 4
    • 0034636023 scopus 로고    scopus 로고
    • Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
    • Bowe, L.M., Coat, G., dePamphilis, C.W., 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc. Natl. Acad. Sci. 97, 4092-4097.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 4092-4097
    • Bowe, L.M.1    Coat, G.2    DePamphilis, C.W.3
  • 6
    • 0001627435 scopus 로고
    • A phylogenetic analysis of American Zamiaceae (Cycadales) using chloroplast DNA restriction fragment length polymorphisms
    • Caputo, P., Stevenson, D.W., Wurtzel, E.T., 1991. A phylogenetic analysis of American Zamiaceae (Cycadales) using chloroplast DNA restriction fragment length polymorphisms. Brittonia 43, 135-145.
    • (1991) Brittonia , vol.43 , pp. 135-145
    • Caputo, P.1    Stevenson, D.W.2    Wurtzel, E.T.3
  • 7
    • 0004087179 scopus 로고
    • Hafner Publishing Company, New York, NY
    • Chamberlain, C.J., 1965. The Living Cycads. Hafner Publishing Company, New York, NY.
    • (1965) The Living Cycads
    • Chamberlain, C.J.1
  • 8
    • 0034636037 scopus 로고    scopus 로고
    • Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
    • Chaw, S., Parkinson, C.L., Cheng, Y., Vincent, T.M., Palmer, J.D., 2000. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc. Natl. Acad. Sci. 97, 4086-4091.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 4086-4091
    • Chaw, S.1    Parkinson, C.L.2    Cheng, Y.3    Vincent, T.M.4    Palmer, J.D.5
  • 9
    • 0031012107 scopus 로고    scopus 로고
    • Molecular phylogeny of extant gymnosperms and seed plant evolution: Analysis of nuclear 18S rRNA sequences
    • Chaw, S., Zharkikh, A., Sung, H., Lau, T., Li, W., 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 14, 56-68.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 56-68
    • Chaw, S.1    Zharkikh, A.2    Sung, H.3    Lau, T.4    Li, W.5
  • 10
    • 0002002208 scopus 로고
    • Major clades and relationships in the "higher" gymnosperms
    • Beck, C.B. (Ed.), Columbia University Press, New York, NY
    • Crane, P.R., 1988. Major clades and relationships in the "higher" gymnosperms. In: Beck, C.B. (Ed.), Origin and Evolution of Gymnosperms. Columbia University Press, New York, NY, pp. 218-272.
    • (1988) Origin and Evolution of Gymnosperms , pp. 218-272
    • Crane, P.R.1
  • 11
    • 0030431040 scopus 로고    scopus 로고
    • Seed plant phylogeny and the relationships of Gnetales
    • Doyle, J.A., 1996. Seed plant phylogeny and the relationships of Gnetales. Int. J. Plant Sci. 157, S3-S39.
    • (1996) Int. J. Plant Sci. , vol.157
    • Doyle, J.A.1
  • 12
    • 0032411093 scopus 로고    scopus 로고
    • Phylogeny of vascular plants
    • Doyle, J.A., 1998. Phylogeny of vascular plants. Ann. Rev. Ecol. Syst. 29, 567-599.
    • (1998) Ann. Rev. Ecol. Syst. , vol.29 , pp. 567-599
    • Doyle, J.A.1
  • 13
    • 0001234321 scopus 로고
    • Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach
    • Doyle, J.A., Donoghue, M.J., 1986. Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Bot. Rev. 52, 321-431.
    • (1986) Bot. Rev. , vol.52 , pp. 321-431
    • Doyle, J.A.1    Donoghue, M.J.2
  • 14
    • 0002594984 scopus 로고
    • A rapid isolation procedure for small quantities of fresh leaf tissue
    • Doyle, J.J., Doyle, J.L., 1987. A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
    • (1987) Phytochem. Bull. , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 15
    • 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
  • 16
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 17
    • 0020933869 scopus 로고
    • Parsimony in systematics: Biological and statistical issues
    • Felsenstein, J., 1983. Parsimony in systematics: biological and statistical issues. Ann. Rev. Ecol. Syst. 14, 313-333.
    • (1983) Ann. Rev. Ecol. Syst. , vol.14 , pp. 313-333
    • Felsenstein, J.1
  • 18
    • 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 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 19
    • 0024887226 scopus 로고
    • A review of fossil cycad megasporophylls, with new evidence of Crossazamia Pomel and its associated leaves from the Lower Permian of Taiyuan, China
    • Gao, Z., Thomas, B.A., 1989. A review of fossil cycad megasporophylls, with new evidence of Crossazamia Pomel and its associated leaves from the Lower Permian of Taiyuan, China. Rev. Palaeobot. Palynol. 60, 205-223.
    • (1989) Rev. Palaeobot. Palynol. , vol.60 , pp. 205-223
    • Gao, Z.1    Thomas, B.A.2
  • 20
    • 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., Bobrova, V., Pahnke, J., Troitsky, A., Antonov, A., Martin, W., 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
  • 21
    • 0033666273 scopus 로고    scopus 로고
    • Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms
    • Graham, S.W., Olmstead, R.G., 2000a. 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
  • 22
    • 0034030879 scopus 로고    scopus 로고
    • Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages
    • Graham, S.W., Olmstead, R.G., 2000b. Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages. Curr. Genet. 37, 183-188.
    • (2000) Curr. Genet. , vol.37 , pp. 183-188
    • Graham, S.W.1    Olmstead, R.G.2
  • 23
    • 0036790003 scopus 로고    scopus 로고
    • Rooting phylogenetic trees with distant outgroups: A case study from the commelinoid monocots
    • Graham, S.W., Olmstead, R.G., Barrett, S.C.H., 2002. Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots. Mol. Biol. Evol. 19, 1769-1781.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1769-1781
    • Graham, S.W.1    Olmstead, R.G.2    Barrett, S.C.H.3
  • 24
    • 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., Reeves, P.A., Burns, A.C.E., Olmstead, R.G., 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
  • 25
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H., Yano, T., 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21, 160-174.
    • (1985) J. Mol. Evol. , vol.21 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 26
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy, M.D., Penny, D., 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
  • 27
    • 0002187494 scopus 로고
    • Evolutionary cladistics and the origin of the angiosperms
    • Joysey, K.A., Friday, E.A. (Eds.), Academic Press, London
    • Hill, C.R., Crane, P.R., 1982. Evolutionary cladistics and the origin of the angiosperms. In: Joysey, K.A., Friday, E.A. (Eds.), Problems of Phylogenetic Reconstruction. Academic Press, London, pp. 269-361.
    • (1982) Problems of Phylogenetic Reconstruction , pp. 269-361
    • Hill, C.R.1    Crane, P.R.2
  • 28
    • 0031436890 scopus 로고    scopus 로고
    • Phylogeny estimation and hypothesis testing using maximum likelihood
    • Huelsenbeck, J.P., Crandall, K.A., 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Ann. Rev. Ecol. Syst. 28, 437-466.
    • (1997) Ann. Rev. Ecol. Syst. , vol.28 , pp. 437-466
    • Huelsenbeck, J.P.1    Crandall, K.A.2
  • 29
    • 0004158930 scopus 로고
    • Smithsoman Institution Press, Washington, DC
    • Jones, D.L., 1993. Cycads of the World. Smithsoman Institution Press, Washington, DC.
    • (1993) Cycads of the World
    • Jones, D.L.1
  • 30
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro, H.N. (Ed.), Academic Press, New York, NY
    • Jukes, T.H., Cantor, C.R., 1969. Evolution of protein molecules. In: Munro, H.N. (Ed.), Mammalian Protein Metabolism. Academic Press, New York, NY, pp. 21-32.
    • (1969) Mammalian Protein Metabolism , pp. 21-32
    • Jukes, T.H.1    Cantor, C.R.2
  • 31
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave, C., Preparata, G., Saccone, C., Serio, G., 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20, 86-93.
    • (1984) J. Mol. Evol. , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 32
    • 0001392984 scopus 로고
    • Cladistics of the Spermatophyta
    • Loconte, H., Stevenson, D.W., 1990. Cladistics of the Spermatophyta. Brittonia 42, 197-211.
    • (1990) Brittonia , vol.42 , pp. 197-211
    • Loconte, H.1    Stevenson, D.W.2
  • 33
    • 0008923176 scopus 로고
    • Cycads: Fossil evidence of late Paleozoic origin
    • Mamay, S.H., 1969. Cycads: fossil evidence of late Paleozoic origin. Science 164, 295-296.
    • (1969) Science , vol.164 , pp. 295-296
    • Mamay, S.H.1
  • 34
  • 35
    • 0033615479 scopus 로고    scopus 로고
    • The root of angiosperm phylogeny inferred from duplicate phytochrome genes
    • Mathews, S., Donoghue, M.J., 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
  • 37
    • 0004582645 scopus 로고
    • Studies of cycad reproduction at Fairchild Tropical Garden
    • Norstog, K.J., 1990. Studies of cycad reproduction at Fairchild Tropical Garden. Mem. New York Bot. Gard. 57, 63-81.
    • (1990) Mem. New York Bot. Gard. , vol.57 , pp. 63-81
    • Norstog, K.J.1
  • 39
    • 0033576614 scopus 로고    scopus 로고
    • Multigene analyses identify the three earliest lineage of extant flowering plants
    • Parkinson, C.L., Adams, K.L., Palmer, J.D., 1999. Multigene analyses identify the three earliest lineage 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
  • 40
    • 0040894933 scopus 로고
    • Estudios numericos en Cycadales. II. Cycadales actuales: Simulacion de arboles evolutivos
    • Petriella, B., Crisci, J.V., 1977. Estudios numericos en Cycadales. II. Cycadales actuales: simulacion de arboles evolutivos. Obra Mus. La Plata 3, 151-159.
    • (1977) Obra Mus. La Plata , vol.3 , pp. 151-159
    • Petriella, B.1    Crisci, J.V.2
  • 44
    • 0027947860 scopus 로고
    • Lignophyte phylogeny and the evolution of spermatophytes: A numerical cladistic analysis
    • Rothwell, G.W., Serbet, R., 1994. Lignophyte phylogeny and the evolution of spermatophytes: a numerical cladistic analysis. Syst. Bot. 19, 443-482.
    • (1994) Syst. Bot. , vol.19 , pp. 443-482
    • Rothwell, G.W.1    Serbet, R.2
  • 45
    • 0036177790 scopus 로고    scopus 로고
    • Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems, and the monophyly of conifers
    • Rydin, C., Källersjö, M., Friis, E.M., 2002. Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: conflicting data, rooting problems, and the monophyly of conifers. Int. J. Plant Sci. 163, 197-214.
    • (2002) Int. J. Plant Sci. , vol.163 , pp. 197-214
    • Rydin, C.1    Källersjö, M.2    Friis, E.M.3
  • 46
    • 0001654063 scopus 로고    scopus 로고
    • Sources of error and confidence intervals in estimating the age of the angiosperms from rbcL and 18S rDNA data
    • Sanderson, M.J., Doyle, J.A., 2001. Sources of error and confidence intervals in estimating the age of the angiosperms from rbcL and 18S rDNA data. Am. J. Bot. 88, 1499-1516.
    • (2001) Am. J. Bot. , vol.88 , pp. 1499-1516
    • Sanderson, M.J.1    Doyle, J.A.2
  • 47
    • 0034069504 scopus 로고    scopus 로고
    • Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
    • Sanderson, M.J., Wojciechowski, M.F., Hu, J.M., Sher Khan, T., Brady, S.G., 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    Sher Khan, T.4    Brady, S.G.5
  • 49
    • 1642272086 scopus 로고
    • Computer-assisted systematics in the Cycadales
    • Stevenson, D.W., Norstog, K.J. (Eds.), Palm and Cycad Societies of Australia Ltd., Queensland
    • Schutzman, B., Dehgan, B., 1993. Computer-assisted systematics in the Cycadales. In: Stevenson, D.W., Norstog, K.J. (Eds.), Proceedings of CYCAD 90, the Second International Conference of Cycad Biology. Palm and Cycad Societies of Australia Ltd., Queensland, pp. 281-289.
    • (1993) Proceedings of CYCAD 90, the Second International Conference of Cycad Biology , pp. 281-289
    • Schutzman, B.1    Dehgan, B.2
  • 50
    • 0033604619 scopus 로고    scopus 로고
    • Angiosperm phylogeny inferred from multiple chloroplast genes as a tool for comparative biology
    • Soltis, P.E., Soltis, D.E., Chase, M.W., 1999. Angiosperm phylogeny inferred from multiple chloroplast genes as a tool for comparative biology. Nature 402, 402-404.
    • (1999) Nature , vol.402 , pp. 402-404
    • Soltis, P.E.1    Soltis, D.E.2    Chase, M.W.3
  • 51
    • 0013103203 scopus 로고
    • Observations on ptyxis, phenology, and trichomes in the Cycadales and their systematic implications
    • Stevenson, D.W., 1981. Observations on ptyxis, phenology, and trichomes in the Cycadales and their systematic implications. Am. J. Bot. 68, 1104-1114.
    • (1981) Am. J. Bot. , vol.68 , pp. 1104-1114
    • Stevenson, D.W.1
  • 52
    • 0000992338 scopus 로고
    • A proposed classification of the Cycadales
    • Abstract
    • Stevenson, D.W., 1985. A proposed classification of the Cycadales. Am. J. Bot. 72, 971-972 (Abstract).
    • (1985) Am. J. Bot. , vol.72 , pp. 971-972
    • Stevenson, D.W.1
  • 53
    • 0002432955 scopus 로고
    • Morphology and systematics of the Cycadales
    • Stevenson, D.W., 1990. Morphology and systematics of the Cycadales. Mem. New York Bot. Gard. 57, 8-55.
    • (1990) Mem. New York Bot. Gard. , vol.57 , pp. 8-55
    • Stevenson, D.W.1
  • 54
    • 0001035344 scopus 로고
    • A formal classification of the extant cycads
    • Stevenson, D.W., 1992. A formal classification of the extant cycads. Brittonia 44, 220-223.
    • (1992) Brittonia , vol.44 , pp. 220-223
    • Stevenson, D.W.1
  • 57
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Sinauer Associates, Sunderland, MA
    • Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, second ed. Sinauer Associates, Sunderland, MA, pp. 407-543.
    • (1996) Molecular Systematics, Second Ed. , pp. 407-543
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 58
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems on the analysis of DNA sequences
    • Tavaré, S., 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lec. Math. Life Sci. 17, 57-86.
    • (1986) Lec. Math. Life Sci. , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 60
    • 0028043489 scopus 로고
    • Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii
    • Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Tsudzuki, T., Sugiura, M., 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. 91, 9794-9798.
    • (1994) Proc. Natl. Acad. Sci. , vol.91 , pp. 9794-9798
    • Wakasugi, T.1    Tsudzuki, J.2    Ito, S.3    Nakashima, K.4    Tsudzuki, T.5    Sugiura, M.6


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