메뉴 건너뛰기




Volumn 89, Issue 10, 2002, Pages 1651-1669

Group II introns as phylogenetic tools: Structure, function, and evolutionary constraints

Author keywords

Chloroplast noncoding DNA; Group II introns; Molecular evolution; Phylogenetic analysis; RNA structure; rpl16 intron

Indexed keywords

ANALYTICAL METHOD; PHYLOGENETICS;

EID: 0036800826     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.89.10.1651     Document Type: Review
Times cited : (109)

References (208)
  • 1
    • 0029670279 scopus 로고    scopus 로고
    • Catalytic role of 2′-hydroxyl groups within a group II intron active site
    • Abramovitz, D. L., R. A. Friedman, And A. M. Pyle. 1996. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271: 1410-1413.
    • (1996) Science , vol.271 , pp. 1410-1413
    • Abramovitz, D.L.1    Friedman, R.A.2    Pyle, A.M.3
  • 2
    • 0035902136 scopus 로고    scopus 로고
    • Molecular phylogeny of the tribe Anthospermeae (Rubiaceae): Systematic and biogeographic implications
    • Anderson, C. L., J. H. E. Rova, And L. Andersson. 2001. Molecular phylogeny of the tribe Anthospermeae (Rubiaceae): Systematic and biogeographic implications. Australian Systematic Botany 14: 231-244.
    • (2001) Australian Systematic Botany , vol.14 , pp. 231-244
    • Anderson, C.L.1    Rova, J.H.E.2    Andersson, L.3
  • 3
    • 0034531021 scopus 로고    scopus 로고
    • A molecular phylogeny of Tropaeolaceae and its systematic implications
    • Andersson, L., And S. Andersson. 2000. A molecular phylogeny of Tropaeolaceae and its systematic implications. Taxon 49: 721-736.
    • (2000) Taxon , vol.49 , pp. 721-736
    • Andersson, L.1    Andersson, S.2
  • 5
    • 0032895759 scopus 로고    scopus 로고
    • The rps16 intron and the phylogeny of the Rubioideae (Rubiaceae)
    • Andersson, L., And J. H. E. Rova. 1999. The rps16 intron and the phylogeny of the Rubioideae (Rubiaceae). Plant Systematics and Evolution 214: 161-186.
    • (1999) Plant Systematics and Evolution , vol.214 , pp. 161-186
    • Andersson, L.1    Rova, J.H.E.2
  • 6
    • 0033923039 scopus 로고    scopus 로고
    • Phylogeny of the Madagascan endemic family Didiereaceae
    • Applequist, W. L., And R. S. Wallace. 2000. Phylogeny of the Madagascan endemic family Didiereaceae. Plant Systematics and Evolution 221: 157-166.
    • (2000) Plant Systematics and Evolution , vol.221 , pp. 157-166
    • Applequist, W.L.1    Wallace, R.S.2
  • 7
    • 0000942405 scopus 로고    scopus 로고
    • Toward a chloroplast DNA phylogeny of the tribe Geonomeae (Palmae)
    • Asmussen, C. B. 1999. Toward a chloroplast DNA phylogeny of the tribe Geonomeae (Palmae). Memoirs of the New York Botanical Garden 83: 121-129.
    • (1999) Memoirs of the New York Botanical Garden , vol.83 , pp. 121-129
    • Asmussen, C.B.1
  • 8
    • 0347420076 scopus 로고    scopus 로고
    • Coding and noncoding plastid DNA in palm systematics
    • Asmussen, C. B., And M. W. Chase. 2001. Coding and noncoding plastid DNA in palm systematics. American Journal of Botany 88: 1103-1117.
    • (2001) American Journal of Botany , vol.88 , pp. 1103-1117
    • Asmussen, C.B.1    Chase, M.W.2
  • 9
    • 0032229886 scopus 로고    scopus 로고
    • Chloroplast DNA characters, phylogeny, and classification of Lathyrus (Fabaceae)
    • Asmussen, C. B., And A. Liston. 1998. Chloroplast DNA characters, phylogeny, and classification of Lathyrus (Fabaceae). American Journal of Botany 85: 387-401.
    • (1998) American Journal of Botany , vol.85 , pp. 387-401
    • Asmussen, C.B.1    Liston, A.2
  • 10
    • 0034130101 scopus 로고    scopus 로고
    • Phylogeny, character evolution, and a new classification of the Calamoid palms
    • Baker, W. J., And J. Dransfield. 2000. Phylogeny, character evolution, and a new classification of the Calamoid palms. Systematic Botany 25: 297-322.
    • (2000) Systematic Botany , vol.25 , pp. 297-322
    • Baker, W.J.1    Dransfield, J.2
  • 11
    • 0034079633 scopus 로고    scopus 로고
    • Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data
    • Baker, W. J., T. A. Hedderson, And J. Dransfield. 2000. Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Molecular Phylogenetics and Evolution 14: 195-217.
    • (2000) Molecular Phylogenetics and Evolution , vol.14 , pp. 195-217
    • Baker, W.J.1    Hedderson, T.A.2    Dransfield, J.3
  • 12
    • 0033760831 scopus 로고    scopus 로고
    • Mitochondrial and chloroplast DNA-based phylogeny of Pelargonium (Geraniaceae)
    • Bakker, F. T., A. Culham, C. E. Pankhurst, And M. Gibby. 2000. Mitochondrial and chloroplast DNA-based phylogeny of Pelargonium (Geraniaceae). American Journal of Botany 87: 727-734.
    • (2000) American Journal of Botany , vol.87 , pp. 727-734
    • Bakker, F.T.1    Culham, A.2    Pankhurst, C.E.3    Gibby, M.4
  • 14
    • 0032148618 scopus 로고    scopus 로고
    • Data sets, partitions, and characters: Philosophies and procedures for analyzing multiple data sets
    • Ballard, J. W. O., M. K. Thayer, A. F. Newton, And E. R. Grismer. 1998. Data sets, partitions, and characters: Philosophies and procedures for analyzing multiple data sets. Systematic Biology 47: 367-396.
    • (1998) Systematic Biology , vol.47 , pp. 367-396
    • Ballard, J.W.O.1    Thayer, M.K.2    Newton, A.F.3    Grismer, E.R.4
  • 15
    • 0032099630 scopus 로고    scopus 로고
    • Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets
    • Baum, D. A., R. L. Small, And J. F. Wendel. 1998. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology 47: 181-207.
    • (1998) Systematic Biology , vol.47 , pp. 181-207
    • Baum, D.A.1    Small, R.L.2    Wendel, J.F.3
  • 16
    • 0025259663 scopus 로고
    • Improvement of PCR amplified DNA sequencing with the aid of detergents
    • Bechmann, B., W. Luke, And G. Hunsmann. 1990. Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Research 18: 1309.
    • (1990) Nucleic Acids Research , vol.18 , pp. 1309
    • Bechmann, B.1    Luke, W.2    Hunsmann, G.3
  • 17
    • 0033000112 scopus 로고    scopus 로고
    • Synonymous nucleotide divergence and saturation: Effects of site-specific variations in codon bias and mutation rates
    • Berg, O. G. 1999. Synonymous nucleotide divergence and saturation: Effects of site-specific variations in codon bias and mutation rates. Journal of Molecular Evolution 48: 398-407.
    • (1999) Journal of Molecular Evolution , vol.48 , pp. 398-407
    • Berg, O.G.1
  • 18
    • 0034104829 scopus 로고    scopus 로고
    • The cyanobacterial origin and vertical transmission of the plastid tRNA(Leu) group-I intron
    • Besendahl, A., Y. L. Qiu, J. D. Palmer, And D. Bhattacharya. 2000. The cyanobacterial origin and vertical transmission of the plastid tRNA(Leu) group-I intron. Current Genetics 37: 12-23.
    • (2000) Current Genetics , vol.37 , pp. 12-23
    • Besendahl, A.1    Qiu, Y.L.2    Palmer, J.D.3    Bhattacharya, D.4
  • 19
    • 0027441281 scopus 로고
    • Trans-splicing of pre-mRNA in plants, animals, and protists
    • Bonen, L. 1993. Trans-splicing of pre-mRNA in plants, animals, and protists. FASEB Journal 7: 40-46.
    • (1993) FASEB Journal , vol.7 , pp. 40-46
    • Bonen, L.1
  • 20
    • 0034691515 scopus 로고    scopus 로고
    • A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron
    • Boudvillain, M., A. De Lencastre, And A. M. Pyle. 2000. A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron. Nature 406: 315-318.
    • (2000) Nature , vol.406 , pp. 315-318
    • Boudvillain, M.1    De Lencastre, A.2    Pyle, A.M.3
  • 21
    • 0032404048 scopus 로고    scopus 로고
    • Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis
    • Boudvillain, M., And A. M. Pyle. 1998. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis. EMBO Journal 17: 7091-7104.
    • (1998) EMBO Journal , vol.17 , pp. 7091-7104
    • Boudvillain, M.1    Pyle, A.M.2
  • 22
    • 0034485919 scopus 로고    scopus 로고
    • Phylogeny and classification of the subfamily Rubioideae (Rubiaceae)
    • Bremer, B., And J. F. Manen. 2000. Phylogeny and classification of the subfamily Rubioideae (Rubiaceae). Plant Systematics and Evolution 225: 43-72.
    • (2000) Plant Systematics and Evolution , vol.225 , pp. 43-72
    • Bremer, B.1    Manen, J.F.2
  • 23
    • 43949160320 scopus 로고
    • Branch support and tree stability
    • Bremer, K. 1994. Branch support and tree stability. Cladistics 10: 295-304.
    • (1994) Cladistics , vol.10 , pp. 295-304
    • Bremer, K.1
  • 24
    • 0035527383 scopus 로고    scopus 로고
    • Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support
    • Buckley, T. R., C. Simon, And G. K. Chambers. 2001. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Systematic Biology 50: 67-86.
    • (2001) Systematic Biology , vol.50 , pp. 67-86
    • Buckley, T.R.1    Simon, C.2    Chambers, G.K.3
  • 25
    • 0001827911 scopus 로고    scopus 로고
    • The intron in chloroplast gene rpl16 is missing from the flowering plant families Geraniaceae, Goodeniaceae, and Plumbaginaceae
    • Campagna, M. L., And S. R. Downie. 1998. The intron in chloroplast gene rpl16 is missing from the flowering plant families Geraniaceae, Goodeniaceae, and Plumbaginaceae. Transactions of the Illinois State Academy of Science 91: 1-11.
    • (1998) Transactions of the Illinois State Academy of Science , vol.91 , pp. 1-11
    • Campagna, M.L.1    Downie, S.R.2
  • 26
    • 0035005937 scopus 로고    scopus 로고
    • Phylogeny and historical biogeography of Lauraceae: Evidence from the chloroplast and nuclear genomes
    • Chanderbali, A. S., H. Van Der Werff, And S. S. Renner. 2001. Phylogeny and historical biogeography of Lauraceae: Evidence from the chloroplast and nuclear genomes. Annals of the Missouri Botanical Gardens 88: 104-134.
    • (2001) Annals of the Missouri Botanical Gardens , vol.88 , pp. 104-134
    • Chanderbali, A.S.1    Van der Werff, H.2    Renner, S.S.3
  • 27
    • 0028569768 scopus 로고
    • Catalytic site components common to both splicing steps of a group II intron
    • Chanfreau, G., And A. Jacquier. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266: 1383-1387.
    • (1994) Science , vol.266 , pp. 1383-1387
    • Chanfreau, G.1    Jacquier, A.2
  • 28
    • 0025810050 scopus 로고
    • The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: A trans-splicing model for this gene-in-pieces
    • Chapdelaine, Y., And L. Bonen. 1991. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: A trans-splicing model for this gene-in-pieces. Cell 65: 465-472.
    • (1991) Cell , vol.65 , pp. 465-472
    • Chapdelaine, Y.1    Bonen, L.2
  • 29
    • 0032878830 scopus 로고    scopus 로고
    • Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of the Araceae family
    • Cho, Y., And J. D. Palmer. 1999. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of the Araceae family. Molecular Biology and Evolution 16: 1155-1165.
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 1155-1165
    • Cho, Y.1    Palmer, J.D.2
  • 31
    • 0031671299 scopus 로고    scopus 로고
    • More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns
    • Chu, V. T., Q. Liu, M. Podar, P. S. Perlman, And A. M. Pyle. 1998. More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns. RNA 4: 1186-1202.
    • (1998) RNA , vol.4 , pp. 1186-1202
    • Chu, V.T.1    Liu, Q.2    Podar, M.3    Perlman, P.S.4    Pyle, A.M.5
  • 32
    • 0001597889 scopus 로고    scopus 로고
    • Molecular phylogenetics of Melastomataceae and Memecylaceae: Implications for character evolution
    • Clausing, G., And S. S. Renner. 2001. Molecular phylogenetics of Melastomataceae and Memecylaceae: Implications for character evolution. American Journal of Botany 88: 486-498.
    • (2001) American Journal of Botany , vol.88 , pp. 486-498
    • Clausing, G.1    Renner, S.S.2
  • 34
    • 0034983477 scopus 로고    scopus 로고
    • Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference
    • Conant, G. C., And P. O. Lewis. 2001. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Molecular Biology and Evolution 18: 1024-1033.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1024-1033
    • Conant, G.C.1    Lewis, P.O.2
  • 35
    • 85036873088 scopus 로고    scopus 로고
    • A preliminary phylogeny of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea) based on SSU rRNA
    • In press
    • Cook, L. G., P. J. Gullan, And H. G. Trueman. In press. A preliminary phylogeny of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea) based on SSU rRNA. Molecular Phylogenetics and Evolution.
    • Molecular Phylogenetics and Evolution
    • Cook, L.G.1    Gullan, P.J.2    Trueman, H.G.3
  • 36
    • 0031552355 scopus 로고    scopus 로고
    • Multiple tertiary interactions involving domain II of group II self-splicing introns
    • Costa, M., E. Deme, A. Jacquier, And F. Michel. 1997. Multiple tertiary interactions involving domain II of group II self-splicing introns. Journal of Molecular Biology 267: 520-536.
    • (1997) Journal of Molecular Biology , vol.267 , pp. 520-536
    • Costa, M.1    Deme, E.2    Jacquier, A.3    Michel, F.4
  • 37
    • 0028921811 scopus 로고
    • Frequent use of the same tertiary motif by self-splicing RNAs
    • Costa, M., And F. Michel. 1995. Frequent use of the same tertiary motif by self-splicing RNAs. EMBO Journal 14: 1276-1285.
    • (1995) EMBO Journal , vol.14 , pp. 1276-1285
    • Costa, M.1    Michel, F.2
  • 38
    • 0033558318 scopus 로고    scopus 로고
    • Tight binding of 5′ exon to domain I of a group II self-splicing intron requires completion of the intron active site
    • Costa, M., And F. Michel. 1999. Tight binding of 5′ exon to domain I of a group II self-splicing intron requires completion of the intron active site. EMBO Journal 18: 1025-1037.
    • (1999) EMBO Journal , vol.18 , pp. 1025-1037
    • Costa, M.1    Michel, F.2
  • 39
    • 0034665039 scopus 로고    scopus 로고
    • A three-dimensional perspective on exon binding by a group II self-splicing intron
    • Costa, M., F. Michel, And E. Westhof. 2000. A three-dimensional perspective on exon binding by a group II self-splicing intron. EMBO Journal I9: 5007-5018.
    • (2000) EMBO Journal , vol.I9 , pp. 5007-5018
    • Costa, M.1    Michel, F.2    Westhof, E.3
  • 40
    • 0034720157 scopus 로고    scopus 로고
    • Retro-transposition of a bacterial group II intron
    • Cousineau, B., S. Lawrence, D. Smith, And M. Belfort. 2000. Retro-transposition of a bacterial group II intron. Nature 404: 1018-1021.
    • (2000) Nature , vol.404 , pp. 1018-1021
    • Cousineau, B.1    Lawrence, S.2    Smith, D.3    Belfort, M.4
  • 41
    • 0029240502 scopus 로고
    • A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants
    • Demesure, B., N. Sodzi, And R. J. Petit. 1995. A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131.
    • (1995) Molecular Ecology , vol.4 , pp. 129-131
    • Demesure, B.1    Sodzi, N.2    Petit, R.J.3
  • 42
    • 0027263683 scopus 로고
    • Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing
    • Dib-Hajj, S. D., S. C. Boulanger, S. K. Hebbar, C. L. Peebles, J. S. Franzen, And P. S. Perlman. 1993. Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing. Nucleic Acids Research 21: 1797-1804.
    • (1993) Nucleic Acids Research , vol.21 , pp. 1797-1804
    • Dib-Hajj, S.D.1    Boulanger, S.C.2    Hebbar, S.K.3    Peebles, C.L.4    Franzen, J.S.5    Perlman, P.S.6
  • 43
    • 0027500136 scopus 로고
    • Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis
    • Dixon, M. T., And D. M. Hillis. 1993. Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Molecular Biology and Evolution 10: 256-267.
    • (1993) Molecular Biology and Evolution , vol.10 , pp. 256-267
    • Dixon, M.T.1    Hillis, D.M.2
  • 44
    • 0034745879 scopus 로고    scopus 로고
    • Chloroplast transformation in Euglena gracilis: Splicing of a group III twintron transcribed from a transgenic psbK operon
    • Doetsch, N. A., M. R. Favreau, N. Kuscuoglu, M. D. Thompson, And R. B. Hallick. 2001. Chloroplast transformation in Euglena gracilis: Splicing of a group III twintron transcribed from a transgenic psbK operon. Current Genetics 39: 49-60.
    • (2001) Current Genetics , vol.39 , pp. 49-60
    • Doetsch, N.A.1    Favreau, M.R.2    Kuscuoglu, N.3    Thompson, M.D.4    Hallick, R.B.5
  • 45
    • 0033502706 scopus 로고    scopus 로고
    • Phylogenetic analysis of chloroplast rps16 intron sequences reveals relationships within the woody southern African Apiaceae subfamily Apioideae
    • Downie, S. R., And D. S. Katz-Downie. 1999. Phylogenetic analysis of chloroplast rps16 intron sequences reveals relationships within the woody southern African Apiaceae subfamily Apioideae. Canadian Journal of Botany 77: 1120-1135.
    • (1999) Canadian Journal of Botany , vol.77 , pp. 1120-1135
    • Downie, S.R.1    Katz-Downie, D.S.2
  • 46
    • 0030208439 scopus 로고    scopus 로고
    • Phylogenetic analysis of Apiaceae subfamily Apioideae using nucleotide sequences from the chloroplast rpoC1 intron
    • Downie, S. R., D. S. Katz-Downie, And K.-J. Cho. 1996. Phylogenetic analysis of Apiaceae subfamily Apioideae using nucleotide sequences from the chloroplast rpoC1 intron. Molecular Phylogenetics and Evolution 6: 1-18.
    • (1996) Molecular Phylogenetics and Evolution , vol.6 , pp. 1-18
    • Downie, S.R.1    Katz-Downie, D.S.2    Cho, K.-J.3
  • 47
    • 0031729009 scopus 로고    scopus 로고
    • Multiple independent losses of the plastid rpoC1 intron in Medicago (Fabaceae) as inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer sequences
    • Downie, S. R., D. S. Katz-Downie, E. J. Rogers, H. L. Zujewski, And E. Small. 1998a. Multiple independent losses of the plastid rpoC1 intron in Medicago (Fabaceae) as inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer sequences. Canadian Journal of Botany 76: 791-803.
    • (1998) Canadian Journal of Botany , vol.76 , pp. 791-803
    • Downie, S.R.1    Katz-Downie, D.S.2    Rogers, E.J.3    Zujewski, H.L.4    Small, E.5
  • 48
    • 0033759668 scopus 로고    scopus 로고
    • A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: Towards a suprageneric classification of subfamily Apioideae
    • Downie, S. R., D. S. Katz-Downie, And M. F. Watson. 2000. A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: Towards a suprageneric classification of subfamily Apioideae. American Journal of Botany 87: 273-292.
    • (2000) American Journal of Botany , vol.87 , pp. 273-292
    • Downie, S.R.1    Katz-Downie, D.S.2    Watson, M.F.3
  • 49
    • 0030451873 scopus 로고    scopus 로고
    • Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNA's
    • Downie, S. R., E. Llanas, And D. S. Katz-Downie. 1996. Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNA's. Systematic Botany 21: 135-151.
    • (1996) Systematic Botany , vol.21 , pp. 135-151
    • Downie, S.R.1    Llanas, E.2    Katz-Downie, D.S.3
  • 50
    • 0026309878 scopus 로고
    • 6 Independent losses of the chloroplast DNA rpl2 intron in dicotyledons - Molecular and phylogenetic implications
    • Downie, S. R., R. G. Olmstead, G. Zurawski, D. E. Soltis, P. S. Soltis, J. C. Watson, And J. D. Palmer. 1991. 6 Independent losses of the chloroplast DNA rpl2 intron in dicotyledons - Molecular and phylogenetic implications. Evolution 45: 1245-1259.
    • (1991) Evolution , vol.45 , pp. 1245-1259
    • Downie, S.R.1    Olmstead, R.G.2    Zurawski, G.3    Soltis, D.E.4    Soltis, P.S.5    Watson, J.C.6    Palmer, J.D.7
  • 51
    • 0002110604 scopus 로고
    • Use of Chloroplast DNA rearrangements in reconstructing plant phylogeny
    • D. E. Soltis et al. [eds.]. Chapman and Hall, New York, New York, USA
    • Downie, S. R., And J. D. Palmer. 1992. Use of Chloroplast DNA rearrangements in reconstructing plant phylogeny. In D. E. Soltis et al. [eds.], Molecular Systematics of Plants, 14-35. Chapman and Hall, New York, New York, USA.
    • (1992) Molecular Systematics of Plants , pp. 14-35
    • Downie, S.R.1    Palmer, J.D.2
  • 52
    • 0027948710 scopus 로고
    • A chloroplast DNA phylogeny of the Caryophyllales based on structural and inverted repeat restriction-site variation
    • Downie, S. R., AND J. D. Palmer. 1994. A chloroplast DNA phylogeny of the Caryophyllales based on structural and inverted repeat restriction-site variation. Systematic Botany 19: 236-252.
    • (1994) Systematic Botany , vol.19 , pp. 236-252
    • Downie, S.R.1    Palmer, J.D.2
  • 53
    • 0032229595 scopus 로고    scopus 로고
    • Molecular systematics of Apiaceae subfamily Apioideae: Phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences
    • Downie, S. R., S. Ramanath, D. S. Katz-Downie, And E. Llanas. 1998b. Molecular systematics of Apiaceae subfamily Apioideae: Phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences. American Journal of Botany 85: 563-591.
    • (1998) American Journal of Botany , vol.85 , pp. 563-591
    • Downie, S.R.1    Ramanath, S.2    Katz-Downie, D.S.3    Llanas, E.4
  • 54
    • 0028835478 scopus 로고
    • Multiple independent losses of two genes and one intron from legume chloroplast genomes
    • Doyle, J. J., J. L. Doyle, And J. D. Palmer. 1995. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Systematic Botany 20: 272-294.
    • (1995) Systematic Botany , vol.20 , pp. 272-294
    • Doyle, J.J.1    Doyle, J.L.2    Palmer, J.D.3
  • 56
    • 0033552870 scopus 로고    scopus 로고
    • Mobile introns: Retrohoming by complete reverse splicing
    • Eickbush, T. H. 1999. Mobile introns: Retrohoming by complete reverse splicing. Current Biology 9: R11-R14.
    • (1999) Current Biology , vol.9
    • Eickbush, T.H.1
  • 57
    • 0029411215 scopus 로고
    • Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana
    • Ems, S. C., C. W. Morden, C. K. Dixon, K. H. Wolfe, C. W. Depamphilis, And J. D. Palmer. 1995. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Molecular Biology 29: 721-733.
    • (1995) Plant Molecular Biology , vol.29 , pp. 721-733
    • Ems, S.C.1    Morden, C.W.2    Dixon, C.K.3    Wolfe, K.H.4    Depamphilis, C.W.5    Palmer, J.D.6
  • 58
    • 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. Systematic Zoology 27: 401-410.
    • (1978) Systematic Zoology , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 59
    • 0020933869 scopus 로고
    • Parsimony in systematics: Biological and statistical issues
    • Felsenstein, J. 1983. Parsimony in systematics: Biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333.
    • (1983) Annual Review of Ecology and Systematics , vol.14 , pp. 313-333
    • Felsenstein, J.1
  • 60
    • 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
  • 61
    • 0034818755 scopus 로고    scopus 로고
    • Taking variation of evolutionary rates between sites into account in inferring phylogenies
    • Felsenstein, J. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. Journal of Molecular Evolution 53: 447-455.
    • (2001) Journal of Molecular Evolution , vol.53 , pp. 447-455
    • Felsenstein, J.1
  • 62
    • 0034789422 scopus 로고    scopus 로고
    • Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters
    • Freudenstein, J. V., And M. W. Chase. 2001. Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters. Systematic Botany 26: 643-657.
    • (2001) Systematic Botany , vol.26 , pp. 643-657
    • Freudenstein, J.V.1    Chase, M.W.2
  • 63
    • 0028093707 scopus 로고
    • Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes
    • Gatesy, J., C. Hayashi, R. DeSalle, And E. Vrba. 1994. Rate limits for mispairing and compensatory change: The mitochondrial ribosomal DNA of antelopes. Evolution 48: 188-196.
    • (1994) Evolution , vol.48 , pp. 188-196
    • Gatesy, J.1    Hayashi, C.2    DeSalle, R.3    Vrba, E.4
  • 65
    • 0344430855 scopus 로고
    • Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses
    • Goldman, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Systematic Zoology 39: 345-361.
    • (1990) Systematic Zoology , vol.39 , pp. 345-361
    • Goldman, N.1
  • 66
    • 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. American Journal of Botany 87: 1712-1730.
    • (2000) American Journal of Botany , vol.87 , pp. 1712-1730
    • Graham, S.W.1    Olmstead, R.G.2
  • 67
    • 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. International Journal of Plant Science 161: S83-S96.
    • (2000) International Journal of Plant Science , vol.161
    • Graham, S.W.1    Reeves, P.A.2    Burns, A.C.E.3    Olmstead, R.G.4
  • 68
    • 0034698288 scopus 로고    scopus 로고
    • Group II introns designed to insert into therapeutically relevant DNA target sites in human cells
    • Guo, H. T., M. Karberg, M. Long, J. P. Jones, B. Sullenger, And A. M. Lambowitz. 2000. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 289: 452-457.
    • (2000) Science , vol.289 , pp. 452-457
    • Guo, H.T.1    Karberg, M.2    Long, M.3    Jones, J.P.4    Sullenger, B.5    Lambowitz, A.M.6
  • 70
    • 0027491314 scopus 로고
    • The phylogenetically predicted base-pairing interactions between alpha and alpha is required for group II intron splicing in vitro
    • Harris-Kerr, C. L., M. Zhang, And C. L. Peebles. 1993. The phylogenetically predicted base-pairing interactions between alpha and alpha is required for group II intron splicing in vitro. Proceedings of the National Academy of Sciences, USA 90: 10 658-10 662.
    • (1993) Proceedings of the National Academy of Sciences, USA , vol.90 , pp. 10658-10662
    • Harris-Kerr, C.L.1    Zhang, M.2    Peebles, C.L.3
  • 71
    • 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. Systematic Zoology 38: 297-309.
    • (1989) Systematic Zoology , vol.38 , pp. 297-309
    • Hendy, M.D.1    Penny, D.2
  • 72
    • 0027983839 scopus 로고
    • Correct in vivo RNA splicing of a mitochondrial intron in algal chloroplasts
    • Herdenberger, F., V. Holländer, And U. Kuck. 1994. Correct in vivo RNA splicing of a mitochondrial intron in algal chloroplasts. Nucleic Acids Research 22: 2869-2875.
    • (1994) Nucleic Acids Research , vol.22 , pp. 2869-2875
    • Herdenberger, F.1    Holländer, V.2    Kuck, U.3
  • 73
    • 0002888491 scopus 로고    scopus 로고
    • Ribosomal DNA sequences and angiosperm systematics
    • P. M. Hollingsworth, R. M. Bateman, and R. J. Gornall [eds.]. Taylor & Francis, London, UK
    • Hershkovitz, M. A., E. A. Zimmer, And W. J. Hahn. 1999. Ribosomal DNA sequences and angiosperm systematics. In P. M. Hollingsworth, R. M. Bateman, and R. J. Gornall [eds.], Molecular Systematics and Plant Evolution, 268-326. Taylor & Francis, London, UK.
    • (1999) Molecular Systematics and Plant Evolution , pp. 268-326
    • Hershkovitz, M.A.1    Zimmer, E.A.2    Hahn, W.J.3
  • 75
    • 0034043777 scopus 로고    scopus 로고
    • The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence
    • Hickson, R. E., C. Simon, And S. W. Perrey. 2000. The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Molecular Biology and Evolution 17: 530-539.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 530-539
    • Hickson, R.E.1    Simon, C.2    Perrey, S.W.3
  • 76
    • 0031952062 scopus 로고    scopus 로고
    • Splicing of the mitochondrial group-II intron rI1: Conserved intron-exon interactions diminish splicing efficiency
    • Holländer, V., And U. Kück. 1998. Splicing of the mitochondrial group-II intron rI1: Conserved intron-exon interactions diminish splicing efficiency. Current Genetics 33: 117-123.
    • (1998) Current Genetics , vol.33 , pp. 117-123
    • Holländer, V.1    Kück, U.2
  • 77
    • 18744427597 scopus 로고    scopus 로고
    • Group II intron splicing in chloroplasts: Identification of mutations determining intron stability and fate of exon RNA
    • Holländer, V., And U. Kück. 1999. Group II intron splicing in chloroplasts: Identification of mutations determining intron stability and fate of exon RNA. Nucleic Acids Research 27: 2345-2353.
    • (1999) Nucleic Acids Research , vol.27 , pp. 2345-2353
    • Holländer, V.1    Kück, U.2
  • 78
    • 0032960288 scopus 로고    scopus 로고
    • Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi
    • Holst-Jensen, A., M. Vaage, T. Schumacher, And S. Johansen. 1999. Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi. Molecular Biology and Evolution 16: 114-126.
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 114-126
    • Holst-Jensen, A.1    Vaage, M.2    Schumacher, T.3    Johansen, S.4
  • 79
    • 0028296307 scopus 로고
    • Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera
    • Hoot, S. B., And J. D. Palmer. 1994. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. Journal of Molecular Evolution 38: 274-281.
    • (1994) Journal of Molecular Evolution , vol.38 , pp. 274-281
    • Hoot, S.B.1    Palmer, J.D.2
  • 80
    • 0033139150 scopus 로고    scopus 로고
    • Effect of nonindependent substitution on phylogenetic accuracy
    • Huelsenbeck, J. P., And R. Neilsen. 1999. Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology 48: 317-328.
    • (1999) Systematic Biology , vol.48 , pp. 317-328
    • Huelsenbeck, J.P.1    Neilsen, R.2
  • 81
    • 0029827383 scopus 로고    scopus 로고
    • Group II introns: Elaborate ribozymes
    • Jacquier, A. 1996. Group II introns: Elaborate ribozymes. Biochimie 78: 474-487.
    • (1996) Biochimie , vol.78 , pp. 474-487
    • Jacquier, A.1
  • 82
    • 0025755708 scopus 로고
    • Splice site selection and role of the lariat in a group II intron
    • Jacquier, A., And Jacquesson-Breuleux. 1991. Splice site selection and role of the lariat in a group II intron. Journal of Molecular Biology 219: 415-428.
    • (1991) Journal of Molecular Biology , vol.219 , pp. 415-428
    • Jacquier, A.1    Jacquesson-Breuleux2
  • 83
    • 0023643081 scopus 로고
    • Multiple exon-binding sites in class II self-splicing intrans
    • Jacquier, A., And F. Michel. 1987. Multiple exon-binding sites in class II self-splicing intrans. Cell 50: 17-29.
    • (1987) Cell , vol.50 , pp. 17-29
    • Jacquier, A.1    Michel, F.2
  • 84
    • 0025344901 scopus 로고
    • Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II self-splicing introns
    • Jacquier, A., And F. Michel. 1990. Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II self-splicing introns. Journal of Molecular Biology 213: 437-447.
    • (1990) Journal of Molecular Biology , vol.213 , pp. 437-447
    • Jacquier, A.1    Michel, F.2
  • 85
    • 0031106356 scopus 로고    scopus 로고
    • Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors
    • Jenkins, B., D. J. Kulhanek, And A. Barkan. 1997. Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. Cell 9: 283-296.
    • (1997) Cell , vol.9 , pp. 283-296
    • Jenkins, B.1    Kulhanek, D.J.2    Barkan, A.3
  • 86
    • 0001528719 scopus 로고    scopus 로고
    • Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae)
    • Jordan, W. C., M. W. Courtney, And J. E. Neigel. 1996. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). American Journal of Botany 83: 430-439.
    • (1996) American Journal of Botany , vol.83 , pp. 430-439
    • Jordan, W.C.1    Courtney, M.W.2    Neigel, J.E.3
  • 87
  • 88
    • 0029997930 scopus 로고    scopus 로고
    • Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA
    • Katayama, H., And Y. Ogihara. 1996. Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Current Genetics 29: 572-581.
    • (1996) Current Genetics , vol.29 , pp. 572-581
    • Katayama, H.1    Ogihara, Y.2
  • 89
    • 0034491886 scopus 로고    scopus 로고
    • The evolution of noncoding chloroplast DNA and its application in plant systematics
    • Kelchner, S. A. 2000. The evolution of noncoding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Gardens 87: 482-498.
    • (2000) Annals of the Missouri Botanical Gardens , vol.87 , pp. 482-498
    • Kelchner, S.A.1
  • 90
    • 0000115544 scopus 로고    scopus 로고
    • A data partition analysis of noncoding sequence evolution in Bontia and Myoporaceae
    • Abstract
    • Kelchner, S. A., R. J. Bayer, R. J. Chinnock, M. D. Crisp, And J. G. West. 2000. A data partition analysis of noncoding sequence evolution in Bontia and Myoporaceae. American Journal of Botany 87: 136 (Abstract).
    • (2000) American Journal of Botany , vol.87 , pp. 136
    • Kelchner, S.A.1    Bayer, R.J.2    Chinnock, R.J.3    Crisp, M.D.4    West, J.G.5
  • 91
    • 0031306828 scopus 로고    scopus 로고
    • Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae)
    • Kelchner, S. A., And L. G. Clark. 1997. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397.
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , pp. 385-397
    • Kelchner, S.A.1    Clark, L.G.2
  • 92
    • 0029811392 scopus 로고    scopus 로고
    • Hairpins create minute inversions in noncoding regions of chloroplast DNA
    • Kelchner, S. A., And J. F. Wendel. 1996. Hairpins create minute inversions in noncoding regions of chloroplast DNA. Current Genetics 30: 259-262.
    • (1996) Current Genetics , vol.30 , pp. 259-262
    • Kelchner, S.A.1    Wendel, J.F.2
  • 93
    • 0030946680 scopus 로고    scopus 로고
    • The structure and function of RuBisCO and their implications for systematic studies
    • Kellogg, E. A., And N. D. Juliano. 1997. The structure and function of RuBisCO and their implications for systematic studies. American Journal of Botany 84: 413-428.
    • (1997) American Journal of Botany , vol.84 , pp. 413-428
    • Kellogg, E.A.1    Juliano, N.D.2
  • 94
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura, M. 1968. Evolutionary rate at the molecular level. Nature 217: 624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 96
    • 0029365329 scopus 로고
    • Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs
    • Kjer, L. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Molecular Phylogenetics and Evolution 4: 314-330.
    • (1995) Molecular Phylogenetics and Evolution , vol.4 , pp. 314-330
    • Kjer, L.M.1
  • 97
    • 0030808127 scopus 로고    scopus 로고
    • A tripartite group II intron in mitochondria of an angiosperm plant
    • Knoop, V., M. Altwasser, And A. Brennicke. 1997. A tripartite group II intron in mitochondria of an angiosperm plant. Molecular and General Genetics 255: 269-276.
    • (1997) Molecular and General Genetics , vol.255 , pp. 269-276
    • Knoop, V.1    Altwasser, M.2    Brennicke, A.3
  • 98
    • 0011129449 scopus 로고
    • Group II introns in plant mitochondria-trans-splicing, RNA editing, evolution and promiscuity
    • A. Brennicke and U. Kück [eds.]. VCH, Weinheim, New York, New York, USA
    • Knoop, V., And A. Brennicke. 1993. Group II introns in plant mitochondria-trans-splicing, RNA editing, evolution and promiscuity. In A. Brennicke and U. Kück [eds.], Plant Mitochondria, 220-232. VCH, Weinheim, New York, New York, USA.
    • (1993) Plant Mitochondria , pp. 220-232
    • Knoop, V.1    Brennicke, A.2
  • 100
    • 0032401749 scopus 로고    scopus 로고
    • A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme
    • Konforti, B. B., Q. Liu, And A. M. Pyle. 1998. A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme. EMBO Journal 17: 7105-7117.
    • (1998) EMBO Journal , vol.17 , pp. 7105-7117
    • Konforti, B.B.1    Liu, Q.2    Pyle, A.M.3
  • 102
    • 0028177080 scopus 로고
    • A simulation of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner, M. K., And J. Felsenstein. 1994. A simulation of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11: 459-468.
    • (1994) Molecular Biology and Evolution , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 103
    • 0024401019 scopus 로고
    • Structure-function relationships in a self-splicing group II intron: A large part of domain II of the mitochondrial intron aI5 is not essential for self-splicing
    • Kwakman, J. H., D. Konings, H. J. Pel, And L. A. Grivell. 1989. Structure-function relationships in a self-splicing group II intron: A large part of domain II of the mitochondrial intron aI5 is not essential for self-splicing. Nucleic Acids Research 17: 4205-4216.
    • (1989) Nucleic Acids Research , vol.17 , pp. 4205-4216
    • Kwakman, J.H.1    Konings, D.2    Pel, H.J.3    Grivell, L.A.4
  • 104
    • 0031431280 scopus 로고    scopus 로고
    • Polymorphism for the presence of the rpl2 intron in chloroplast genomes of Bauhinia (Leguminosae)
    • Lai, M., J. Sceppa, J. A. Ballenger, J. J. Doyle, And R. P. Wunderlin. 1997. Polymorphism for the presence of the rpl2 intron in chloroplast genomes of Bauhinia (Leguminosae). Systematic Botany 22: 519-528.
    • (1997) Systematic Botany , vol.22 , pp. 519-528
    • Lai, M.1    Sceppa, J.2    Ballenger, J.A.3    Doyle, J.J.4    Wunderlin, R.P.5
  • 106
    • 0032957760 scopus 로고    scopus 로고
    • Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1
    • Laroche, J., and J. Bousquet. 1999. Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1. Molecular Biology and Evolution 16: 441-452.
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 441-452
    • Laroche, J.1    Bousquet, J.2
  • 107
    • 0028033047 scopus 로고
    • Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers
    • Lazowska, J., B. Meunier, and C. Macadre. 1994. Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers. EMBO Journal 13: 4963-4972.
    • (1994) EMBO Journal , vol.13 , pp. 4963-4972
    • Lazowska, J.1    Meunier, B.2    Macadre, C.3
  • 108
    • 0026660411 scopus 로고
    • Constraints on the evolution of plastid introns: The group II intron in the gene encoding tRNA-Val(UAC)
    • Learn, G. H. J., J. S. Shore, G. R. Furnier, G. Zurawski, and M. T. Clegg. 1992. Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC). Molecular Biology and Evolution 9: 856-871.
    • (1992) Molecular Biology and Evolution , vol.9 , pp. 856-871
    • Learn, G.H.J.1    Shore, J.S.2    Furnier, G.R.3    Zurawski, G.4    Clegg, M.T.5
  • 109
    • 0034045269 scopus 로고    scopus 로고
    • Phylogenetic analysis of cpDNA restriction sites and rps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa
    • Lee, B.-Y., and S. R. Downie. 2000. Phylogenetic analysis of cpDNA restriction sites and rps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa. Plant Systematics and Evolution 221: 35-60.
    • (2000) Plant Systematics and Evolution , vol.221 , pp. 35-60
    • Lee, B.-Y.1    Downie, S.R.2
  • 110
    • 0000521631 scopus 로고    scopus 로고
    • A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences
    • Lee, J., and T. Hymowitz. 2001. A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences. American Journal of Botany 88: 2064-2073.
    • (2001) American Journal of Botany , vol.88 , pp. 2064-2073
    • Lee, J.1    Hymowitz, T.2
  • 111
    • 0002948868 scopus 로고    scopus 로고
    • Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
    • D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.]. Kluwer Academic, Boston, Massachusetts, USA
    • Lewis, P. O. 1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II: DNA sequencing, 132-163. Kluwer Academic, Boston, Massachusetts, USA.
    • (1998) Molecular Systematics of Plants II: DNA Sequencing , pp. 132-163
    • Lewis, P.O.1
  • 112
    • 0030958291 scopus 로고    scopus 로고
    • Phylogeny and classification of Fumariaceae, with emphasis on Dicentra s.1., based on the plastid gene rps16 intron
    • Liden, M., T. Fukuhara, J. Rylander, and B. Oxelman. 1997. Phylogeny and classification of Fumariaceae, with emphasis on Dicentra s.1., based on the plastid gene rps16 intron. Plant Systematics and Evolution 206: 411-420.
    • (1997) Plant Systematics and Evolution , vol.206 , pp. 411-420
    • Liden, M.1    Fukuhara, T.2    Rylander, J.3    Oxelman, B.4
  • 113
    • 0027952084 scopus 로고
    • The phylogenetic position of the genus Astragalus (Fabaceae): Evidence from the chloroplast genes rpoC1 and rpoC2
    • Liston, A., and J. A. Wheeler. 1994. The phylogenetic position of the genus Astragalus (Fabaceae): evidence from the chloroplast genes rpoC1 and rpoC2. Biochemical Systematics and Ecology 22: 377-388.
    • (1994) Biochemical Systematics and Ecology , vol.22 , pp. 377-388
    • Liston, A.1    Wheeler, J.A.2
  • 115
    • 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. Molecular Biology and Evolution 11: 605-612.
    • (1994) Molecular Biology and Evolution , vol.11 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 116
    • 0034351388 scopus 로고    scopus 로고
    • Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology
    • Lutzoni, F., P. Wagner, V. Reeb, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49: 628-651.
    • (2000) Systematic Biology , vol.49 , pp. 628-651
    • Lutzoni, F.1    Wagner, P.2    Reeb, V.3    Zoller, S.4
  • 118
    • 0001705679 scopus 로고    scopus 로고
    • Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
    • Maddison, D. R., M. D. Baker, and K. A. Ober. 1999. Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae). Systematic Entomology 24: 103-138.
    • (1999) Systematic Entomology , vol.24 , pp. 103-138
    • Maddison, D.R.1    Baker, M.D.2    Ober, K.A.3
  • 119
    • 0031789680 scopus 로고    scopus 로고
    • Trans-splicing group II introns in plant mitochondria: The complete ser of cis-arranged homologs in ferns, fern allies, and a hornwort
    • Malek, O., and V. Knoop. 1998. Trans-splicing group II introns in plant mitochondria: the complete ser of cis-arranged homologs in ferns, fern allies, and a hornwort. RNA 4: 1599-1609.
    • (1998) RNA , vol.4 , pp. 1599-1609
    • Malek, O.1    Knoop, V.2
  • 120
    • 0033947771 scopus 로고    scopus 로고
    • The codon-degeneracy model of molecular evolution
    • McClellan, D. A. 2000. The codon-degeneracy model of molecular evolution. Journal of Molecular Evolution 50: 131-140.
    • (2000) Journal of Molecular Evolution , vol.50 , pp. 131-140
    • McClellan, D.A.1
  • 121
    • 0021092830 scopus 로고
    • Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members
    • Michel, F., and B. Dujon. 1983. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members. EMBO Journal 2: 33-38.
    • (1983) EMBO Journal , vol.2 , pp. 33-38
    • Michel, F.1    Dujon, B.2
  • 122
    • 0029066770 scopus 로고
    • Structure and activities of group II introns
    • Michel, F., and J.-L. Ferat. 1995. Structure and activities of group II introns. Annual Review of Biochemistry 64: 435-461.
    • (1995) Annual Review of Biochemistry , vol.64 , pp. 435-461
    • Michel, F.1    Ferat, J.-L.2
  • 123
    • 0024428420 scopus 로고
    • Comparative and functional anatomy of group II catalytic introns - A review
    • Michel, F., K. Umesono, and H. Ozeki. 1989. Comparative and functional anatomy of group II catalytic introns-a review. Gene 82: 5-30.
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 124
    • 0033750527 scopus 로고    scopus 로고
    • Deletion of a conserved dinucleotide inhibits the second step of group II intron splicing
    • Mikheeva, S., H. L. Murray, H. Zhou, B. M. Turczyk, and K. A. Jarrell. 2000. Deletion of a conserved dinucleotide inhibits the second step of group II intron splicing. RNA 6: 1509-1515.
    • (2000) RNA , vol.6 , pp. 1509-1515
    • Mikheeva, S.1    Murray, H.L.2    Zhou, H.3    Turczyk, B.M.4    Jarrell, K.A.5
  • 126
    • 0027434086 scopus 로고
    • Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function
    • Mohr, G., P. S. Perlman, and A. M. Lambowitz. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Research 21: 4991-4997.
    • (1993) Nucleic Acids Research , vol.21 , pp. 4991-4997
    • Mohr, G.1    Perlman, P.S.2    Lambowitz, A.M.3
  • 127
    • 0034161995 scopus 로고    scopus 로고
    • Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences
    • Mohr, G., D. Smith, M. Belfort, and A. M. Lambowitz. 2000. Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes and Development 14: 559-573.
    • (2000) Genes and Development , vol.14 , pp. 559-573
    • Mohr, G.1    Smith, D.2    Belfort, M.3    Lambowitz, A.M.4
  • 129
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa
    • Morrison, D. A., and J. T. Ellis. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Molecular Biology and Evolution 14: 428-441.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 130
    • 0034350373 scopus 로고    scopus 로고
    • Comparison of three methods for estimating internal support on phylogenetic trees
    • Mort, M. E., P. S. Soltis, D. E. Soltis, and M. L. Mabry. 2000. Comparison of three methods for estimating internal support on phylogenetic trees. Systematic Biology 49: 160-170.
    • (2000) Systematic Biology , vol.49 , pp. 160-170
    • Mort, M.E.1    Soltis, P.S.2    Soltis, D.E.3    Mabry, M.L.4
  • 131
    • 0027382204 scopus 로고
    • Transposition of group II intron all in yeast and invasion of mitochondrial genes at new locations
    • Mueller, M. W., M. Allmaier, R. Eskes, and R. J. Schweyen. 1993. Transposition of group II intron all in yeast and invasion of mitochondrial genes at new locations. Nature 366: 174-176.
    • (1993) Nature , vol.366 , pp. 174-176
    • Mueller, M.W.1    Allmaier, M.2    Eskes, R.3    Schweyen, R.J.4
  • 132
    • 0028900996 scopus 로고
    • Evolutionary analyses of DNA sequences subject to constraints on secondary structure
    • Muse, S. V. 1995. Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429-1439.
    • (1995) Genetics , vol.139 , pp. 1429-1439
    • Muse, S.V.1
  • 134
    • 0001329538 scopus 로고    scopus 로고
    • Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA
    • D. S. Soltis, P. S. Soltis, and J. J. Doyle [eds.]. Chapman and Hall, New York, New York, USA
    • Olmstead, R. G., P. A. Reeves, and A. C. Yen. 1998. Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA. In D. S. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II: DNA sequencing, 164-187, Chapman and Hall, New York, New York, USA.
    • (1998) Molecular Systematics of Plants II: DNA Sequencing , pp. 164-187
    • Olmstead, R.G.1    Reeves, P.A.2    Yen, A.C.3
  • 135
    • 0032855292 scopus 로고    scopus 로고
    • Relationships of the Buddlejaceae s.1. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data
    • Oxelman, B., M. Backlund, and B. Bremer. 1999. Relationships of the Buddlejaceae s.1. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data. Systematic Botany 24: 164-182.
    • (1999) Systematic Botany , vol.24 , pp. 164-182
    • Oxelman, B.1    Backlund, M.2    Bremer, B.3
  • 136
    • 0030919759 scopus 로고    scopus 로고
    • Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae)
    • Oxelman, B., M. Liden, and D. Berglund. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206: 393-410.
    • (1997) Plant Systematics and Evolution , vol.206 , pp. 393-410
    • Oxelman, B.1    Liden, M.2    Berglund, D.3
  • 138
  • 139
    • 0002021422 scopus 로고    scopus 로고
    • The origin and evolution of plastids and their genomes
    • D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Kluwer Academic, Boston, Massachusetts, USA
    • Palmer, J. D., and C. F. Delwiche. 1998. The origin and evolution of plastids and their genomes. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II: DNA sequencing, 375-409. Kluwer Academic, Boston, Massachusetts, USA.
    • (1998) Molecular Systematics of Plants II: DNA Sequencing , pp. 375-409
    • Palmer, J.D.1    Delwiche, C.F.2
  • 142
    • 0033832102 scopus 로고    scopus 로고
    • Phylogeny of the Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-trnF(GAA) intergenic spacer
    • Persson, C. 2000. Phylogeny of the Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-trnF(GAA) intergenic spacer. Nordic Journal of Botany 20: 257-269.
    • (2000) Nordic Journal of Botany , vol.20 , pp. 257-269
    • Persson, C.1
  • 143
    • 0036270658 scopus 로고    scopus 로고
    • Phylogeny of Hibiscus and the tribe Hibisceae (Malvaceae) using chloroplast DNA sequences of ndhF and the rpl16 intron
    • Pfeil, B. E., C. L. Brubaker, L. A. Craven, and M. D. Crisp. 2002. Phylogeny of Hibiscus and the tribe Hibisceae (Malvaceae) using chloroplast DNA sequences of ndhF and the rpl16 intron. Systematic Botany 27: 333-350.
    • (2002) Systematic Botany , vol.27 , pp. 333-350
    • Pfeil, B.E.1    Brubaker, C.L.2    Craven, L.A.3    Crisp, M.D.4
  • 144
    • 0034089550 scopus 로고    scopus 로고
    • Searching for the taxonomic position of the African genus Colletoecema (Rubiaceae): Morphology and anatomy compared to an rps16-intron analysis of the Rubioideae
    • Piesschaert, F., L. Andersson, S. Jansen, S. Dessein, E. Robbrecht, and E. Smets. 2000. Searching for the taxonomic position of the African genus Colletoecema (Rubiaceae): morphology and anatomy compared to an rps16-intron analysis of the Rubioideae. Canadian Journal of Botany 78: 288-304.
    • (2000) Canadian Journal of Botany , vol.78 , pp. 288-304
    • Piesschaert, F.1    Andersson, L.2    Jansen, S.3    Dessein, S.4    Robbrecht, E.5    Smets, E.6
  • 145
    • 0033065716 scopus 로고    scopus 로고
    • Photocrosslinking of 4-thio uracil-containing RNAs supports a side-by-side arrangement of domains 5 and 6 of a group II intron
    • Podar, M., and P. S. Perlman. 1999. Photocrosslinking of 4-thio uracil-containing RNAs supports a side-by-side arrangement of domains 5 and 6 of a group II intron. RNA 5: 318-329.
    • (1999) RNA , vol.5 , pp. 318-329
    • Podar, M.1    Perlman, P.S.2
  • 146
    • 0031857783 scopus 로고    scopus 로고
    • The two steps of group II intron self-splicing are mechanistically distinguishable
    • Podar, M., P. S. Perlman, and R. A. Padgett. 1998. The two steps of group II intron self-splicing are mechanistically distinguishable. RNA 4: 890-900.
    • (1998) RNA , vol.4 , pp. 890-900
    • Podar, M.1    Perlman, P.S.2    Padgett, R.A.3
  • 147
    • 0034847822 scopus 로고    scopus 로고
    • Inferring the history of the polyploid Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences
    • Popp, M., and B. Oxelman. 2001. Inferring the history of the polyploid Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences. Molecular Phylogenetics and Evolution 20: 474-481.
    • (2001) Molecular Phylogenetics and Evolution , vol.20 , pp. 474-481
    • Popp, M.1    Oxelman, B.2
  • 148
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • Posada, D., and K. A. Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50: 580-601.
    • (2001) Systematic Biology , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.2
  • 149
    • 0002319075 scopus 로고    scopus 로고
    • Catalytic reaction mechanisms and structural features of group II intron ribozymes
    • F. Eckstein and D. M. J. Lilley [eds.]. Springer Verlag, New York, New York, USA
    • Pyle, A. M. 1996. Catalytic reaction mechanisms and structural features of group II intron ribozymes. In F. Eckstein and D. M. J. Lilley [eds.], Catalytic RNA, 75-107. Springer Verlag, New York, New York, USA.
    • (1996) Catalytic RNA , pp. 75-107
    • Pyle, A.M.1
  • 150
    • 0026808975 scopus 로고
    • Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
    • Reeves, J. H. 1992. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. Journal of Molecular Evolution 35: 17-31.
    • (1992) Journal of Molecular Evolution , vol.35 , pp. 17-31
    • Reeves, J.H.1
  • 151
    • 0033298279 scopus 로고    scopus 로고
    • Circumscription and phylogeny of the Laurales: Evidence from molecular and morphological data
    • Renner, S. S. 1999. Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data. American Journal of Botany 86: 1301-1315.
    • (1999) American Journal of Botany , vol.86 , pp. 1301-1315
    • Renner, S.S.1
  • 152
    • 0033679591 scopus 로고    scopus 로고
    • What is the relationship among Hernandiaceae, Lauraceae, and Monimiaceae, and why is this question so difficult to answer?
    • Renner, S. S., and A. S. Chanderbali. 2000. What is the relationship among Hernandiaceae, Lauraceae, and Monimiaceae, and why is this question so difficult to answer? International Journal of Plant Sciences 161: S109-S119.
    • (2000) International Journal of Plant Sciences , vol.161
    • Renner, S.S.1    Chanderbali, A.S.2
  • 153
    • 0034350327 scopus 로고    scopus 로고
    • Timing transantarctic disjunctions in the Atherospermataceae (Laurales): Evidence from coding and noncoding chloroplast sequences
    • Renner. S. S., D. B. Foreman, and D. Murray. 2000. Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences. Systematic Biology 49: 579-591.
    • (2000) Systematic Biology , vol.49 , pp. 579-591
    • Renner, S.S.1    Foreman, D.B.2    Murray, D.3
  • 154
    • 0001111764 scopus 로고
    • Polymorphism, hybridization, and variable evolutionary rate in molecular phylogenies
    • P. S. Soltis, D. E. Soltis, and J. J. Doyle [eds.]. Chapman and Hall, New York, New York, USA
    • Ritland, K., and J. E. Eckenwalder. 1992. Polymorphism, hybridization, and variable evolutionary rate in molecular phylogenies. In P. S. Soltis, D. E. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants, 404-428. Chapman and Hall, New York, New York, USA.
    • (1992) Molecular Systematics of Plants , pp. 404-428
    • Ritland, K.1    Eckenwalder, J.E.2
  • 156
    • 0031725368 scopus 로고    scopus 로고
    • Two co-existing mechanisms account for the large-scale deletions of mitochondrial DNA in Podospora anserina that involve the 5′ border of a group-II intron
    • Sainsard-Chanet, A., O. Begel, and Y. D'Aubenton-Carafa. 1998. Two co-existing mechanisms account for the large-scale deletions of mitochondrial DNA in Podospora anserina that involve the 5′ border of a group-II intron. Current Genetics 34: 326-335.
    • (1998) Current Genetics , vol.34 , pp. 326-335
    • Sainsard-Chanet, A.1    Begel, O.2    D'Aubenton-Carafa, Y.3
  • 158
    • 0035085506 scopus 로고    scopus 로고
    • Phylogenetic analyses of Aurantioideae (Rutaceae) based on noncoding plastid DNA sequences and phytochemical features
    • Samuel, R., F. Ehrendorfer, M. W. Chase, and H. Greger. 2001. Phylogenetic analyses of Aurantioideae (Rutaceae) based on noncoding plastid DNA sequences and phytochemical features. Plant Biology 3: 77-87.
    • (2001) Plant Biology , vol.3 , pp. 77-87
    • Samuel, R.1    Ehrendorfer, F.2    Chase, M.W.3    Greger, H.4
  • 159
    • 0029526909 scopus 로고
    • Objections to bootstrapping phylogenies: A critique
    • Sanderson, M. J. 1995. Objections to bootstrapping phylogenies: a critique. Systematic Biology 44: 299-320.
    • (1995) Systematic Biology , vol.44 , pp. 299-320
    • Sanderson, M.J.1
  • 160
  • 161
    • 0023644230 scopus 로고
    • Self-splicing of group II introns in vitro: Lariat formation and 3′-splice site selection in mutant RNAs
    • Schmelzer, C., and M. W. Müller. 1987. Self-splicing of group II introns in vitro: lariat formation and 3′-splice site selection in mutant RNAs. Cell 51: 753-762.
    • (1987) Cell , vol.51 , pp. 753-762
    • Schmelzer, C.1    Müller, M.W.2
  • 162
    • 0022446227 scopus 로고
    • Self-splicing of group II introns in vitro: Mapping of the branch point and mutational inhibition of lariat formation
    • Schmelzer, C., and R. J. Schweyen. 1986. Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell 46: 557-565.
    • (1986) Cell , vol.46 , pp. 557-565
    • Schmelzer, C.1    Schweyen, R.J.2
  • 163
    • 0032229320 scopus 로고    scopus 로고
    • Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences
    • Schnabel, A., and J. F. Wendel. 1998. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. American Journal of Botany 85: 1753-1765.
    • (1998) American Journal of Botany , vol.85 , pp. 1753-1765
    • Schnabel, A.1    Wendel, J.F.2
  • 164
    • 0028087047 scopus 로고
    • The plant mitochondrial genome: Physical structure, information content, RNA editing, and gene migration to the nucleus
    • Schuster, W., and A. Brennicke. 1994. The plant mitochondrial genome: physical structure, information content, RNA editing, and gene migration to the nucleus. Annual Review of Plant Physiology and Plant Molecular Biology 45: 61-78.
    • (1994) Annual Review of Plant Physiology and Plant Molecular Biology , vol.45 , pp. 61-78
    • Schuster, W.1    Brennicke, A.2
  • 165
    • 0000548921 scopus 로고
    • Rapid radiation of North American desert genera of the Papaveraceae: Evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments
    • Schwarzbach, A. E., and J. W. Kadereit. 1995. Rapid radiation of North American desert genera of the Papaveraceae: evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments. Plant Systematics and Evolution 9: 159-170.
    • (1995) Plant Systematics and Evolution , vol.9 , pp. 159-170
    • Schwarzbach, A.E.1    Kadereit, J.W.2
  • 167
    • 0034019179 scopus 로고    scopus 로고
    • Recombinant mitochondrial DNA molecules suggest a template switching ability for group-II-intron reverse transcriptase
    • Sellem, C. H., O. Begel, and A. Sainsard-Chanet. 2000. Recombinant mitochondrial DNA molecules suggest a template switching ability for group-II-intron reverse transcriptase. Current Genetics 37: 24-28.
    • (2000) Current Genetics , vol.37 , pp. 24-28
    • Sellem, C.H.1    Begel, O.2    Sainsard-Chanet, A.3
  • 168
    • 0034350427 scopus 로고    scopus 로고
    • Gaps as characters in sequence-based phylogenetic analyses
    • Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
    • (2000) Systematic Biology , vol.49 , pp. 369-381
    • Simmons, M.P.1    Ochoterena, H.2
  • 169
    • 0032229478 scopus 로고    scopus 로고
    • The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group
    • Small, R. L., J. A. Ryburn, R. C. Cronn, T. Seelanan, and J. F. Wendel. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
    • (1998) American Journal of Botany , vol.85 , pp. 1301-1315
    • Small, R.L.1    Ryburn, J.A.2    Cronn, R.C.3    Seelanan, T.4    Wendel, J.F.5
  • 170
    • 0002687565 scopus 로고    scopus 로고
    • Molecular evolution of 18S rDNA in angiosperms: Implications for character weighting in phylogenetic analysis
    • D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.]. Kluwer Academic, Boston, Massachusetts, USA
    • Soltis, P. S., and D. E. Soltis. 1998. Molecular evolution of 18S rDNA in angiosperms: implications for character weighting in phylogenetic analysis. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular sytematics of plants II: DNA sequencing, 188-210. Kluwer Academic, Boston, Massachusetts, USA.
    • (1998) Molecular Sytematics of Plants II: DNA Sequencing , pp. 188-210
    • Soltis, P.S.1    Soltis, D.E.2
  • 171
    • 0028834744 scopus 로고
    • Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals
    • Springer, M., L. J. Hollar, and A. Burk. 1995. Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. Molecular Biology and Evolution 12: 1138-1150.
    • (1995) Molecular Biology and Evolution , vol.12 , pp. 1138-1150
    • Springer, M.1    Hollar, L.J.2    Burk, A.3
  • 172
    • 0034350429 scopus 로고    scopus 로고
    • Invariable sites models and their use in phylogeny reconstruction
    • Steel, M., D. Huson, and P. J. Lockhart. 2000. Invariable sites models and their use in phylogeny reconstruction. Systematic Biology 49: 225-232.
    • (2000) Systematic Biology , vol.49 , pp. 225-232
    • Steel, M.1    Huson, D.2    Lockhart, P.J.3
  • 173
    • 0034035066 scopus 로고    scopus 로고
    • Parsimony, likelihood, and the role of models in molecular phylogenetics
    • Steel, M., and D. Penny. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Molecular Biology and Evolution 17: 839-850.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 839-850
    • Steel, M.1    Penny, D.2
  • 174
    • 0029880314 scopus 로고    scopus 로고
    • The effect of topology on estimates of among-site rate variation
    • Sullivan, J., K. E. Holsinger, and C. Simon. 1996. The effect of topology on estimates of among-site rate variation. Journal of Molecular Evolution 42: 308-312.
    • (1996) Journal of Molecular Evolution , vol.42 , pp. 308-312
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 175
    • 0035527373 scopus 로고    scopus 로고
    • Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
    • Sullivan, J., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Systematic Biology 50: 723-729.
    • (2001) Systematic Biology , vol.50 , pp. 723-729
    • Sullivan, J.1    Swofford, D.L.2
  • 177
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. Hillis, C. Moritz, and B. Mable [eds.]. Sinauer, Sunderland, Massachusetts, USA
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. hillis. 1996, Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. Mable [eds.], Molecular systematics, 407-514. Sinauer, Sunderland, Massachusetts, USA.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 178
    • 0032940932 scopus 로고    scopus 로고
    • Ribozymes: The characteristics and properties of catalytic RNAs
    • Tanner, N. K. 1999. Ribozymes: the characteristics and properties of catalytic RNAs. FEMS Microbiology Reviews 23: 257-275.
    • (1999) FEMS Microbiology Reviews , vol.23 , pp. 257-275
    • Tanner, N.K.1
  • 179
    • 0034844560 scopus 로고    scopus 로고
    • CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin
    • Till, B., C. Schmitz-Linneweber, R. Williams-Carrier, and A. Barkan. 2001. CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA 7: 1227-1238.
    • (2001) RNA , vol.7 , pp. 1227-1238
    • Till, B.1    Schmitz-Linneweber, C.2    Williams-Carrier, R.3    Barkan, A.4
  • 180
    • 0034910710 scopus 로고    scopus 로고
    • Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases
    • Toor, N., G. Hausner, and S. Zimmerly. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7: 1142-1152.
    • (2001) RNA , vol.7 , pp. 1142-1152
    • Toor, N.1    Hausner, G.2    Zimmerly, S.3
  • 181
    • 0033744204 scopus 로고    scopus 로고
    • Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
    • Tufféry, P., and P. Darlu. 2000. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Molecular Biology and Evolution 17: 1753-1759.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 1753-1759
    • Tufféry, P.1    Darlu, P.2
  • 182
    • 0031149251 scopus 로고    scopus 로고
    • Links between maximum likelihood and maximum parsimony under a simple model of site substitution
    • Tuffley, C., and M. Steel. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bulletin of Mathematical Biology 59: 581-607.
    • (1997) Bulletin of Mathematical Biology , vol.59 , pp. 581-607
    • Tuffley, C.1    Steel, M.2
  • 183
    • 0028997284 scopus 로고
    • Evolutionary transfer of ORF-containing group-I introns between different subcellular compartments (chloroplast and mitochondrion)
    • Turmel, M., V. Cote, C. Otis, J. P. Mercer, M. W. Gray, K. M. Lonergan, and C. Lemieux. 1995. Evolutionary transfer of ORF-containing group-I introns between different subcellular compartments (chloroplast and mitochondrion). Molecular Biology and Evolution 12: 533-545.
    • (1995) Molecular Biology and Evolution , vol.12 , pp. 533-545
    • Turmel, M.1    Cote, V.2    Otis, C.3    Mercer, J.P.4    Gray, M.W.5    Lonergan, K.M.6    Lemieux, C.7
  • 184
    • 0034232357 scopus 로고    scopus 로고
    • The G-U wobble base pair: A fundamental building block of RNA structure crucial to RNA function in diverse biological systems
    • Varani, G., and W. H. McClain. 2000. The G-U wobble base pair: a fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Reports 1: 18-23.
    • (2000) EMBO Reports , vol.1 , pp. 18-23
    • Varani, G.1    McClain, W.H.2
  • 185
    • 0027309533 scopus 로고
    • Rates and patterns of base change in the small subunit ribosomal RNA gene
    • Vawter, L., and W. M. Brown. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134: 597-608.
    • (1993) Genetics , vol.134 , pp. 597-608
    • Vawter, L.1    Brown, W.M.2
  • 186
    • 0345062264 scopus 로고    scopus 로고
    • Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants
    • Vogerl, J., T. Börner, and W. R. Hess. 1999. Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. Nucleic Acids Research 27: 3866-3874.
    • (1999) Nucleic Acids Research , vol.27 , pp. 3866-3874
    • Vogerl, J.1    Börner, T.2    Hess, W.R.3
  • 187
    • 0034524865 scopus 로고    scopus 로고
    • Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data
    • Wallander, E., and V. A. Albert. 2000. Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data. American Journal of Botany 87: 1827-1841.
    • (2000) American Journal of Botany , vol.87 , pp. 1827-1841
    • Wallander, E.1    Albert, V.A.2
  • 188
    • 0033301379 scopus 로고    scopus 로고
    • Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences
    • Wang, X.-R., Y. Tsumura, H. Yoshimaru, K. Nagasaka, and A. E. Szmidt. 1999. Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. American Journal of Botany 86: 1742-1753.
    • (1999) American Journal of Botany , vol.86 , pp. 1742-1753
    • Wang, X.-R.1    Tsumura, Y.2    Yoshimaru, H.3    Nagasaka, K.4    Szmidt, A.E.5
  • 189
    • 0033180584 scopus 로고    scopus 로고
    • A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA
    • Wank, H., J. SanFilippo, R. N. Singh, M. Matsuura, and A. M. Lambowitz. 1999. A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA. Molecular Cell 4: 239-250.
    • (1999) Molecular Cell , vol.4 , pp. 239-250
    • Wank, H.1    SanFilippo, J.2    Singh, R.N.3    Matsuura, M.4    Lambowitz, A.M.5
  • 191
    • 0033679561 scopus 로고    scopus 로고
    • Molecular phylogeny of Old World Trifolium (Fabaceae), based on plastid and nuclear markers
    • Watson, L. E., H. Sayed-Ahmed, and A. Badr. 2000. Molecular phylogeny of Old World Trifolium (Fabaceae), based on plastid and nuclear markers. Plant Systematics and Evolution 224: 153-171.
    • (2000) Plant Systematics and Evolution , vol.224 , pp. 153-171
    • Watson, L.E.1    Sayed-Ahmed, H.2    Badr, A.3
  • 192
    • 0026957846 scopus 로고
    • Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae)
    • Wesson, D. M., C. H. Porter, and F. H. Collins. 1992. Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae). Molecular Phylogenetics and Evolution 1: 253-269.
    • (1992) Molecular Phylogenetics and Evolution , vol.1 , pp. 253-269
    • Wesson, D.M.1    Porter, C.H.2    Collins, F.H.3
  • 193
    • 0023672228 scopus 로고
    • Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implicafions
    • Wheeler, W. C., and R. L. Honeycutt. 1988. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implicafions. Molecular Biology and Evolution 5: 90-96.
    • (1988) Molecular Biology and Evolution , vol.5 , pp. 90-96
    • Wheeler, W.C.1    Honeycutt, R.L.2
  • 194
    • 0034350323 scopus 로고    scopus 로고
    • Phylogenetic relationships among the Phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes
    • Wilgenbusch, J., and K. DeQueiroz. 2000. Phylogenetic relationships among the Phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612.
    • (2000) Systematic Biology , vol.49 , pp. 592-612
    • Wilgenbusch, J.1    DeQueiroz, K.2
  • 195
    • 0024600983 scopus 로고
    • An improved method for direct sequencing PCR amplified material using dimethyl sulfoxide
    • Winship, P. R. 1989. An improved method for direct sequencing PCR amplified material using dimethyl sulfoxide. Nucleic Acids Research 17: 1266.
    • (1989) Nucleic Acids Research , vol.17 , pp. 1266
    • Winship, P.R.1
  • 196
    • 0025864763 scopus 로고
    • Trans-splicing in Oenothera mitochondria: nadl mRNAs are edited in exon and trans-splicing group II intron sequences
    • Wissinger, B., W. Schuster, and A. Brennicke. 1991. Trans-splicing in Oenothera mitochondria: nadl mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65: 473-482.
    • (1991) Cell , vol.65 , pp. 473-482
    • Wissinger, B.1    Schuster, W.2    Brennicke, A.3
  • 197
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe, K. H., W.-H. Li, and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA 84: 9054-9058.
    • (1987) Proceedings of the National Academy of Sciences, USA , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.-H.2    Sharp, P.M.3
  • 198
    • 0026447426 scopus 로고
    • Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant
    • Wolfe, K. H., C. W. Morden, and J. D. Palmer. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences, USA 89: 10648-10652.
    • (1992) Proceedings of the National Academy of Sciences, USA , vol.89 , pp. 10648-10652
    • Wolfe, K.H.1    Morden, C.W.2    Palmer, J.D.3
  • 199
    • 0032566493 scopus 로고    scopus 로고
    • Group II intron mobility in yeast mitochondria - Target DNA-primed reverse transcription activity of all and reverse splicing into DNA transposition sites in vitro
    • Yang, J., G. Mohr, P. S. Perlman, and A. M. Lambowitz. 1998. Group II intron mobility in yeast mitochondria-target DNA-primed reverse transcription activity of all and reverse splicing into DNA transposition sites in vitro. Journal of Molecular Biology 282: 505-523.
    • (1998) Journal of Molecular Biology , vol.282 , pp. 505-523
    • Yang, J.1    Mohr, G.2    Perlman, P.S.3    Lambowitz, A.M.4
  • 200
    • 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. Journal of Molecular Evolution 39: 306-314.
    • (1994) Journal of Molecular Evolution , vol.39 , pp. 306-314
    • Yang, Z.1
  • 201
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367-372.
    • (1996) Trends in Ecology and Evolution , vol.11 , pp. 367-372
    • Yang, Z.1
  • 202
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation
    • Yang, Z., N. Goldman, and A. Friday. 1994. Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Molecular Biology and Evolution 11: 316-324.
    • (1994) Molecular Biology and Evolution , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 203
    • 0033636041 scopus 로고    scopus 로고
    • Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants
    • Young, N. D., and C. W. DePamphilis. 2000. Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants. Molecular Biology and Evolution 17: 1933-1941.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 1933-1941
    • Young, N.D.1    DePamphilis, C.W.2
  • 204
    • 0034022498 scopus 로고    scopus 로고
    • Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data
    • Zhang, W. 2000. Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data. Molecular Phylogenetics and Evolution 15: 135-146.
    • (2000) Molecular Phylogenetics and Evolution , vol.15 , pp. 135-146
    • Zhang, W.1
  • 206
    • 0028859580 scopus 로고
    • A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility
    • Zimmerly, S., H. Guo, R. Eskes, J. Yang, P. S. Perlman, and A. M. Lambowitz. 1995a. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83: 529-538.
    • (1995) Cell , vol.83 , pp. 529-538
    • Zimmerly, S.1    Guo, H.2    Eskes, R.3    Yang, J.4    Perlman, P.S.5    Lambowitz, A.M.6
  • 207
    • 0029162089 scopus 로고
    • Group II intron mobility occurs by target DNA-primed reverse transcriptase
    • Zimmerly, S., H. Guo, P. S. Perlman, and A. M. Lambowitz. 1995b. Group II intron mobility occurs by target DNA-primed reverse transcriptase. Cell 82: 545-554.
    • (1995) Cell , vol.82 , pp. 545-554
    • Zimmerly, S.1    Guo, H.2    Perlman, P.S.3    Lambowitz, A.M.4
  • 208
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.