메뉴 건너뛰기




Volumn 49, Issue 1, 2000, Pages 101-113

Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l.

Author keywords

Apocynaceae s.l.; Character performance; Character weighting; Codon constraints; Functional constraints; Protein structure; Rescaled consistency index

Indexed keywords

RBCL PROTEIN, PLASTID; RIBULOSEBISPHOSPHATE CARBOXYLASE;

EID: 0034350371     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150050207410     Document Type: Article
Times cited : (50)

References (54)
  • 2
    • 0001228401 scopus 로고
    • Character-state weighting for cladistic analysis of protein-coding DNA sequences
    • ALBERT, V. A., M. W. CHASE, AND B. D. MISHLER. 1993. Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Mo. Bot. Gard. 80:752-766.
    • (1993) Ann. Mo. Bot. Gard. , vol.80 , pp. 752-766
    • Albert, V.A.1    Chase, M.W.2    Mishler, B.D.3
  • 4
    • 84983713476 scopus 로고    scopus 로고
    • Phylogenetic relationships within the gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae
    • in press. in press
    • BACKLUND, M., B. OXELMAN, AND B. BREMER, in press. Phylogenetic relationships within the Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae. Am. J. Bot. (in press).
    • Am. J. Bot.
    • Backlund, M.1    Oxelman, B.2    Bremer, B.3
  • 5
    • 0001091518 scopus 로고    scopus 로고
    • Subfamilial and tribal relationships in the rubiaceae based on rbcL sequence data
    • in press
    • BREMER, B., K. ANDREASEN, AND D. OLSSON. in press. Subfamilial and tribal relationships in the Rubiaceae based on rbcL sequence data. Ann. Mo. Bot. Gard. 82:383-397.
    • Ann. Mo. Bot. Gard. , vol.82 , pp. 383-397
    • Bremer, B.1    Andreasen, K.2    Olsson, D.3
  • 6
    • 84989486128 scopus 로고
    • Combinable component consensus
    • BREMER, K. 1990. Combinable component consensus. Cladistics 6:369-372.
    • (1990) Cladistics , vol.6 , pp. 369-372
    • Bremer, K.1
  • 8
    • 0032085607 scopus 로고    scopus 로고
    • Critical reexamination of palynological characters used to delimit Asclepiadaceae in comparison to the molecular phylogeny obtained from plastid matK sequences
    • CIVEYREL, L., A. LE THOMAS, K. FERGUSON, AND M. W. CHASE. 1998. Critical reexamination of palynological characters used to delimit Asclepiadaceae in comparison to the molecular phylogeny obtained from plastid matK sequences. Mol. Phylogenet. Evol. 9:517-527.
    • (1998) Mol. Phylogenet. Evol. , vol.9 , pp. 517-527
    • Civeyrel, L.1    Le Thomas, A.2    Ferguson, K.3    Chase, M.W.4
  • 9
    • 0028191812 scopus 로고
    • Phylogeny of the genus Pyramimonas (Prasino-phyceae, Chlorophyta) inferred from the rbcL gene
    • DAUGBJERG, N., . MOESTRUP, AND P. ARCTANDER. 1994. Phylogeny of the genus Pyramimonas (Prasino-phyceae, Chlorophyta) inferred from the rbcL gene. J. Phycol. 30:991-999.
    • (1994) J. Phycol. , vol.30 , pp. 991-999
    • Daugbjerg, N.1    Moestrup2    Arctander, P.3
  • 12
    • 84963028421 scopus 로고
    • A successive approximations approach to character weighting
    • FARRIS, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18:374-385.
    • (1969) Syst. Zool. , vol.18 , pp. 374-385
    • Farris, J.S.1
  • 13
    • 84983540175 scopus 로고
    • The retention index and the rescaled consistency index
    • FARRIS, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417-419.
    • (1989) Cladistics , vol.5 , pp. 417-419
    • Farris, J.S.1
  • 14
    • 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. 27:401-411.
    • (1978) Syst. Zool. , vol.27 , pp. 401-411
    • Felsenstein, J.1
  • 15
    • 84983695724 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
  • 16
    • 0029826321 scopus 로고    scopus 로고
    • Systematic studies of the antarctic species of the Phyllophoraceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis
    • FREDERICQ, S., AND M. E. RAMIÌREZ. 1996. Systematic studies of the antarctic species of the Phyllophoraceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis. Hydrobiologia 326/327:137-143.
    • (1996) Hydrobiologia , pp. 137-143
    • Fredericq, S.1    RamiÌrez, M.E.2
  • 17
    • 0027463557 scopus 로고
    • Ribosomal RNA trees misleading?
    • HASEGAWA, M., AND T. HASHIMOTO. 1993. Ribosomal RNA trees misleading? Nature 361:23.
    • (1993) Nature , vol.361 , pp. 23
    • Hasegawa, M.1    Hashimoto, T.2
  • 18
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
    • (1989) Syst. Zool. , vol.38 , pp. 297-309
    • Hendy, M.D.1    Penny, D.2
  • 19
    • 0027722963 scopus 로고
    • Analysis of DNA sequence data: Phylogenetic inference
    • HILLIS, D. M., M. W. ALLARD, AND M. M. MIYAMOTO. 1993. Analysis of DNA sequence data: Phylogenetic inference. Methods Enzymol. 224:456-487.
    • (1993) Methods Enzymol. , vol.224 , pp. 456-487
    • Hillis, D.M.1    Allard, M.W.2    Miyamoto, M.M.3
  • 20
    • 12044253190 scopus 로고
    • An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
    • HILLIS, D. M., AND. J. J. BULL. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
    • (1993) Syst. Biol. , vol.42 , pp. 182-192
    • Hillis, D.M.1    Bull, J.J.2
  • 21
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-8.
    • (1995) Syst. Biol. , vol.44 , pp. 17-18
    • Huelsenbeck, J.P.1
  • 22
    • 0025764044 scopus 로고
    • Evolution of the cytochrome b gene of mammals
    • IRWIN, D. T., T. D. KOCHER, AND A. C. WILSON. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32:128-144.
    • (1991) J. Mol. Evol. , vol.32 , pp. 128-144
    • Irwin, D.T.1    Kocher, T.D.2    Wilson, A.C.3
  • 23
    • 0002074574 scopus 로고
    • Angiosperm family pairs: Preliminary phylogenetic analyses
    • JUDD, W. S., R. W. SANDERS, AND M. J. DONOGHUE. 1994. Angiosperm family pairs: Preliminary phylogenetic analyses. Harv. Pap. Bot. 5:1-51.
    • (1994) Harv. Pap. Bot. , vol.5 , pp. 1-51
    • Judd, W.S.1    Sanders, R.W.2    Donoghue, M.J.3
  • 24
    • 0032420129 scopus 로고    scopus 로고
    • Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plant and flowering plants
    • KAÌLLERSJOÌ, M., J. S. FARRIS, M. W. CHASE, B. BREMER, M. F. FAY, C. J. HUMPHRIES, G. PETERSEN, O. SEBERG, AND K. BREMER. 1998. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plant and flowering plants. Plant Syst. Evol. 213:259-287.
    • (1998) Plant Syst. Evol. , vol.213 , pp. 259-287
    • KaÌllersjoÌ, M.1    Farris, J.S.2    Chase, M.W.3    Bremer, B.4    Fay, M.F.5    Humphries, C.J.6    Petersen, G.7    Seberg, O.8    Bremer, K.9
  • 25
    • 0030946680 scopus 로고    scopus 로고
    • The structure and function of RuBisCO and their implication for systematic studies
    • KELLOGG, E. A., AND N. D. JULIANO. 1997. The structure and function of RuBisCO and their implication for systematic studies. Am. J. Bot. 84:413-428.
    • (1997) Am. J. Bot. , vol.84 , pp. 413-428
    • Kellogg, E.A.1    Juliano, N.D.2
  • 27
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea
    • KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
    • (1989) J. Mol. Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 28
    • 0025160560 scopus 로고
    • Crystallographic analysis of ribulose-1,5-bisphosphate carboxylase from spinach at 2.4 aÌ resolution
    • KNIGHT, S., I. ANDERSSON, AND C.-I. BRAÌNDEÌN. 1990. Crystallographic analysis of ribulose-1,5-bisphosphate carboxylase from spinach at 2.4 AÌ resolution. J. Mol. Biol. 215:113-160.
    • (1990) J. Mol. Biol. , vol.215 , pp. 113-160
    • Knight, S.1    Andersson, I.2    BraÌndeÌn, C.-I.3
  • 29
    • 0002149670 scopus 로고
    • Taxa of the apocynaceae above the genus level. Series of revisions of Apocynaceae XXXVIII
    • LEEUWENBERG, A. J. M. 1994. Taxa of the Apocynaceae above the genus level. Series of revisions of Apocynaceae XXXVIII. Wageningen Agric. Univ. Pap. 94: 45-60.
    • (1994) Wageningen Agric. Univ. Pap. , vol.94 , pp. 45-60
    • Leeuwenberg, A.J.M.1
  • 30
    • 0000496243 scopus 로고    scopus 로고
    • Cynanchum-rhodostegiella-Vincetoxicum-Tylophora (Asclepiadaceae): New considerations on an old problem
    • LIEDE, S. 1996. Cynanchum-Rhodostegiella-Vincetoxicum-Tylophora (Asclepiadaceae): New considerations on an old problem. Taxon 45:193-211.
    • (1996) Taxon , vol.45 , pp. 193-211
    • Liede, S.1
  • 31
    • 0028077939 scopus 로고
    • Tribal disposition of genera in the Asclepiadaceae
    • LIEDE, S., AND F. ALBERS. 1994. Tribal disposition of genera in the Asclepiadaceae. Taxon 43:201-231.
    • (1994) Taxon , vol.43 , pp. 201-231
    • Liede, S.1    Albers, F.2
  • 32
    • 0028361182 scopus 로고
    • Recovering evolutionary trees under a more realistic model of sequence evolution
    • LOCKHART, P. J., M. A. STEEL, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 34
    • 0028456067 scopus 로고
    • Phylogenetic analysis of green plant rbcL sequences
    • MANHART, J. R. 1994. Phylogenetic analysis of green plant rbcL sequences. Mol. Phylogenet. Evol. 3:114-127.
    • (1994) Mol. Phylogenet. Evol. , vol.3 , pp. 114-127
    • Manhart, J.R.1
  • 36
    • 0001329538 scopus 로고    scopus 로고
    • Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA
    • (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York
    • OLMSTEAD, R. G., P. A. REEVES, AND A. C. YEN. 1998. Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA. Pages 164-187. In Molecular systematics of plants, Volume 2; DNA sequencing (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York.
    • (1998) Molecular Systematics of Plants, Volume 2; DNA Sequencing , vol.2 , pp. 164-187
    • Olmstead, R.G.1    Reeves, P.A.2    Yen, A.C.3
  • 37
    • 0026660413 scopus 로고
    • A simple method for estimating and testing minimum-evolution trees
    • RHZETSKY, A., AND M. NEI. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 945-967
    • Rhzetsky, A.1    Nei, M.2
  • 38
    • 0004282518 scopus 로고
    • SAS Institute Inc., Cary, North Carolina
    • SAS INSTITUTE. 1990. SAS/STAT User's guide, 6. SAS Institute Inc., Cary, North Carolina.
    • (1990) SAS/STAT User's Guide, 6.
  • 40
    • 0032229387 scopus 로고    scopus 로고
    • Morphology and molecular data in phylogenetic fraternity - The tribe Wrightieae (Apocynaceae) revisited
    • SENNBLAD, B., M. E. ENDRESS, AND B. BREMER. 1998. Morphology and molecular data in phylogenetic fraternity - the tribe Wrightieae (Apocynaceae) revisited. Am. J. Bot. 85:1143-1158.
    • (1998) Am. J. Bot. , vol.85 , pp. 1143-1158
    • Sennblad, B.1    Endress, M.E.2    Bremer, B.3
  • 42
    • 0028251187 scopus 로고
    • Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers
    • SIMON, C., F. FRATI, A. BECKENBACH, B. CRESPI, H. LIU, AND P. FLOOK. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
    • (1994) Ann. Entomol. Soc. Am. , vol.87 , pp. 651-701
    • Simon, C.1    Frati, F.2    Beckenbach, A.3    Crespi, B.4    Liu, H.5    Flook, P.6
  • 44
    • 0002687565 scopus 로고    scopus 로고
    • Molecular evolution of 18S rDNA in angiosperms: Implications for character weighting in phylogenetic analysis
    • (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York
    • SOLTIS, P. S., AND D. E. SOLTIS. 1998. Molecular evolution of 18S rDNA in angiosperms: Implications for character weighting in phylogenetic analysis. Pages 188-210. In Molecular systematics of plants, Volume 2; DNA sequencing (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York.
    • (1998) Molecular Systematics of Plants, Volume 2; DNA Sequencing , vol.2 , pp. 188-210
    • Soltis, P.S.1    Soltis, D.E.2
  • 45
    • 0027180533 scopus 로고
    • Confidence in evolutionary trees from biological data
    • STEEL, M. A., P. J. LOCKHART, AND D. PENNY. 1993. Confidence in evolutionary trees from biological data. Nature 364:440-442.
    • (1993) Nature , vol.364 , pp. 440-442
    • Steel, M.A.1    Lockhart, P.J.2    Penny, D.3
  • 46
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • STRIMMER, K., AND A. VON HAESLER. 1996. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haesler, A.2
  • 49
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts
    • SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 50
    • 0002766501 scopus 로고
    • The genus Microloma (Asclepiadaceae)
    • WANNTORP, H.-E. 1988. The genus Microloma (Asclepiadaceae). Opera Bot. 98:1-69.
    • (1988) Opera Bot. , vol.98 , pp. 1-69
    • Wanntorp, H.-E.1
  • 51
    • 0023672228 scopus 로고
    • Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications
    • WHEELER, W. C., AND R. L. HONEYCUTT. 1988. Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications. Mol. Biol. Evol. 5:90-96.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 90-96
    • Wheeler, W.C.1    Honeycutt, R.L.2
  • 52
    • 0001336098 scopus 로고
    • Phylogenetic relationships of Cornus L. Sensu lato and putative relatives inferred from rbcL sequence data
    • XIANG, Q.-Y., D. E. SOLTIS, D. R. MORGAN, AND P. S. SOLTIS. 1993. Phylogenetic relationships of Cornus L. sensu lato and putative relatives inferred from rbcL sequence data. Ann. Mo. Bot. Gard. 80:723-734.
    • (1993) Ann. Mo. Bot. Gard. , vol.80 , pp. 723-734
    • Xiang, Q.-Y.1    Soltis, D.E.2    Morgan, D.R.3    Soltis, P.S.4
  • 53
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • YANG, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39: 306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 54
    • 0029878719 scopus 로고    scopus 로고
    • Phylogenetic analysis using parsimony and likelihood methods
    • YANG, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. J Mol. Evol. 42:294-307.
    • (1996) J Mol. Evol. , vol.42 , pp. 294-307
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.