메뉴 건너뛰기




Volumn 54, Issue 2, 2005, Pages 183-196

Towards building the tree of life: A simulation study for all angiosperm genera

Author keywords

Angiosperms; Maximum parsimony; Monte Carlo simulations; Neighbor joining; Taxon sampling; Tree of life

Indexed keywords

ANGIOSPERM; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER SIMULATION; GENETICS; METHODOLOGY; MONTE CARLO METHOD; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPRODUCIBILITY; SAMPLE SIZE;

EID: 19044382857     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150590923254     Document Type: Article
Times cited : (29)

References (64)
  • 1
    • 0037355121 scopus 로고    scopus 로고
    • Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes
    • Adkins, R. M., A. H. Walton, and R. L. Honeycutt. 2003. Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol. Phylogenet. Evol. 26:409-420.
    • (2003) Mol. Phylogenet. Evol. , vol.26 , pp. 409-420
    • Adkins, R.M.1    Walton, A.H.2    Honeycutt, R.L.3
  • 2
    • 0037841805 scopus 로고    scopus 로고
    • The deep roots of eukaryotes
    • Baldauf, S. L. 2003. The deep roots of eukaryotes. Science 300:1703-1706.
    • (2003) Science , vol.300 , pp. 1703-1706
    • Baldauf, S.L.1
  • 3
    • 0035222013 scopus 로고    scopus 로고
    • Scaling of accuracy in extremely large phylogenetic trees
    • (R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, eds.). World Scientific Publishing Company, River Edge, New Jersey
    • Bininda-Emonds, O. R. P., S. G. Brady, J. Kim, and M. J. Sanderson. 2000. Scaling of accuracy in extremely large phylogenetic trees. Pages 547-558 in Pacific Symposium on Biocomputing 6 (R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, eds.). World Scientific Publishing Company, River Edge, New Jersey.
    • (2000) Pacific Symposium on Biocomputing 6 , pp. 547-558
    • Bininda-Emonds, O.R.P.1    Brady, S.G.2    Kim, J.3    Sanderson, M.J.4
  • 5
    • 0032575125 scopus 로고    scopus 로고
    • Gene sequences, collaboration, and analysis of large data sets
    • Chase, M. W., and A. V. Cox. 1998. Gene sequences, collaboration, and analysis of large data sets. Austr. Syst. Bot. 11:215-229.
    • (1998) Austr. Syst. Bot. , vol.11 , pp. 215-229
    • Chase, M.W.1    Cox, A.V.2
  • 6
    • 0036943052 scopus 로고    scopus 로고
    • Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle
    • Desper, R., and O. Gascuel. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle. J. Comp. Biol. 9: 687-705.
    • (2002) J. Comp. Biol. , vol.9 , pp. 687-705
    • Desper, R.1    Gascuel, O.2
  • 8
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • Eisen, J. A., and C. M. Fraser. 2003. Phylogenomics: Intersection of evolution and genomics. Science 300:1706-1707.
    • (2003) Science , vol.300 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 9
    • 33845518635 scopus 로고    scopus 로고
    • Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule
    • Erdös, P. L., M. A. Steel, L. A. Székely, and T. J. Warnow. 1997. Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule. Comput. Artif. Intell. 16:217-227.
    • (1997) Comput. Artif. Intell. , vol.16 , pp. 217-227
    • Erdös, P.L.1    Steel, M.A.2    Székely, L.A.3    Warnow, T.J.4
  • 11
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 12
    • 0029103137 scopus 로고
    • A new method for evaluating the shape of large phylogenies
    • Fusco, G., and Q. C. B. Cronk. 1995. A new method for evaluating the shape of large phylogenies. J. Theor. Biol. 175:235-243.
    • (1995) J. Theor. Biol. , vol.175 , pp. 235-243
    • Fusco, G.1    Cronk, Q.C.B.2
  • 13
    • 0030807655 scopus 로고    scopus 로고
    • BioNJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel, O. 1997. BioNJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 14
    • 0028887457 scopus 로고
    • Success of maximum-likelihood phylogeny inference in the 4-taxon case
    • Gaut, B. S., and P. O. Lewis. 1995. Success of maximum-likelihood phylogeny inference in the 4-taxon case. Mol. Biol. Evol. 12:152-162.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 152-162
    • Gaut, B.S.1    Lewis, P.O.2
  • 15
    • 19044396954 scopus 로고
    • Amniote phylogeny and the importance of fossils
    • Gauthier, J., A. G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 12:152-162.
    • (1988) Cladistics , vol.12 , pp. 152-162
    • Gauthier, J.1    Kluge, A.G.2    Rowe, T.3
  • 16
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
    • (1998) Syst. Biol. , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 17
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 18
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
    • (1985) J. Mol. Evol. , vol.21 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 19
    • 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
  • 20
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 21
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:1-8.
    • (1998) Syst. Biol. , vol.47 , pp. 1-8
    • Hillis, D.M.1
  • 22
    • 0028362880 scopus 로고
    • Application and accuracy of molecular phylogenies
    • Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264: 671-677.
    • (1994) Science , vol.264 , pp. 671-677
    • Hillis, D.M.1    Huelsenbeck, J.P.2    Cunningham, C.W.3
  • 23
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference
    • Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference. Syst. Biol. 52:124-126.
    • (2003) Syst. Biol. , vol.52 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.D.2    McGuire, J.A.3    Zwickl, D.J.4
  • 24
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • Huelsenbeck, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44: 17-48.
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 25
    • 0242655936 scopus 로고    scopus 로고
    • Frequent inconsistency of parsimony under a simple model of cladogenesis
    • Huelsenbeck, J. P., and K. M. Lander. 2003. Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst. Biol. 52:641-648.
    • (2003) Syst. Biol. , vol.52 , pp. 641-648
    • Huelsenbeck, J.P.1    Lander, K.M.2
  • 26
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 27
    • 0032773940 scopus 로고    scopus 로고
    • Homoplasy increases phylogenetic structure
    • Källersjö, M., V. A. Albert, and J. S. Farris. 1999. Homoplasy increases phylogenetic structure. Cladistics 15:91-93.
    • (1999) Cladistics , vol.15 , pp. 91-93
    • Källersjö, M.1    Albert, V.A.2    Farris, J.S.3
  • 28
    • 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 plants and flowering plants
    • Källersjö, 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 plants and flowering plants. Plant Syst. Evol. 213:259-287.
    • (1998) Plant Syst. Evol. , vol.213 , pp. 259-287
    • Källersjö, 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
  • 29
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • Kim, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
    • (1996) Syst. Biol. , vol.45 , pp. 363-374
    • Kim, J.1
  • 30
    • 0032028996 scopus 로고    scopus 로고
    • Large-scale phylogenies and measuring the performance of phylogenetic estimators
    • Kim, J. 1998. Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47:43-60.
    • (1998) Syst. Biol. , vol.47 , pp. 43-60
    • Kim, J.1
  • 31
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 32
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B., and D. L. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 34
    • 0038518202 scopus 로고    scopus 로고
    • Preserving the Tree of Life
    • Mace, G. M., J. L. Gittleman, and A. Purvis. 2003. Preserving the Tree of Life. Science 300:1707-1709.
    • (2003) Science , vol.300 , pp. 1707-1709
    • Mace, G.M.1    Gittleman, J.L.2    Purvis, A.3
  • 35
    • 0033680155 scopus 로고    scopus 로고
    • Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal DNA data
    • Miadlikowska, J., and F. Lutzoni. 2000. Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal DNA data. Int. J. Plant Sci. 161:925-958.
    • (2000) Int. J. Plant Sci. , vol.161 , pp. 925-958
    • Miadlikowska, J.1    Lutzoni, F.2
  • 36
    • 1542341051 scopus 로고    scopus 로고
    • Major patterns of actinopterygian phylogenies: A new perspective based on >200 complete mitochondrial DNA sequences
    • Miya, M., and M. Nishida. 2002. Major patterns of actinopterygian phylogenies: A new perspective based on >200 complete mitochondrial DNA sequences. Integr. Comp. Biol. 42:1280.
    • (2002) Integr. Comp. Biol. , vol.42 , pp. 1280
    • Miya, M.1    Nishida, M.2
  • 37
    • 0035207848 scopus 로고    scopus 로고
    • Rate acceleration and long-branch attraction in a conserved gene of cryptic Daphniid (Crustaceae) species
    • Omilian, A. R., and D. J. Taylor. 2001. Rate acceleration and long-branch attraction in a conserved gene of cryptic Daphniid (Crustaceae) species. Mol. Biol. Evol. 18:2201-2212.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2201-2212
    • Omilian, A.R.1    Taylor, D.J.2
  • 38
    • 0002310070 scopus 로고    scopus 로고
    • Building phylogenies: Are the big easy?
    • Purvis, A., and D. L. J. Quicke. 1997. Building phylogenies: Are the big easy? Trends Ecol. Evol. 12:49-50.
    • (1997) Trends Ecol. Evol. , vol.12 , pp. 49-50
    • Purvis, A.1    Quicke, D.L.J.2
  • 40
    • 0035527380 scopus 로고    scopus 로고
    • Changing the landscape: A new strategy for estimating large phylogenies
    • Quicke, D. L. J., J. Taylor, and A. Purvis. 2001. Changing the landscape: A new strategy for estimating large phylogenies. Syst. Biol. 50:60-66.
    • (2001) Syst. Biol. , vol.50 , pp. 60-66
    • Quicke, D.L.J.1    Taylor, J.2    Purvis, A.3
  • 41
  • 42
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new methods of phylogenetic inference
    • Rannala, B., and Z. H. Yang. 1996. Probability distribution of molecular evolutionary trees: A new methods of phylogenetic inference. J. Mol. Evol. 43:304-311.
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.H.2
  • 43
    • 0032407089 scopus 로고    scopus 로고
    • Fast Fitch - Parsimony algorithms for large data sets
    • Ronquist, F. 1998. Fast Fitch - Parsimony algorithms for large data sets. Cladistics 14:387-400.
    • (1998) Cladistics , vol.14 , pp. 387-400
    • Ronquist, F.1
  • 45
    • 0036005526 scopus 로고    scopus 로고
    • Building supertrees: An empirical assessment using the grass family (Poaceae)
    • Salamin, N., T. R. Hodkinson, and V. Savolainen. 2002. Building supertrees: An empirical assessment using the grass family (Poaceae). Syst. Biol. 51:112-126.
    • (2002) Syst. Biol. , vol.51 , pp. 112-126
    • Salamin, N.1    Hodkinson, T.R.2    Savolainen, V.3
  • 46
    • 0042695888 scopus 로고    scopus 로고
    • The challenge of constructing large phylogenetic trees
    • Sanderson, M. J., and A. C. Driskell. 2003. The challenge of constructing large phylogenetic trees. Trends Plant Sci. 8: 374-379.
    • (2003) Trends Plant Sci. , vol.8 , pp. 374-379
    • Sanderson, M.J.1    Driskell, A.C.2
  • 48
    • 0036699890 scopus 로고    scopus 로고
    • Phylogeny reconstruction and functional constraints in organellar genomes: Plastid atpB and rbcL sequences versus animal mitochondrion
    • Savolainen, V., M. W. Chase, N. Salamin, D. E. Soltis, P. S. Soltis, A. J. Lopez, O. Fedrigo, and G. J. P. Naylor. 2002. Phylogeny reconstruction and functional constraints in organellar genomes: Plastid atpB and rbcL sequences versus animal mitochondrion. Syst. Biol. 51:638-647.
    • (2002) Syst. Biol. , vol.51 , pp. 638-647
    • Savolainen, V.1    Chase, M.W.2    Salamin, N.3    Soltis, D.E.4    Soltis, P.S.5    Lopez, A.J.6    Fedrigo, O.7    Naylor, G.J.P.8
  • 50
    • 0001541744 scopus 로고    scopus 로고
    • A supertree method for rooted trees
    • Semple, C., and M. Steel. 2000. A supertree method for rooted trees. Discrete Appl. Math. 105: 147-158.
    • (2000) Discrete Appl. Math. , vol.105 , pp. 147-158
    • Semple, C.1    Steel, M.2
  • 53
    • 2242465833 scopus 로고    scopus 로고
    • Sufficient conditions for two tree reconstruction techniques to succeed on sufficiently long sequences
    • Steel, M. 2001. Sufficient conditions for two tree reconstruction techniques to succeed on sufficiently long sequences. SIAM J. Discrete Math. 14:36-48.
    • (2001) SIAM J. Discrete Math. , vol.14 , pp. 36-48
    • Steel, M.1
  • 54
    • 0001774956 scopus 로고    scopus 로고
    • Measuring global diversity and its decline
    • (M. Reaka-Kudla, D. E. Wilson, and E. O. Wilson, eds.). Joseph Henry Press, Washington, DC
    • Stork, N. E. 1997. Measuring global diversity and its decline. Pages 41-68 in Biodiversity II: Understanding and protecting our biological resources (M. Reaka-Kudla, D. E. Wilson, and E. O. Wilson, eds.). Joseph Henry Press, Washington, DC.
    • (1997) Biodiversity II: Understanding and Protecting Our Biological Resources , pp. 41-68
    • Stork, N.E.1
  • 55
    • 0030310648 scopus 로고    scopus 로고
    • Accuracy of neighbor joining for n-taxon trees
    • Strimmer, K., and A. von Haeseler. 1996. Accuracy of neighbor joining for n-taxon trees. Syst. Biol. 45: 516-523.
    • (1996) Syst. Biol. , vol.45 , pp. 516-523
    • Strimmer, K.1    Von Haeseler, A.2
  • 56
    • 0002618746 scopus 로고    scopus 로고
    • Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics
    • Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mamml. Evol. 4:77-86.
    • (1997) J. Mamml. Evol. , vol.4 , pp. 77-86
    • Sullivan, J.1    Swofford, D.L.2
  • 58
    • 0001336205 scopus 로고    scopus 로고
    • Phylogeny reconstruction
    • (D. M. Hillis, C. Moritz and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts
    • Swofford, D. L., G. K. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogeny reconstruction. 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.K.2    Waddell, P.J.3    Hillis, D.M.4
  • 59
    • 0038191149 scopus 로고    scopus 로고
    • Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms
    • Telford, M. J., A. E. Lockyer, C. Cartwright-Finch, and D. T. J. Littlewood. 2003. Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms. Proc. R. Soc. Lond. B 270:1077-1083.
    • (2003) Proc. R. Soc. Lond. B , vol.270 , pp. 1077-1083
    • Telford, M.J.1    Lockyer, A.E.2    Cartwright-Finch, C.3    Littlewood, D.T.J.4
  • 60
    • 0038825263 scopus 로고    scopus 로고
    • Accelerated likelihood surface exploration: The likelihood ratchet
    • Vos. R. A. 2003. Accelerated likelihood surface exploration: The likelihood ratchet. Syst. Biol. 52:368-373.
    • (2003) Syst. Biol. , vol.52 , pp. 368-373
    • Vos, R.A.1
  • 61
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequence with variable rates over sites: Approximate methods
    • Yang, Z. H. 1994. Maximum likelihood phylogenetic estimation from DNA sequence with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.H.1
  • 62
    • 0032028624 scopus 로고    scopus 로고
    • On the best evolutionary rate for phylogenetic analysis
    • Yang, Z. H. 1998. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47:125-133.
    • (1998) Syst. Biol. , vol.47 , pp. 125-133
    • Yang, Z.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.