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Volumn 8, Issue 8, 2003, Pages 374-379

The challenge of constructing large phylogenetic trees

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EMBRYOPHYTA;

EID: 0042695888     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1360-1385(03)00165-1     Document Type: Review
Times cited : (83)

References (57)
  • 3
    • 0000031660 scopus 로고
    • Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL
    • Chase, M.W. et al. (1993) Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Garden 80, 528-580
    • (1993) Ann. Missouri Bot. Garden , vol.80 , pp. 528-580
    • Chase, M.W.1
  • 4
    • 0034350426 scopus 로고    scopus 로고
    • Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences
    • Savolainen, V. et al. (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 49, 306-362
    • (2000) Syst. Biol. , vol.49 , pp. 306-362
    • Savolainen, V.1
  • 5
    • 0032025585 scopus 로고    scopus 로고
    • Inferring complex phylogenies using parsimony: An empirical approach using three large DNA data sets for angiosperms
    • Soltis, D.E. et al. (1998) Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms. Syst. Biol. 47, 32-42
    • (1998) Syst. Biol. , vol.47 , pp. 32-42
    • Soltis, D.E.1
  • 6
    • 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
    • Kallersjo, M. et al. (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
    • Kallersjo, M.1
  • 7
    • 0036125446 scopus 로고    scopus 로고
    • Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA)
    • Lee, Y. et al. (2002) Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA). Genome Res. 12, 493-502
    • (2002) Genome Res. , vol.12 , pp. 493-502
    • Lee, Y.1
  • 9
    • 0036800892 scopus 로고    scopus 로고
    • Phylogeny of seed plants based on evidence from eight genes
    • Soltis, D. et al. (2002) Phylogeny of seed plants based on evidence from eight genes. Am. J. Bot. 89, 1670-1681
    • (2002) Am. J. Bot. , vol.89 , pp. 1670-1681
    • Soltis, D.1
  • 10
    • 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
  • 11
    • 0034350422 scopus 로고    scopus 로고
    • More taxa or more characters revisited: Combining data from nuclear protein-coding genes for phylogenetic analyses of Noctuidea (Insecta Lepidoptera)
    • Mitchell, A. et al. (2000) More taxa or more characters revisited: combining data from nuclear protein-coding genes for phylogenetic analyses of Noctuidea (Insecta Lepidoptera). Syst. Biol. 49, 202-224
    • (2000) Syst. Biol. , vol.49 , pp. 202-224
    • Mitchell, A.1
  • 12
    • 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
  • 13
    • 0033480324 scopus 로고    scopus 로고
    • A few logs suffice to build (almost) all trees (I)
    • Erdos, P.L. et al. (1999) A few logs suffice to build (almost) all trees (I). Random Structures & Algorithms 14, 153-184
    • (1999) Random Structures & Algorithms , vol.14 , pp. 153-184
    • Erdos, P.L.1
  • 14
    • 0035222013 scopus 로고    scopus 로고
    • Scaling of accuracy in extremely large phylogenetic trees
    • Altman, R.B. et al., eds. World Scientific, Singapore/River Edge, NJ, USA
    • Bininda-Emonds, O.R.P. et al. (2001) Scaling of accuracy in extremely large phylogenetic trees. In Pacific Symposium on Biocomputing 2001 (Altman, R.B. et al., eds), pp. 547-558, World Scientific, Singapore/River Edge, NJ, USA
    • (2001) Pacific Symposium on Biocomputing 2001 , pp. 547-558
    • Bininda-Emonds, O.R.P.1
  • 15
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 16
    • 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
  • 17
    • 0037022379 scopus 로고    scopus 로고
    • The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
    • Bapteste, E. et al. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. U. S. A. 99, 1414-1419
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 1414-1419
    • Bapteste, E.1
  • 18
    • 0037370533 scopus 로고    scopus 로고
    • Probabilistic analysis indicates discordant gene trees in chloroplast evolution
    • Vogl, C. et al. (2003) Probabilistic analysis indicates discordant gene trees in chloroplast evolution. J. Mol. Evol. 56, 330-340
    • (2003) J. Mol. Evol. , vol.56 , pp. 330-340
    • Vogl, C.1
  • 19
    • 0033920569 scopus 로고    scopus 로고
    • Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
    • Adachi, J. et al. (2000) Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50, 348-358
    • (2000) J. Mol. Evol. , vol.50 , pp. 348-358
    • Adachi, J.1
  • 20
    • 0036899796 scopus 로고    scopus 로고
    • Whole chloroplast genome comparison of rice, maize, and wheat: Implications for chloroplast gene diversification and phylogeny of cereals
    • Matsuoka, Y. et al. (2002) Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Mol. Biol. Evol. 19, 2084-2091
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2084-2091
    • Matsuoka, Y.1
  • 21
    • 0032225748 scopus 로고    scopus 로고
    • Does adding characters with missing data increase or decrease phylogenetic accuracy?
    • Wiens, J.J. (1998) Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47, 625-640
    • (1998) Syst. Biol. , vol.47 , pp. 625-640
    • Wiens, J.J.1
  • 22
    • 0036554650 scopus 로고    scopus 로고
    • Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions
    • Kearney, M. (2002) Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Syst. Biol. 51, 369-381
    • (2002) Syst. Biol. , vol.51 , pp. 369-381
    • Kearney, M.1
  • 23
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 24
    • 0031224822 scopus 로고    scopus 로고
    • Analyzing large data sets: rbcL 500 revisited
    • Rice, K.A. et al. (1997) Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46, 554-563
    • (1997) Syst. Biol. , vol.46 , pp. 554-563
    • Rice, K.A.1
  • 25
    • 0035527377 scopus 로고    scopus 로고
    • Stochastic search strategy for estimation of maximum likelihood phylogenetic trees
    • Salter, L.A. and Pearl, D.K. (2001) Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Syst. Biol. 50, 7-17
    • (2001) Syst. Biol. , vol.50 , pp. 7-17
    • Salter, L.A.1    Pearl, D.K.2
  • 26
    • 0033857959 scopus 로고    scopus 로고
    • NJML: A hybrid algorithm for the neighbor-joining and maximum-likelihood methods
    • Ota, S. and Li, W-H. (2000) NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. Mol. Biol. Evol. 17, 1401-1409
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1401-1409
    • Ota, S.1    Li, W.-H.2
  • 28
    • 0032099099 scopus 로고    scopus 로고
    • Parallel implementation of DNAml program on message-passing architectures
    • Ceron, C. et al. (1998) Parallel implementation of DNAml program on message-passing architectures. Parallel Computing 24, 701-716
    • (1998) Parallel Computing , vol.24 , pp. 701-716
    • Ceron, C.1
  • 29
    • 0034819230 scopus 로고    scopus 로고
    • Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny
    • Katoh, K. et al. (2001) Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53, 477-484
    • (2001) J. Mol. Evol. , vol.53 , pp. 477-484
    • Katoh, K.1
  • 30
    • 0037379673 scopus 로고    scopus 로고
    • Phylogeny estimation: Traditional and Bayesian approaches
    • Holder, M. and Lewis, P.O. (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4, 275-284
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 275-284
    • Holder, M.1    Lewis, P.O.2
  • 31
    • 0033504552 scopus 로고    scopus 로고
    • The Parsimony Ratchet, a new method for rapid parsimony analysis
    • Nixon, K.C. (1999) The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407-414
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1
  • 32
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B. and Simon, D.L. (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
  • 33
    • 0034351392 scopus 로고    scopus 로고
    • Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae)
    • Sanderson, M.J. and Wojciechowski, M.F. (2000) Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49, 671-685
    • (2000) Syst. Biol. , vol.49 , pp. 671-685
    • Sanderson, M.J.1    Wojciechowski, M.F.2
  • 34
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki, Y. et al. (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. U. S. A. 99, 16138-16143
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 16138-16143
    • Suzuki, Y.1
  • 35
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    • Alfaro, M. et al. (2003) Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20, 255-266
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 255-266
    • Alfaro, M.1
  • 36
    • 0035749071 scopus 로고    scopus 로고
    • Bacterial molecular phylogeny using supertree approach
    • Daubin, V. et al. (2001) Bacterial molecular phylogeny using supertree approach. Genome Inform. Ser. Workshop Genome Inform. 12, 155-164
    • (2001) Genome Inform. Ser. Workshop Genome Inform. , vol.12 , pp. 155-164
    • Daubin, V.1
  • 37
    • 0035793857 scopus 로고    scopus 로고
    • Molecular and morphological supertrees for eutherian (placental) mammals
    • Liu, F-G.R. et al. (2001) Molecular and morphological supertrees for eutherian (placental) mammals. Science 291, 1786-1789
    • (2001) Science , vol.291 , pp. 1786-1789
    • Liu, F.-G.R.1
  • 38
    • 0037035383 scopus 로고    scopus 로고
    • A genus-level supertree of the Dinosauria
    • Pisani, D. et al. (2002) A genus-level supertree of the Dinosauria. Proc. R. Soc. London Ser. B Biol. Sci. 269, 915-921
    • (2002) Proc. R. Soc. London Ser. B Biol. Sci. , vol.269 , pp. 915-921
    • Pisani, D.1
  • 39
    • 0000710057 scopus 로고    scopus 로고
    • Molecular phylogeny of the 'temperate herbaceous tribes' of papilionoid legumes: A supertree approach
    • Polhill, R.M., Raven, P.H., et al. eds, Royal Botanical Gardens, Kew, Surrey, UK
    • Wojciechowski, M.F. et al. (2000) Molecular phylogeny of the 'temperate herbaceous tribes' of papilionoid legumes: a supertree approach. Advances in Legume Systematics (Vol. 9) (Polhill, R.M., Raven, P.H., et al. eds), pp. 277-298, Royal Botanical Gardens, Kew, Surrey, UK
    • (2000) Advances in Legume Systematics , vol.9 , pp. 277-298
    • Wojciechowski, M.F.1
  • 40
    • 0036005526 scopus 로고    scopus 로고
    • Building supertrees: An empirical assessment using the grass family (Poaceae)
    • Salamin, N. et al. (2002) Building supertrees: an empirical assessment using the grass family (Poaceae). Syst. Biol. 51, 136-150
    • (2002) Syst. Biol. , vol.51 , pp. 136-150
    • Salamin, N.1
  • 41
    • 0001741936 scopus 로고    scopus 로고
    • Relationship of the order Apiales to subclass Asteridae: A re-evaluation of morphological characters based on insights from molecular data
    • Plunkett, G.M. (2001) Relationship of the order Apiales to subclass Asteridae: a re-evaluation of morphological characters based on insights from molecular data. Edinburgh J. Bot. 58, 183-200
    • (2001) Edinburgh J. Bot. , vol.58 , pp. 183-200
    • Plunkett, G.M.1
  • 42
    • 0002529938 scopus 로고
    • When are phylogeny estimates from molecular and morphological data incongruent?
    • Miyamoto, M.M. and Cracraft, J., eds, Oxford University Press
    • Swofford, D.L. (1991) When are phylogeny estimates from molecular and morphological data incongruent? In Phylogenetic Analysis of DNA Sequences (Miyamoto, M.M. and Cracraft, J., eds) pp. 295-333, Oxford University Press
    • (1991) Phylogenetic Analysis of DNA Sequences , pp. 295-333
    • Swofford, D.L.1
  • 43
    • 0036698966 scopus 로고    scopus 로고
    • Resolution of a supertree/supermatrix paradox
    • Gatesy, J. et al. (2002) Resolution of a supertree/supermatrix paradox. Syst. Biol. 51, 652-664
    • (2002) Syst. Biol. , vol.51 , pp. 652-664
    • Gatesy, J.1
  • 44
    • 0036005524 scopus 로고    scopus 로고
    • Matrix representation with parsimony, taxonomic congruence, and total evidence
    • Pisani, D. and Wilkinson, M. (2002) Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst. Biol. 51, 151-155
    • (2002) Syst. Biol. , vol.51 , pp. 151-155
    • Pisani, D.1    Wilkinson, M.2
  • 45
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
    • Bininda-Emonds, O.R.P. and Sanderson, M.J. (2001) Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst. Biol. 50, 565-579
    • (2001) Syst. Biol. , vol.50 , pp. 565-579
    • Bininda-Emonds, O.R.P.1    Sanderson, M.J.2
  • 46
    • 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
  • 47
    • 0034733685 scopus 로고    scopus 로고
    • Accommodating phylogenetic uncertainty in evolutionary studies
    • Huelsenbeck, J.P. et al. (2000) Accommodating phylogenetic uncertainty in evolutionary studies. Science 288, 2349-2350
    • (2000) Science , vol.288 , pp. 2349-2350
    • Huelsenbeck, J.P.1
  • 48
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • Page, R.D.M. and Charleston, M.A. (1997) From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7, 231-240
    • (1997) Mol. Phylogenet. Evol. , vol.7 , pp. 231-240
    • Page, R.D.M.1    Charleston, M.A.2
  • 49
    • 0037036630 scopus 로고    scopus 로고
    • Going nuclear: Gene family evolution and vertebrate phylogeny reconciled
    • Cotton, J.A. and Page, R.D.M. (2002) Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc. R. Soc. London Ser. B Biol. Sci. 269, 1555-1561
    • (2002) Proc. R. Soc. London Ser. B Biol. Sci. , vol.269 , pp. 1555-1561
    • Cotton, J.A.1    Page, R.D.M.2
  • 50
    • 0038158155 scopus 로고    scopus 로고
    • Obtaining maximal concatenated phylogenetic data sets from large sequence databases
    • Sanderson, M.J. et al. (2003) Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20, 1036-1042
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1036-1042
    • Sanderson, M.J.1
  • 51
    • 0037774102 scopus 로고    scopus 로고
    • Consensus algorithms for the generation of all maximal bicliques
    • Rutgers University, Piscataway, NJ, USA
    • Alexe, G. et al. (2002) Consensus algorithms for the generation of all maximal bicliques. DIMACS Technical Report 2002-52, Rutgers University, Piscataway, NJ, USA (http://dimacs.rutgers.edu/TechnicalReports/2002.html)
    • (2002) DIMACS Technical Report 2002-52
    • Alexe, G.1
  • 53
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • Sanderson, M.J. et al. (1998) Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13, 105-109
    • (1998) Trends Ecol. Evol. , vol.13 , pp. 105-109
    • Sanderson, M.J.1
  • 54
    • 0036931408 scopus 로고    scopus 로고
    • The (super)tree of life: Procedures, problems, and prospects
    • Bininda-Emonds, O.R.P. et al. (2002) The (super)tree of life: procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33, 265-290
    • (2002) Annu. Rev. Ecol. Syst. , vol.33 , pp. 265-290
    • Bininda-Emonds, O.R.P.1
  • 56
    • 0001541744 scopus 로고    scopus 로고
    • A supertree method for rooted trees
    • Semple, C. and Steel, M. (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
  • 57
    • 0001567207 scopus 로고
    • Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions
    • Aho, A.V. et al. (1981) Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10, 405-421
    • (1981) SIAM J. Comput. , vol.10 , pp. 405-421
    • Aho, A.V.1


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