메뉴 건너뛰기




Volumn 39, Issue 1 SPEC. ISS., 2006, Pages 86-102

Tree disagreement: Measuring and testing incongruence in phylogenies

Author keywords

Actinobacillus; Caulobacter; cpa; Erwinia; ILD; Kishino Hasegawa; LILD; Mannheimia; Pasteurella; Rodrigo test; rpoB; Shimodaira Hasegawa; SOWH; Symmetric difference; tadA; Templeton; Total evidence; Vibrio; WCI; Yersinia

Indexed keywords

ALGORITHMS; BACTERIA; DATA PROCESSING; ERROR ANALYSIS; GENES; TESTING;

EID: 31344454068     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2005.08.008     Document Type: Review
Times cited : (103)

References (98)
  • 1
    • 0000147290 scopus 로고
    • The implications of congruence in Menidia
    • M.F. Mickevich, and J.S. Farris The implications of congruence in Menidia Syst Zool 30 1981 351 370
    • (1981) Syst Zool , vol.30 , pp. 351-370
    • Mickevich, M.F.1    Farris, J.S.2
  • 3
  • 4
    • 0030816742 scopus 로고    scopus 로고
    • Can three incongruence tests predict when data should be combined?
    • C.W. Cunningham Can three incongruence tests predict when data should be combined? Mol Biol Evol 14 7 1997 733 740
    • (1997) Mol Biol Evol , vol.14 , Issue.7 , pp. 733-740
    • Cunningham, C.W.1
  • 5
    • 0031224810 scopus 로고    scopus 로고
    • Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods
    • C.W. Cunningham Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods Syst Biol 46 3 1997 464 478
    • (1997) Syst Biol , vol.46 , Issue.3 , pp. 464-478
    • Cunningham, C.W.1
  • 6
    • 0034512402 scopus 로고    scopus 로고
    • Noise and incongruence: Interpreting results of the incongruence length difference test
    • K. Dolphin, R. Belshaw, C.D. Orme, and D.L. Quicke Noise and incongruence: interpreting results of the incongruence length difference test Mol Phylogenet Evol 17 3 2000 401 406
    • (2000) Mol Phylogenet Evol , vol.17 , Issue.3 , pp. 401-406
    • Dolphin, K.1    Belshaw, R.2    Orme, C.D.3    Quicke, D.L.4
  • 7
    • 0036221248 scopus 로고    scopus 로고
    • When does the incongruence length difference test fail?
    • P. Darlu, and G. Lecointre When does the incongruence length difference test fail? Mol Biol Evol 19 4 2002 432 437
    • (2002) Mol Biol Evol , vol.19 , Issue.4 , pp. 432-437
    • Darlu, P.1    Lecointre, G.2
  • 8
    • 0036005517 scopus 로고    scopus 로고
    • Increased congruence does not necessarily indicate increased phylogenetic accuracy-the behavior of the incongruence length difference test in mixed-model analyses
    • M. Dowton, and A.D. Austin Increased congruence does not necessarily indicate increased phylogenetic accuracy-the behavior of the incongruence length difference test in mixed-model analyses Syst Biol 51 1 2002 19 31
    • (2002) Syst Biol , vol.51 , Issue.1 , pp. 19-31
    • Dowton, M.1    Austin, A.D.2
  • 9
    • 0036699888 scopus 로고    scopus 로고
    • The utility of the incongruence length difference test
    • F.K. Barker, and F.M. Lutzoni The utility of the incongruence length difference test Syst Biol 51 4 2002 625 637
    • (2002) Syst Biol , vol.51 , Issue.4 , pp. 625-637
    • Barker, F.K.1    Lutzoni, F.M.2
  • 11
    • 0035527350 scopus 로고    scopus 로고
    • Failure of the ILD to determine data combinability for slow loris phylogeny
    • A.D. Yoder, J.A. Irwin, and B.A. Payseur Failure of the ILD to determine data combinability for slow loris phylogeny Syst Biol 50 3 2001 408 424
    • (2001) Syst Biol , vol.50 , Issue.3 , pp. 408-424
    • Yoder, A.D.1    Irwin, J.A.2    Payseur, B.A.3
  • 12
    • 0035065311 scopus 로고    scopus 로고
    • Uninformative characters and apparent conflict between molecules and morphology
    • M.S. Lee Uninformative characters and apparent conflict between molecules and morphology Mol Biol Evol 18 4 2001 676 680
    • (2001) Mol Biol Evol , vol.18 , Issue.4 , pp. 676-680
    • Lee, M.S.1
  • 13
    • 1642356002 scopus 로고    scopus 로고
    • Congruence versus phylogenetic accuracy: Revisiting the incongruence length difference test
    • A.L. Hipp, J.C. Hall, and K.J. Sytsma Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test Syst Biol 53 1 2004 81 89
    • (2004) Syst Biol , vol.53 , Issue.1 , pp. 81-89
    • Hipp, A.L.1    Hall, J.C.2    Sytsma, K.J.3
  • 14
    • 0030311441 scopus 로고    scopus 로고
    • Testing for phylogenetic conflict among molecular data sets in the tribe triticeae (graminneae)
    • R.J. Mason-Gamer, and E.A. Kellogg Testing for phylogenetic conflict among molecular data sets in the tribe triticeae (graminneae) Syst Biol 45 4 1996 524 545
    • (1996) Syst Biol , vol.45 , Issue.4 , pp. 524-545
    • Mason-Gamer, R.J.1    Kellogg, E.A.2
  • 15
    • 0021084212 scopus 로고
    • Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes
    • A.R. Templeton Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes Evolution 37 1983 221 244
    • (1983) Evolution , vol.37 , pp. 221-244
    • Templeton, A.R.1
  • 16
    • 0034350428 scopus 로고    scopus 로고
    • A new method to localize and test the significance of incongruence: Detecting domain shuffling in the nuclear receptor superfamily
    • J.W. Thornton, and R. DeSalle A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily Syst Biol 49 2 2000 183 201
    • (2000) Syst Biol , vol.49 , Issue.2 , pp. 183-201
    • Thornton, J.W.1    Desalle, R.2
  • 17
    • 0036375811 scopus 로고    scopus 로고
    • Detection of recombination among Salmonella enterica strains using the incongruence length difference test
    • E.W. Brown, M.L. Kotewicz, and T.A. Cebula Detection of recombination among Salmonella enterica strains using the incongruence length difference test Mol Phylogenet Evol 24 1 2002 102 120
    • (2002) Mol Phylogenet Evol , vol.24 , Issue.1 , pp. 102-120
    • Brown, E.W.1    Kotewicz, M.L.2    Cebula, T.A.3
  • 18
    • 0034774688 scopus 로고    scopus 로고
    • Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors
    • N.A. Shevchuk, and M.W. Allard Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors Mol Phylogenet Evol 21 1 2001 43 54
    • (2001) Mol Phylogenet Evol , vol.21 , Issue.1 , pp. 43-54
    • Shevchuk, N.A.1    Allard, M.W.2
  • 19
    • 0031371067 scopus 로고    scopus 로고
    • Multiple sources of character information and the phylogeny of Hawaiian drosophilids
    • R.H. Baker, and R. DeSalle Multiple sources of character information and the phylogeny of Hawaiian drosophilids Syst Biol 46 4 1997 654 673
    • (1997) Syst Biol , vol.46 , Issue.4 , pp. 654-673
    • Baker, R.H.1    Desalle, R.2
  • 20
    • 0347093471 scopus 로고    scopus 로고
    • Decreasing the effects of horizontal gene transfer on bacterial phylogeny: The Escherichia coli case study
    • P. Escobar-Paramo, A. Sabbagh, P. Darlu, O. Pradillon, C. Vaury, and E. Denamur Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study Mol Phylogenet Evol 30 1 2004 243 250
    • (2004) Mol Phylogenet Evol , vol.30 , Issue.1 , pp. 243-250
    • Escobar-Paramo, P.1    Sabbagh, A.2    Darlu, P.3    Pradillon, O.4    Vaury, C.5    Denamur, E.6
  • 21
    • 12944281550 scopus 로고    scopus 로고
    • Total evidence require exclusion of phylogenetically misleading data
    • G. Lecointre, and P. Deleporte Total evidence require exclusion of phylogenetically misleading data Zool Scripta 34 2005 101 117
    • (2005) Zool Scripta , vol.34 , pp. 101-117
    • Lecointre, G.1    Deleporte, P.2
  • 22
    • 0031741481 scopus 로고    scopus 로고
    • Escherichia coli molecular phylogeny using the incongruence length difference test
    • G. Lecointre, L. Rachdi, P. Darlu, and E. Denamur Escherichia coli molecular phylogeny using the incongruence length difference test Mol Biol Evol 15 12 1998 1685 1695
    • (1998) Mol Biol Evol , vol.15 , Issue.12 , pp. 1685-1695
    • Lecointre, G.1    Rachdi, L.2    Darlu, P.3    Denamur, E.4
  • 23
    • 0038617707 scopus 로고    scopus 로고
    • The widespread colonization Island of Actinobacillus actinomycetemcomitans
    • P.J. Planet, S.C. Kachlany, D.H. Fine, R. DeSalle, and D.H. Figurski The widespread colonization Island of Actinobacillus actinomycetemcomitans Nat Genet 34 2 2003 193 198
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 193-198
    • Planet, P.J.1    Kachlany, S.C.2    Fine, D.H.3    Desalle, R.4    Figurski, D.H.5
  • 24
    • 7444241447 scopus 로고    scopus 로고
    • Detecting phylogenetic incongruence using BIONJ: An improvement of the ILD test
    • M. Zelwer, and V. Daubin Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test Mol Phylogenet Evol 33 3 2004 687 693
    • (2004) Mol Phylogenet Evol , vol.33 , Issue.3 , pp. 687-693
    • Zelwer, M.1    Daubin, V.2
  • 25
    • 84960612286 scopus 로고
    • Cladistic permutation tests for monophyly and nonmonophyly
    • D.P. Faith Cladistic permutation tests for monophyly and nonmonophyly Syst Zool 40 1991 366 375
    • (1991) Syst Zool , vol.40 , pp. 366-375
    • Faith, D.P.1
  • 26
    • 0000443251 scopus 로고    scopus 로고
    • The PTP is meaningless, T-PTP is contradictory: A reply to Trueman
    • J.M. Carpenter, P.A. Goloboff, and J.S. Farris The PTP is meaningless, T-PTP is contradictory: a reply to Trueman Cladistics 14 1998 105 116
    • (1998) Cladistics , vol.14 , pp. 105-116
    • Carpenter, J.M.1    Goloboff, P.A.2    Farris, J.S.3
  • 27
    • 0030310653 scopus 로고    scopus 로고
    • The topology-dependent permutation test for monophyly does not test for monophyly
    • D. Swofford, J.L. Thorne, J. Felsenstein, and B.M. Wiegmann The topology-dependent permutation test for monophyly does not test for monophyly Syst Biol 45 1996 575 579
    • (1996) Syst Biol , vol.45 , pp. 575-579
    • Swofford, D.1    Thorne, J.L.2    Felsenstein, J.3    Wiegmann, B.M.4
  • 29
    • 0023688014 scopus 로고
    • Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences
    • E.M. Prager, and A.C. Wilson Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences J Mol Evol 27 4 1988 326 335
    • (1988) J Mol Evol , vol.27 , Issue.4 , pp. 326-335
    • Prager, E.M.1    Wilson, A.C.2
  • 30
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
    • H. Kishino, T. Miyata, and M. Hasegawa Maximum likelihood inference of protein phylogeny and the origin of chloroplasts J Mol Evol 31 1990 151 160
    • (1990) J Mol Evol , vol.31 , pp. 151-160
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 31
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
    • H. Kishino, and M. Hasegawa 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 2 1989 170 179
    • (1989) J Mol Evol , vol.29 , Issue.2 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 32
    • 0030328811 scopus 로고    scopus 로고
    • A likelihood ratio test to detect conflicting phylogenetic signal
    • J.P. Huelsenbeck, and J.J. Bull A likelihood ratio test to detect conflicting phylogenetic signal Syst Biol 45 1996 92 98
    • (1996) Syst Biol , vol.45 , pp. 92-98
    • Huelsenbeck, J.P.1    Bull, J.J.2
  • 33
    • 0033635534 scopus 로고    scopus 로고
    • Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests
    • P.J. Waddell, H. Kishino, and R. Ota Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests Mol Biol Evol 17 12 2000 1988 1992
    • (2000) Mol Biol Evol , vol.17 , Issue.12 , pp. 1988-1992
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 34
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • N. Goldman Statistical tests of models of DNA substitution J Mol Evol 36 1993 182 198
    • (1993) J Mol Evol , vol.36 , pp. 182-198
    • Goldman, N.1
  • 35
    • 0034351387 scopus 로고    scopus 로고
    • Likelihood-based tests of topologies in phylogenetics
    • N. Goldman, J.P. Anderson, and A.G. Rodrigo Likelihood-based tests of topologies in phylogenetics Syst Biol 49 2000 652 670
    • (2000) Syst Biol , vol.49 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 36
    • 0024454601 scopus 로고
    • Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders
    • M. Hasegawa, and H. Kishino Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders Jpn J Genet 64 4 1989 243 258
    • (1989) Jpn J Genet , vol.64 , Issue.4 , pp. 243-258
    • Hasegawa, M.1    Kishino, H.2
  • 37
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D.M. Hillis C. Moritz B.K. Mable Sinauer Sunderland, Mass
    • D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis Phylogenetic inference D.M. Hillis C. Moritz B.K. Mable Molecular systematics 1996 Sinauer Sunderland, Mass 407 514
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 38
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol Biol Evol 17 1999 1114 1116
    • (1999) Mol Biol Evol , vol.17 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 39
    • 7744247581 scopus 로고    scopus 로고
    • An application of multiple comparison techniques to model selection
    • H. Shimodaira, and M. Hasegawa An application of multiple comparison techniques to model selection Ann Inst Stat Math 50 1998 1 13
    • (1998) Ann Inst Stat Math , vol.50 , pp. 1-13
    • Shimodaira, H.1    Hasegawa, M.2
  • 40
    • 41049111540 scopus 로고    scopus 로고
    • Inferring confidence sets of possibly misspecified gene trees
    • K. Strimmer, and A. Rambaut Inferring confidence sets of possibly misspecified gene trees Proc Biol Sci 269 1487 2002 137 142
    • (2002) Proc Biol Sci , vol.269 , Issue.1487 , pp. 137-142
    • Strimmer, K.1    Rambaut, A.2
  • 41
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • H. Shimodaira An approximately unbiased test of phylogenetic tree selection Syst Biol 51 3 2002 492 508
    • (2002) Syst Biol , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 42
    • 0036623259 scopus 로고    scopus 로고
    • Model misspecification and probabilistic tests of topology: Evidence from empirical data sets
    • T.R. Buckley Model misspecification and probabilistic tests of topology: evidence from empirical data sets Syst Biol 51 3 2002 509 523
    • (2002) Syst Biol , vol.51 , Issue.3 , pp. 509-523
    • Buckley, T.R.1
  • 43
    • 0029261787 scopus 로고
    • Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique
    • A. Zharkikh, and W.H. Li Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique Mol Phylogenet Evol 4 1 1995 44 63
    • (1995) Mol Phylogenet Evol , vol.4 , Issue.1 , pp. 44-63
    • Zharkikh, A.1    Li, W.H.2
  • 44
    • 0038586502 scopus 로고    scopus 로고
    • Confidence regions and hypothesis tests for topologies using generalized least squares
    • E. Susko Confidence regions and hypothesis tests for topologies using generalized least squares Mol Biol Evol 20 6 2003 862 868
    • (2003) Mol Biol Evol , vol.20 , Issue.6 , pp. 862-868
    • Susko, E.1
  • 46
    • 0033084970 scopus 로고    scopus 로고
    • Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant
    • P.J. Waddell, Y. Cao, J. Hauf, and M. Hasegawa Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant Syst Biol 48 1 1999 31 53
    • (1999) Syst Biol , vol.48 , Issue.1 , pp. 31-53
    • Waddell, P.J.1    Cao, Y.2    Hauf, J.3    Hasegawa, M.4
  • 47
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo
    • Z. Yang, and B. Rannala Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo Mol Biol Evol 14 1997 717 724
    • (1997) Mol Biol Evol , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 48
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • B. Larget, and D.L. Simon Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees Mol Biol Evol 16 1999 750 759
    • (1999) Mol Biol Evol , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 49
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • J.P. Huelsenbeck, F. Ronquist, R. Nielsen, and J.P. Bollback Bayesian inference of phylogeny and its impact on evolutionary biology Science 294 5550 2001 2310 2314
    • (2001) Science , vol.294 , Issue.5550 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 50
    • 0036806280 scopus 로고    scopus 로고
    • Potential applications and pitfalls of Bayesian inference of phylogeny
    • J.P. Huelsenbeck, B. Larget, R.E. Miller, and F. Ronquist Potential applications and pitfalls of Bayesian inference of phylogeny Syst Biol 51 5 2002 673 688
    • (2002) Syst Biol , vol.51 , Issue.5 , pp. 673-688
    • Huelsenbeck, J.P.1    Larget, B.2    Miller, R.E.3    Ronquist, F.4
  • 51
    • 0037461032 scopus 로고    scopus 로고
    • How Bayes tests of molecular phylogenies compare with frequentist approaches
    • S. Aris-Brosou How Bayes tests of molecular phylogenies compare with frequentist approaches Bioinformatics 19 5 2003 618 624
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 618-624
    • Aris-Brosou, S.1
  • 52
    • 0000857757 scopus 로고    scopus 로고
    • Measuring topological incongruence by extending character techniques
    • W. Wheeler Measuring topological incongruence by extending character techniques Cladistics 15 1999 131 135
    • (1999) Cladistics , vol.15 , pp. 131-135
    • Wheeler, W.1
  • 53
    • 1642519173 scopus 로고    scopus 로고
    • A classification of consensus methods for phylogenetics
    • M.F. Janowitz F.-J. Lapointe F.R. McMorris B. Mirkin F.S. Roberts American Mathematics Society Providence, Rhode Island
    • D. Bryant A classification of consensus methods for phylogenetics M.F. Janowitz F.-J. Lapointe F.R. McMorris B. Mirkin F.S. Roberts Bioconsensus 2003 American Mathematics Society Providence, Rhode Island
    • (2003) Bioconsensus
    • Bryant, D.1
  • 54
    • 0033916185 scopus 로고    scopus 로고
    • RadCon: Phylogenetic tree comparison and consensus
    • J.L. Thorley, and R.D. Page RadCon: phylogenetic tree comparison and consensus Bioinformatics 16 5 2000 486 487
    • (2000) Bioinformatics , vol.16 , Issue.5 , pp. 486-487
    • Thorley, J.L.1    Page, R.D.2
  • 55
    • 12044252586 scopus 로고
    • Distributions of tree comparison metrics-some new results
    • M. Steel, and D. Penny Distributions of tree comparison metrics-some new results Syst Biol 42 2 1993 126 141
    • (1993) Syst Biol , vol.42 , Issue.2 , pp. 126-141
    • Steel, M.1    Penny, D.2
  • 56
    • 84959758123 scopus 로고
    • Congruence between morphometric and allozyme data for Menidia species: A reappraisal
    • D.H. Colless Congruence between morphometric and allozyme data for Menidia species: a reappraisal Syst Biol 29 3 1980 288 299
    • (1980) Syst Biol , vol.29 , Issue.3 , pp. 288-299
    • Colless, D.H.1
  • 57
    • 0000347343 scopus 로고
    • Consensus indices in comparing classifications
    • F.J. Rohlf Consensus indices in comparing classifications Math Biosci 59 1982 131 144
    • (1982) Math Biosci , vol.59 , pp. 131-144
    • Rohlf, F.J.1
  • 58
    • 0000941526 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • A.G. Kluge, and J.S. Farris Quantitative phyletics and the evolution of anurans Syst Zool 38 1969 1 32
    • (1969) Syst Zool , vol.38 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 59
    • 84963071608 scopus 로고
    • On comparing the shapes of taxonomic trees
    • J.S. Farris On comparing the shapes of taxonomic trees Syst Zool 22 1973 50 54
    • (1973) Syst Zool , vol.22 , pp. 50-54
    • Farris, J.S.1
  • 60
    • 0002844544 scopus 로고
    • Combining Trees as a way of combining datasets for phylogenetic inference, and the desirability of combining gene trees
    • B.R. Baum Combining Trees as a way of combining datasets for phylogenetic inference, and the desirability of combining gene trees Taxon 41 1992 3 10
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 61
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • M.A. Ragan Phylogenetic inference based on matrix representation of trees Mol Phylogenet Evol 1 1 1992 53 58
    • (1992) Mol Phylogenet Evol , vol.1 , Issue.1 , pp. 53-58
    • Ragan, M.A.1
  • 62
    • 0027104018 scopus 로고
    • Matrix representation in reconstructing phylogenetic relationships among the eukaryotes
    • M.A. Ragan Matrix representation in reconstructing phylogenetic relationships among the eukaryotes Biosystems 28 1-3 1992 47 55
    • (1992) Biosystems , vol.28 , Issue.1-3 , pp. 47-55
    • Ragan, M.A.1
  • 63
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • D.F. Robinson, and L.R. Foulds Comparison of phylogenetic trees Math Biosci 53 1981 131 147
    • (1981) Math Biosci , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 64
    • 84959752542 scopus 로고
    • Comparison of undirected phylogenetic trees based on subtrees of 4 evolutionary units
    • G.F. Estabrook, F.R. McMorris, and C.A. Meacham Comparison of undirected phylogenetic trees based on subtrees of 4 evolutionary units Syst Zool 34 1985 193 200
    • (1985) Syst Zool , vol.34 , pp. 193-200
    • Estabrook, G.F.1    McMorris, F.R.2    Meacham, C.A.3
  • 65
    • 0018117949 scopus 로고
    • On the similarity of dendrograms
    • M.S. Waterman, and T.F. Smith On the similarity of dendrograms Theor Biol 73 1978 789 800
    • (1978) Theor Biol , vol.73 , pp. 789-800
    • Waterman, M.S.1    Smith, T.F.2
  • 66
    • 12044252724 scopus 로고
    • Trees from languages and genes are very similar
    • D. Penny, E.E. Watson, and M. Steel Trees from languages and genes are very similar Syst Biol 42 1993 382 384
    • (1993) Syst Biol , vol.42 , pp. 382-384
    • Penny, D.1    Watson, E.E.2    Steel, M.3
  • 67
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • M.K. Kuhner, and J. Felsenstein A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates Mol Biol Evol 11 3 1994 459 468
    • (1994) Mol Biol Evol , vol.11 , Issue.3 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 68
    • 0002506482 scopus 로고    scopus 로고
    • On consensus, confidence, and "total evidence"
    • R.D. Page On consensus, confidence, and "total evidence" Cladistics 12 1996 83 92
    • (1996) Cladistics , vol.12 , pp. 83-92
    • Page, R.D.1
  • 69
    • 0001466544 scopus 로고
    • A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree
    • A.G. Rodrigo, M. Kelly-Borges, P.R. Bergquist, and P.L. Bergquist A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree N Z J Bot 31 1993 257 268
    • (1993) N Z J Bot , vol.31 , pp. 257-268
    • Rodrigo, A.G.1    Kelly-Borges, M.2    Bergquist, P.R.3    Bergquist, P.L.4
  • 70
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree [see comments]
    • W.F. Doolittle Phylogenetic classification and the universal tree [see comments] Science 284 5423 1999 2124 2129
    • (1999) Science , vol.284 , Issue.5423 , pp. 2124-2129
    • Doolittle, W.F.1
  • 71
    • 0036360035 scopus 로고    scopus 로고
    • Re-examining microbial evolution through the lens of horizontal transfer
    • DeSalle R, Giribet G, Wheeler W, editors. New York: Birkhauser-Verlag; Exs
    • Planet PJ. Re-examining microbial evolution through the lens of horizontal transfer. In: DeSalle R, Giribet G, Wheeler W, editors. Molecular systematics and evolution: theory and practice. New York: Birkhauser-Verlag; Exs 2002;92:247-303.
    • (2002) Molecular Systematics and Evolution: Theory and Practice , vol.92 , pp. 247-303
    • Planet, P.J.1
  • 72
  • 73
    • 0036898759 scopus 로고    scopus 로고
    • Prokaryotic evolution in light of gene transfer
    • J.P. Gogarten, W.F. Doolittle, and J.G. Lawrence Prokaryotic evolution in light of gene transfer Mol Biol Evol 19 12 2002 2226 2238
    • (2002) Mol Biol Evol , vol.19 , Issue.12 , pp. 2226-2238
    • Gogarten, J.P.1    Doolittle, W.F.2    Lawrence, J.G.3
  • 74
    • 0242490943 scopus 로고    scopus 로고
    • Lateral gene transfer: When will adolescence end?
    • J.G. Lawrence, and H. Hendrickson Lateral gene transfer: when will adolescence end? Mol Microbiol 50 3 2003 739 749
    • (2003) Mol Microbiol , vol.50 , Issue.3 , pp. 739-749
    • Lawrence, J.G.1    Hendrickson, H.2
  • 75
    • 0033758854 scopus 로고    scopus 로고
    • Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea
    • S.C. Kachlany, P.J. Planet, M.K. Bhattacharjee, E. Kollia, R. DeSalle, and D.H. Fine Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea J Bacteriol 182 21 2000 6169 6176
    • (2000) J Bacteriol , vol.182 , Issue.21 , pp. 6169-6176
    • Kachlany, S.C.1    Planet, P.J.2    Bhattacharjee, M.K.3    Kollia, E.4    Desalle, R.5    Fine, D.H.6
  • 76
    • 0035449036 scopus 로고    scopus 로고
    • Genes for tight adherence of Actinobacillus actinomycetemcomitans: From plaque to plague to pond scum
    • S.C. Kachlany, P.J. Planet, R. DeSalle, D.H. Fine, and D.H. Figurski Genes for tight adherence of Actinobacillus actinomycetemcomitans: from plaque to plague to pond scum Trends Microbiol 9 9 2001 429 437
    • (2001) Trends Microbiol , vol.9 , Issue.9 , pp. 429-437
    • Kachlany, S.C.1    Planet, P.J.2    Desalle, R.3    Fine, D.H.4    Figurski, D.H.5
  • 77
    • 0034999675 scopus 로고    scopus 로고
    • Flp-1, the first representative of a new pilin gene subfamily, is required for non-specific adherence of Actinobacillus actinomycetemcomitans
    • S.C. Kachlany, P.J. Planet, R. Desalle, D.H. Fine, D.H. Figurski, and J.B. Kaplan flp-1, the first representative of a new pilin gene subfamily, is required for non-specific adherence of Actinobacillus actinomycetemcomitans Mol Microbiol 40 3 2001 542 554
    • (2001) Mol Microbiol , vol.40 , Issue.3 , pp. 542-554
    • Kachlany, S.C.1    Planet, P.J.2    Desalle, R.3    Fine, D.H.4    Figurski, D.H.5    Kaplan, J.B.6
  • 78
    • 0038132217 scopus 로고    scopus 로고
    • Tight-adherence genes of Actinobacillus actinomycetemcomitans are required for virulence in a rat model
    • H.C. Schreiner, K. Sinatra, J.B. Kaplan, D. Furgang, S.C. Kachlany, and P.J. Planet Tight-adherence genes of Actinobacillus actinomycetemcomitans are required for virulence in a rat model Proc Natl Acad Sci USA 100 12 2003 7295 7300
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.12 , pp. 7295-7300
    • Schreiner, H.C.1    Sinatra, K.2    Kaplan, J.B.3    Furgang, D.4    Kachlany, S.C.5    Planet, P.J.6
  • 79
    • 0036266632 scopus 로고    scopus 로고
    • Haemophilus ducreyi requires the flp gene cluster for microcolony formation in vitro
    • J.R. Nika, J.L. Latimer, C.K. Ward, R.J. Blick, N.J. Wagner, and L.D. Cope Haemophilus ducreyi requires the flp gene cluster for microcolony formation in vitro Infect Immun 70 6 2002 2965 2975
    • (2002) Infect Immun , vol.70 , Issue.6 , pp. 2965-2975
    • Nika, J.R.1    Latimer, J.L.2    Ward, C.K.3    Blick, R.J.4    Wagner, N.J.5    Cope, L.D.6
  • 81
    • 0033822730 scopus 로고    scopus 로고
    • Identification of Pasteurella multocida virulence genes in a septicemic mouse model using signature-tagged mutagenesis
    • T.E. Fuller, M.J. Kennedy, and D.E. Lowery Identification of Pasteurella multocida virulence genes in a septicemic mouse model using signature-tagged mutagenesis Microb Pathog 29 1 2000 25 38
    • (2000) Microb Pathog , vol.29 , Issue.1 , pp. 25-38
    • Fuller, T.E.1    Kennedy, M.J.2    Lowery, D.E.3
  • 82
    • 4644273625 scopus 로고    scopus 로고
    • Identification of specific in vivo-induced (ivi) genes in Yersinia ruckeri and analysis of ruckerbactin, a catecholate siderophore iron acquisition system
    • L. Fernandez, I. Marquez, and J.A. Guijarro Identification of specific in vivo-induced (ivi) genes in Yersinia ruckeri and analysis of ruckerbactin, a catecholate siderophore iron acquisition system Appl Environ Microbiol 70 9 2004 5199 5207
    • (2004) Appl Environ Microbiol , vol.70 , Issue.9 , pp. 5199-5207
    • Fernandez, L.1    Marquez, I.2    Guijarro, J.A.3
  • 83
    • 0035957004 scopus 로고    scopus 로고
    • Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification
    • P.J. Planet, S.C. Kachlany, R. DeSalle, and D.H. Figurski Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification Proc Natl Acad Sci USA 98 5 2001 2503 2508
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.5 , pp. 2503-2508
    • Planet, P.J.1    Kachlany, S.C.2    Desalle, R.3    Figurski, D.H.4
  • 84
    • 0034816350 scopus 로고    scopus 로고
    • Nonspecific adherence and fibril biogenesis by Actinobacillus actinomycetemcomitans: TadA protein is an ATPase
    • M.K. Bhattacharjee, S.C. Kachlany, D.H. Fine, and D.H. Figurski Nonspecific adherence and fibril biogenesis by Actinobacillus actinomycetemcomitans: TadA protein is an ATPase J Bacteriol 183 20 2001 5927 5936
    • (2001) J Bacteriol , vol.183 , Issue.20 , pp. 5927-5936
    • Bhattacharjee, M.K.1    Kachlany, S.C.2    Fine, D.H.3    Figurski, D.H.4
  • 85
    • 0030669211 scopus 로고    scopus 로고
    • RpoB sequence analysis as a novel basis for bacterial identification
    • C. Mollet, M. Drancourt, and D. Raoult rpoB sequence analysis as a novel basis for bacterial identification Mol Microbiol 26 5 1997 1005 1011
    • (1997) Mol Microbiol , vol.26 , Issue.5 , pp. 1005-1011
    • Mollet, C.1    Drancourt, M.2    Raoult, D.3
  • 86
    • 12344263811 scopus 로고    scopus 로고
    • ORFcurator: Molecular curation of genes and gene clusters in prokaryotic organisms
    • J.A. Rosenfeld, I.N. Sarkar, P.J. Planet, D.H. Figurski, and R. DeSalle ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms Bioinformatics 20 18 2004 3462 3465
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3462-3465
    • Rosenfeld, J.A.1    Sarkar, I.N.2    Planet, P.J.3    Figurski, D.H.4    Desalle, R.5
  • 87
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • T.A. Hall BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp Ser 41 1999 95 98
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 89
    • 0031811061 scopus 로고    scopus 로고
    • Jungles: A new solution to the host/parasite phylogeny reconciliation problem
    • M.A. Charleston Jungles: a new solution to the host/parasite phylogeny reconciliation problem Math Biosci 149 2 1998 191 223
    • (1998) Math Biosci , vol.149 , Issue.2 , pp. 191-223
    • Charleston, M.A.1
  • 90
    • 0033278654 scopus 로고    scopus 로고
    • How should species phylogenies be inferred from sequence data?
    • J.B. Slowinski, and R.D. Page How should species phylogenies be inferred from sequence data? Syst Biol 48 4 1999 814 825
    • (1999) Syst Biol , vol.48 , Issue.4 , pp. 814-825
    • Slowinski, J.B.1    Page, R.D.2
  • 91
    • 84959806898 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes)
    • A.G. Kluge A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes) Syst Zool 38 1989 1 25
    • (1989) Syst Zool , vol.38 , pp. 1-25
    • Kluge, A.G.1
  • 92
    • 0027501821 scopus 로고
    • Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology
    • D.J. Eernisse, and A.G. Kluge Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology Mol Biol Evol 10 6 1993 1170 1195
    • (1993) Mol Biol Evol , vol.10 , Issue.6 , pp. 1170-1195
    • Eernisse, D.J.1    Kluge, A.G.2
  • 93
    • 0035527376 scopus 로고    scopus 로고
    • Are the fossil data really at odds with the molecular data? Morphological evidence for cetartiodactyla phylogeny reexamined
    • G.J. Naylor, and D.C. Adams Are the fossil data really at odds with the molecular data? Morphological evidence for cetartiodactyla phylogeny reexamined Syst Biol 50 3 2001 444 453
    • (2001) Syst Biol , vol.50 , Issue.3 , pp. 444-453
    • Naylor, G.J.1    Adams, D.C.2
  • 94
    • 0042592785 scopus 로고    scopus 로고
    • On simultaneous analysis
    • K.C. Nixon, and J.M. Carpenter On simultaneous analysis Cladistics 12 1996 221 241
    • (1996) Cladistics , vol.12 , pp. 221-241
    • Nixon, K.C.1    Carpenter, J.M.2
  • 96
    • 0028922906 scopus 로고
    • Testing the covarion hypothesis of molecular evolution
    • M.M. Miyamoto, and W.M. Fitch Testing the covarion hypothesis of molecular evolution Mol Biol Evol 12 3 1995 503 513
    • (1995) Mol Biol Evol , vol.12 , Issue.3 , pp. 503-513
    • Miyamoto, M.M.1    Fitch, W.M.2
  • 97
    • 12044258419 scopus 로고
    • Weighting, partitioning, and combining data in phylogenetic analysis
    • P.T. Chippindale, and J.J. Wiens Weighting, partitioning, and combining data in phylogenetic analysis Syst Biol 43 1994 278 287
    • (1994) Syst Biol , vol.43 , pp. 278-287
    • Chippindale, P.T.1    Wiens, J.J.2
  • 98
    • 0001546577 scopus 로고
    • Separate vs combined analysis of phylogenetic evidence
    • A. de Queiroz, M.J. Donoghue, and J. Kim Separate vs combined analysis of phylogenetic evidence Annu Rev Ecol Syst 26 1995 657 681
    • (1995) Annu Rev Ecol Syst , vol.26 , pp. 657-681
    • De Queiroz, A.1    Donoghue, M.J.2    Kim, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.