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Volumn 47, Issue 1, 1998, Pages 61-76

Amphioxus Mitochondrial DNA, Chordate Phylogeny, and the Limits of Inference Based on Comparisons of Sequences

Author keywords

Amphioxus; Chordate phylogeny; Homoplasy; Molecular systematics; mtDNA; Phylogenetic inference

Indexed keywords

MITOCHONDRIAL DNA;

EID: 0032028997     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351598261030     Document Type: Article
Times cited : (191)

References (50)
  • 1
    • 0000266922 scopus 로고
    • Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index
    • ARCHIE, J. W. 1989. Homoplasy excess ratios: New indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. Syst. Zool. 38:253-269.
    • (1989) Syst. Zool. , vol.38 , pp. 253-269
    • Archie, J.W.1
  • 3
    • 0000367652 scopus 로고
    • The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
    • BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
    • (1988) Evolution , vol.42 , pp. 795-803
    • Bremer, K.1
  • 4
    • 0029027331 scopus 로고
    • A highly conserved nuclear gene for low-level phylogenetics: Elongation factor-la recovers morphology-based tree for heliothine moths
    • CHO, S., A. MITCHELL, J. C. REGIER, C. MITTER, R. W. POOLE, T. P. FRIEDLANDER, AND S. ZHAO. 1995. A highly conserved nuclear gene for low-level phylogenetics: Elongation factor-la recovers morphology-based tree for heliothine moths. Mol. Biol. Evol. 12: 650-656.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 650-656
    • Cho, S.1    Mitchell, A.2    Regier, J.C.3    Mitter, C.4    Poole, R.W.5    Friedlander, T.P.6    Zhao, S.7
  • 6
    • 0029096506 scopus 로고
    • Sampling properties of DNA sequence data in phylogenetic analysis
    • CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis.Mol. Biol. Evol. 12:814-822.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 814-822
    • Cummings, M.P.1    Otto, S.P.2    Wakeley, J.3
  • 8
    • 0027501821 scopus 로고
    • Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules and morphology
    • EERNISSE, D. J., AND A. KLUGE. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules and morphology. Mol. Biol. Evol. 10:1170-1195.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1170-1195
    • Eernisse, D.J.1    Kluge, A.2
  • 10
    • 84963028421 scopus 로고
    • A successive approximation approach to character weighting
    • FARRIS, J. S. 1969. A successive approximation approach to character weighting. Syst. Zool. 18:374-385.
    • (1969) Syst. Zool. , vol.18 , pp. 374-385
    • Farris, J.S.1
  • 11
    • 0001151063 scopus 로고
    • The logical basis of phylogenetic analysis
    • (N. I. Platnick. and V. A. Funk, eds.). Columbia Press, New York
    • FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume II (N. I. Platnick. and V. A. Funk, eds.). Columbia Press, New York.
    • (1983) Advances in Cladistics , vol.2 , pp. 7-36
    • Farris, J.S.1
  • 12
    • 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
  • 13
    • 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 27:401-416.
    • (1978) Syst. Zool , vol.27 , pp. 401-416
    • Felsenstein, J.1
  • 14
    • 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
  • 15
    • 0014092973 scopus 로고
    • A method for estimating the number of invariant amino acid positions in a gene using cytochrome c as a model case
    • FITCH, W. M., AND E. MARGOLIASH. 1967. A method for estimating the number of invariant amino acid positions in a gene using cytochrome c as a model case. Biochem. Genet. 1:65-71.
    • (1967) Biochem. Genet. , vol.1 , pp. 65-71
    • Fitch, W.M.1    Margoliash, E.2
  • 16
    • 0024258114 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 4:105-209.
    • (1988) Cladistics , vol.4 , pp. 105-209
    • Gauthier, J.1    Kluge, A.G.2    Rowe, T.3
  • 17
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
    • (1993) J. Mol. Evol. , vol.36 , pp. 182-198
    • Goldman, N.1
  • 18
    • 12044254698 scopus 로고
    • Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates
    • GRAYBEAL, A. 1994. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates. Syst. Biol. 43: 174-193.
    • (1994) Syst. Biol. , vol.43 , pp. 174-193
    • Graybeal, A.1
  • 19
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • GU, X., Y.-X. FU, AND W-H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12: 546-557.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 546-557
    • Gu, X.1    Fu, Y.-X.2    Li, W.-H.3
  • 20
    • 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
  • 21
    • 0002063701 scopus 로고
    • Discriminating between phylogenetic signal and random noise in DNA sequences
    • (M. M. Miyamoto and J. Cracraft, eds). Oxford Univ. Press, New York
    • HILLIS, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. Pages 278-294 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds). Oxford Univ. Press, New York.
    • (1991) Phylogenetic Analysis of DNA Sequences , pp. 278-294
    • Hillis, D.M.1
  • 22
    • 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
  • 23
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 24
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • (H. N. Munro, ed.). Academic Press, New York
    • JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 25
    • 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
  • 26
    • 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
  • 27
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the 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 of the Hominoidea. J. Mol. Evol. 29:170-179.
    • (1989) J. Mol. Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 28
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • LANAVE, C., G. PREPARATA, C. SACCONE, AND G. SERIO. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
    • (1984) J. Mol. Evol. , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 30
    • 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
  • 31
    • 0000229302 scopus 로고
    • Heads and tails: A chordate phylogeny
    • MAISEY, J. G. 1986. Heads and tails: A chordate phylogeny. Cladistics 2:201-256.
    • (1986) Cladistics , vol.2 , pp. 201-256
    • Maisey, J.G.1
  • 32
    • 0001911916 scopus 로고
    • Phylogeny of early vertebrate skeletal induction and ossification patterns
    • (M. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum, New York
    • MAISEY, J. G. 1988. Phylogeny of early vertebrate skeletal induction and ossification patterns. Evolutionary biology, Volume 22 (M. Hecht, B. Wallace, and G. T. Prance, eds.). Plenum, New York.
    • (1988) Evolutionary Biology , vol.22
    • Maisey, J.G.1
  • 33
    • 0029619271 scopus 로고
    • The importance of base composition in the correct assessment of genetic distance
    • PESOLE, G., G. DELLISANTI, G. PREPARATA, AND C. SACCONE. 1995. The importance of base composition in the correct assessment of genetic distance. J. Mol. Evol. 41:1124-1127.
    • (1995) J. Mol. Evol. , vol.41 , pp. 1124-1127
    • Pesole, G.1    Dellisanti, G.2    Preparata, G.3    Saccone, C.4
  • 34
    • 0028578194 scopus 로고
    • Can the Cambrian explosion be inferred through molecular phylogeny?
    • PHILIPPE H. A. CHENUIL, AND A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Development (suppl.):15-25.
    • (1994) Development , Issue.SUPPL. , pp. 15-25
    • Philippe, H.1    Chenuil, A.2    Adoutte, A.3
  • 35
  • 36
    • 0030045281 scopus 로고    scopus 로고
    • Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
    • RUSSO, C. A. M, N. TAKEZAKI, AND M. NEI. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 525-536
    • Russo, C.A.M.1    Takezaki, N.2    Nei, M.3
  • 37
    • 0024457184 scopus 로고
    • DNA microenvironments and the molecular clock
    • SACCONE, C., G. PESOLE, AND G. PREPARATA. 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29:407-411.
    • (1989) J. Mol. Evol. , vol.29 , pp. 407-411
    • Saccone, C.1    Pesole, G.2    Preparata, G.3
  • 38
    • 0025317141 scopus 로고
    • Influence of base composition on quantitative estimates of gene evolution
    • SACCONE, C., C. LANAVE, G. PESOLE, AND G. PREPARATA. 1990. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183:570-583.
    • (1990) Methods Enzymol. , vol.183 , pp. 570-583
    • Saccone, C.1    Lanave, C.2    Pesole, G.3    Preparata, G.4
  • 40
    • 0027180533 scopus 로고
    • Confidence in evolutionary trees from biological sequence data
    • STEEL, M. A., P. J. LOCKHART, AND D. PENNY. 1993. Confidence in evolutionary trees from biological sequence data. Nature 364:440-442.
    • (1993) Nature , vol.364 , pp. 440-442
    • Steel, M.A.1    Lockhart, P.J.2    Penny, D.3
  • 41
    • 43949153645 scopus 로고
    • Recovering a tree from the leaf colorations it generates under a Markov model
    • STEEL, M. A. 1994. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7:19-23.
    • (1994) Appl. Math. Lett. , vol.7 , pp. 19-23
    • Steel, M.A.1
  • 42
    • 0028807391 scopus 로고
    • Among-site rate variation and phylogenetic analysis of 12S rRNA data in sigmodontine rodents
    • SULLIVAN, J., K. E. HOLSINGER, AND C. SIMON. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA data in sigmodontine rodents. Mol. Biol. Evol. 12:988-1001.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 988-1001
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 43
    • 0029880314 scopus 로고    scopus 로고
    • The effect of topology on estimates of among site rate variation
    • SULLIVAN, J., K. E. HOLSINCER, AND C. SIMON. 1996. The effect of topology on estimates of among site rate variation. J. Mol. Evol. 42:308-312.
    • (1996) J. Mol. Evol. , vol.42 , pp. 308-312
    • Sullivan, J.1    Holsincer, K.E.2    Simon, C.3
  • 44
    • 85083613110 scopus 로고    scopus 로고
    • Uncertainty in estimating parameters of mixed-distribution models of rate heterogeneity
    • submitted to
    • SULLIVAN, J., D. L. SWOFFORD, AND G. J. P. NAYLOR. Uncertainty in estimating parameters of mixed-distribution models of rate heterogeneity. (submitted to Syst. Biol.)
    • Syst. Biol.
    • Sullivan, J.1    Swofford, D.L.2    Naylor, G.J.P.3
  • 45
    • 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, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
    • (1996) Molecular Systematics, 2nd Edition , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 46
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems on the analysis of DNA sequences
    • TAVARÉ, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lec. Math. Life Sci. 17:57-86.
    • (1986) Lec. Math. Life Sci. , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 47
    • 0001897782 scopus 로고
    • Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data
    • (B. Weir, ed.). Marcel Dekker, New York
    • TEMPLETON, A. R. 1983. Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. Pages 151-179 in Statistical analysis of DNA sequence data (B. Weir, ed.). Marcel Dekker, New York.
    • (1983) Statistical Analysis of DNA Sequence Data , pp. 151-179
    • Templeton, A.R.1
  • 48
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 50
    • 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


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