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Volumn 52, Issue 3, 2003, Pages 352-367

Failed refutations: Further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration

Author keywords

Assumptions; Corroboration; Karl Popper; Likelihood; Parsimony; Philosophy; Phylogenetics; Probability

Indexed keywords

ARTICLE; KNOWLEDGE; PHILOSOPHY; PHYLOGENY; STATISTICAL MODEL; SYSTEM ANALYSIS;

EID: 0038487291     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150309324     Document Type: Article
Times cited : (30)

References (41)
  • 1
    • 0001321005 scopus 로고
    • An evaluation of cladistic and character analyses as hypothetico-deductive procedures, and the consequences for character weighting
    • BRYANT, H. 1989. An evaluation of cladistic and character analyses as hypothetico-deductive procedures, and the consequences for character weighting. Syst. Zool. 38:214-227.
    • (1989) Syst. Zool. , vol.38 , pp. 214-227
    • Bryant, H.1
  • 2
    • 0002381098 scopus 로고
    • Hybrid origin of a unisexual species of whiptail lizard, Cnemidophorus neomexicanus, in western North America: New evidence and a review
    • COLE, C. J., H. C. DESSAUER, AND G. BARROWCLOUGH. 1988. Hybrid origin of a unisexual species of whiptail lizard, Cnemidophorus neomexicanus, in western North America: New evidence and a review. Am. Mus. Novit. 2905:1-38.
    • (1988) Am. Mus. Novit. , vol.2905 , pp. 1-38
    • Cole, C.J.1    Dessauer, H.C.2    Barrowclough, G.3
  • 3
    • 0035527346 scopus 로고    scopus 로고
    • Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration
    • DE QUEIROZ, K., AND S. POE. 2001. Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Syst. Biol. 50:305-321.
    • (2001) Syst. Biol. , vol.50 , pp. 305-321
    • De Queiroz, K.1    Poe, S.2
  • 4
    • 0004128472 scopus 로고
    • Cambridge Univ. Press, Cambridge, U.K. [Expanded edition published by Johns Hopkins Univ. Press, Baltimore, Maryland, 1992.]
    • EDWARDS, A. W. F. 1972. Likelihood. Cambridge Univ. Press, Cambridge, U.K. [Expanded edition published by Johns Hopkins Univ. Press, Baltimore, Maryland, 1992.]
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 5
    • 38249008775 scopus 로고
    • On corroboration: A reply to Carpenter
    • FAITH, D. P. 1992. On corroboration: A reply to Carpenter. Cladistics 8:265-273.
    • (1992) Cladistics , vol.8 , pp. 265-273
    • Faith, D.P.1
  • 6
    • 11944264422 scopus 로고
    • Probability, parsimony, and Popper
    • FAITH, D. P., AND P. S. CRANSTON. 1992. Probability, parsimony, and Popper. Syst. Biol. 41:252-257.
    • (1992) Syst. Biol. , vol.41 , pp. 252-257
    • Faith, D.P.1    Cranston, P.S.2
  • 7
    • 0035527351 scopus 로고    scopus 로고
    • Towards an inclusive philosophy of phylogenetic inference
    • FAITH, D. P., AND J. W. H. TRUEMAN. 2001. Towards an inclusive philosophy of phylogenetic inference. Syst. Biol. 50:331-350.
    • (2001) Syst. Biol. , vol.50 , pp. 331-350
    • Faith, D.P.1    Trueman, J.W.H.2
  • 8
    • 0001151063 scopus 로고
    • The logical basis of phylogenetic analysis
    • (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York
    • FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
    • (1983) Advances in Cladistics , vol.2 , pp. 7-36
    • Farris, J.S.1
  • 9
    • 0038767589 scopus 로고
    • Entropy and fruit flies
    • FARRIS, J. S. 1989. Entropy and fruit flies. Cladistics 5:103-108.
    • (1989) Cladistics , vol.5 , pp. 103-108
    • Farris, J.S.1
  • 10
    • 0000375117 scopus 로고
    • Conjectures and refutations
    • FARRIS, J. S. 1995. Conjectures and refutations. Cladistics 11:105-118.
    • (1995) Cladistics , vol.11 , pp. 105-118
    • Farris, J.S.1
  • 11
    • 0035527348 scopus 로고    scopus 로고
    • Popper and likelihood versus "Popper.*"
    • FARRIS, J. S., A. G. KLUGE, AND J. M. CARPENTER. 2001. Popper and likelihood versus "Popper.*" Syst. Biol. 50:438-444.
    • (2001) Syst. Biol. , vol.50 , pp. 438-444
    • Farris, J.S.1    Kluge, A.G.2    Carpenter, J.M.3
  • 12
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility will be positively misleading
    • FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 13
    • 0002385657 scopus 로고
    • An introduction to the logic of phylogeny reconstruction
    • (J. Cracraft and N. Eldredge, eds.). Columbia Univ. Press, New York
    • GAFFNEY, E. S. 1979. An introduction to the logic of phylogeny reconstruction. Pages 79-111 in Phylogenetic analysis and paleontology (J. Cracraft and N. Eldredge, eds.). Columbia Univ. Press, New York.
    • (1979) Phylogenetic Analysis and Paleontology , pp. 79-111
    • Gaffney, E.S.1
  • 14
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA sequence evolution
    • GOLDMAN, N. 1993. Statistical tests of models of DNA sequence evolution. J. Mol. Evol. 36:182-198.
    • (1993) J. Mol. Evol. , vol.36 , pp. 182-198
    • Goldman, N.1
  • 15
    • 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
  • 17
    • 0030902563 scopus 로고    scopus 로고
    • Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
    • HUELSENBECK, J. P., AND B. RANNALA. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.
    • (1997) Science , vol.276 , pp. 227-232
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 18
    • 0031430478 scopus 로고    scopus 로고
    • Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics
    • KLUGE, A. G. 1997a. Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics. Zool. Scr. 26:349-360.
    • (1997) Zool. Scr. , vol.26 , pp. 349-360
    • Kluge, A.G.1
  • 19
    • 0031395952 scopus 로고    scopus 로고
    • Testability and the refutation and corroboration of cladistic hypotheses
    • KLUGE, A. G. 1997b. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81-96.
    • (1997) Cladistics , vol.13 , pp. 81-96
    • Kluge, A.G.1
  • 20
    • 0035527349 scopus 로고    scopus 로고
    • Philosophical conjectures and their refutation
    • KLUGE, A. G. 2001. Philosophical conjectures and their refutation. Syst. Biol. 50:322-330.
    • (2001) Syst. Biol. , vol.50 , pp. 322-330
    • Kluge, A.G.1
  • 21
    • 0002479337 scopus 로고
    • Falsification and the methodology of scientific research programmes
    • (I. Lakatos and A. Musgrave, eds.). Cambridge Univ. Press, Cambridge, U.K.
    • LAKATOS, I. 1970. Falsification and the methodology of scientific research programmes. Pages 91-196 in Criticism and the growth of knowledge (I. Lakatos and A. Musgrave, eds.). Cambridge Univ. Press, Cambridge, U.K.
    • (1970) Criticism and the Growth of Knowledge , pp. 91-196
    • Lakatos, I.1
  • 22
    • 0035527403 scopus 로고    scopus 로고
    • Catalyzing bacterial speciation: Correlating lateral transfer with genetic headroom
    • LAWRENCE, J. G. 2001. Catalyzing bacterial speciation: Correlating lateral transfer with genetic headroom. Syst. Biol. 50:479-496.
    • (2001) Syst. Biol. , vol.50 , pp. 479-496
    • Lawrence, J.G.1
  • 23
    • 0002948868 scopus 로고    scopus 로고
    • Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
    • (D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds.). Kluwer Academic, Boston
    • LEWIS, P. O. 1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Pages 132-163 in Molecular systematics of plants. II. DNA sequencing (D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds.). Kluwer Academic, Boston.
    • (1998) Molecular Systematics of Plants. II. DNA Sequencing , pp. 132-163
    • Lewis, P.O.1
  • 24
    • 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
  • 25
    • 0000924146 scopus 로고
    • Hybrids and phylogenetic systematics. I. Patterns of character expression in hybrids and their implications for cladistic analysis
    • MCDADE, L. 1990. Hybrids and phylogenetic systematics. I. Patterns of character expression in hybrids and their implications for cladistic analysis. Evolution 44:1685-1700.
    • (1990) Evolution , vol.44 , pp. 1685-1700
    • McDade, L.1
  • 27
    • 0003432081 scopus 로고
    • Basic Books, New York. [2nd edition published by Harper and Row, New York, 1968.]
    • POPPER, K. R. 1962. Conjectures and refutations. Basic Books, New York. [2nd edition published by Harper and Row, New York, 1968.]
    • (1962) Conjectures and Refutations
    • Popper, K.R.1
  • 29
    • 0029526909 scopus 로고
    • Objections to bootstrapping phylogenies: A critique
    • SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
    • (1995) Syst. Biol. , vol.44 , pp. 299-320
    • Sanderson, M.J.1
  • 30
    • 0344430832 scopus 로고    scopus 로고
    • Probabilism and phylogenetic inference
    • SIDDALL, M. E., AND A. G. KLUGE. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-336.
    • (1997) Cladistics , vol.13 , pp. 313-336
    • Siddall, M.E.1    Kluge, A.G.2
  • 32
    • 0034035066 scopus 로고    scopus 로고
    • Parsimony, likelihood, and the role of models in molecular phylogenetics
    • STEEL, M., AND D. PENNY. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 839-850
    • Steel, M.1    Penny, D.2
  • 33
    • 0001140522 scopus 로고
    • Phylogeny reconstruction
    • (D. M. Hillis and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts
    • SWOFFORD, D. L., AND G. J. OLSEN. 1990. Phylogeny reconstruction. Pages 411-501 in Molecular systematics, 1st edition (D. M. Hillis and C. Moritz, eds.). Sinauer, Sunderland, Massachusetts.
    • (1990) Molecular Systematics, 1st Edition , pp. 411-501
    • Swofford, D.L.1    Olsen, G.J.2
  • 34
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, 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, 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
  • 35
    • 0035527406 scopus 로고    scopus 로고
    • Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
    • SWOFFORD, D. L., P. J. WADDELL, J. P. HUELSENBECK, P. G. FOSTER, P. O. LEWIS, AND J. S. ROGERS. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
    • (2001) Syst. Biol. , vol.50 , pp. 525-539
    • Swofford, D.L.1    Waddell, P.J.2    Huelsenbeck, J.P.3    Foster, P.G.4    Lewis, P.O.5    Rogers, J.S.6
  • 36
    • 0031149251 scopus 로고    scopus 로고
    • Links between maximum likelihood and maximum parsimony under a simple model of site substitution
    • TUFFLEY, C., AND M. STEEL. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581-607.
    • (1997) Bull. Math. Biol. , vol.59 , pp. 581-607
    • Tuffley, C.1    Steel, M.2
  • 37
    • 84959834965 scopus 로고
    • Karl R. Popper, systematics, and classification: A reply to Walter Bock and other evolutionary taxonomists
    • WILEY, E. O. 1975. Karl R. Popper, systematics, and classification: A reply to Walter Bock and other evolutionary taxonomists. Syst. Zool. 24:233-243.
    • (1975) Syst. Zool. , vol.24 , pp. 233-243
    • Wiley, E.O.1
  • 38
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • YANG, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 39
    • 0029878719 scopus 로고    scopus 로고
    • Phylogenetic analysis using parsimony and likelihood methods
    • YANG, Z. 1996a. 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
  • 40
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • YANG, Z. 1996b. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 41
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • YANG, Z., N. GOLDMAN, AND A. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:316-324.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3


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