SEARCH

SEARCH BY CITATION

References

  • 1
    Arnold, E.N. 1981. Estimating phylogenies at low taxonomic levels. Z. Zool. Syst. Evolutionsforsch. 19: 1 35.
  • 2
    Arnold, E.N. 1990. Why do morphological phylogenies vary in quality? A study based on the comparative history of lizard clades. Proc. R. Soc. London B 240: 135 172.
  • 3
    Ball, I. 1983. On groups, existence, and the ordering of nature. Syst. Zool. 32: 446 451.
  • 4
    Bishop, M. & Friday, A.E. 1985. Evolutionary trees from nucleic acid and protein sequences. Proceedings R. Soc. London B 226: 271 302.
  • 5
    Bock, W.J. 1977. Foundations and methods of evolutionary classification. In: Major Patterns in Vertebrate Evolution (M. K. Hecht, P. C. Goody & B. M. Hecht, eds), pp. 851–895. Plenum Press, New York, USA.
  • 6
    Bock, W.J. 1981. Functional adaptive analysis in evolutionary classification. Amer. Zool. 21: 5 20.
  • 7
    Brady, R. 1985. On the independence of systematics. Cladistics 1: 113 126.
  • 8
    Brady, R. 1994. Explanation, description, and the meaning of ‘transformation’ in taxonomic evidence. In: Models in Phylogeny Reconstruction (R. W. Scotland, D. J. Siebert & D. M. Williams, eds), pp. 11–29. Clarendon Press, Oxford.
  • 9
    Brown, W.M., Praeger, E.M., Wang, A., Wilson, A.C. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18: 225 239.
  • 10
    Bryant, H.N. 1989. An evaluation of cladistic and character analyses as hypothetico-deductive procedures, and the consequences for character weighting. Syst. Zool. 38: 214 227.
  • 11
    Bryant, H.N. 1991. The polarization of character transformations in phylogenetic systematics: role of axiomatic and auxiliary assumptions. Syst. Zool. 40: 433 445.
  • 12
    Bull, J.J. & Charnov, E.L. 1985. On irreversible evolution. Evolution 39: 1149 1155.
  • 13
    Dollo, L. 1893. Les Lois de l’evolution. Bull. Soc. Belge Géol. Pal. Hydr. 7: 164 166.
  • 14
    Farris, J.S. 1983. The logical basis of phylogenetic systematics. In: Advances in Cladistics (N. I. Platnick & V. A. Funk, eds), pp. 7–36. Columbia University Press, New York.
  • 15
    Felsenstein, J. 1978. Cases in which parsimony or compatability methods will be positively misleading. Syst. Zool. 27: 401 410.
  • 16
    Fisher, D.C. 1981. The role of functional analysis in phylogenetic inference: examples from the history of the Xiphosura. Amer. Zool. 21: 47 62.
  • 17
    Fisher, D.C. 1995. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. In: Interpreting the Hierarchy of Nature: from Systematic Patterns to Evolutionary Process Theories (L. Grande & O. Rieppel, eds), pp. 133–171. Academic Press, New York.
  • 18
    Friday, A.E. 1987. Models of evolutionary change and the estimation of evolutionary trees. Oxford Surv. Evol. Biol. 4: 61 88.
  • 19
    Gaffney, E.S. 1979. An introduction to the logic of phylogenetic reconstruction. In: Phylogenetic Analysis and Paleontology (J. Cracraft & N. Eldredge, eds), pp. 79–111. Columbia University Press, New York.
  • 20
    Gallis, F. 1996. The application of functional morphology to evolutionary studies. Trends Ecol. Evol. 11: 124 129.
  • 21
    Gardiner, B.G. 1982. Tetrapod classification. Zool. J. Linnean Soc. 74: 207 232.
  • 22
    Gardiner, B.G. 1993. Haematothermia: warm-blooded amniotes. Cladistics 9: 369 395.
  • 23
    Goldman, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Syst. Zool. 39: 345 361.
  • 24
    Goloboff, P.A. 1997. Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs. Cladistics 13: 225 245.
  • 25
    Gould, S.J. 1977. Ontogeny and Phylogeny. Belknap Press, Cambridge, MA.
  • 26
    Greer, A.E., Caputo, V., Lanza, B., Palmieri R. 1998. Observations on limb reduction in the scincid lizard genus Chalcides. J. Herp. 32: 244 252.
  • 27
    Harvey, P.H. & Pagel, M.D. 1991. The Comparative Method in Evolutionary Biology. Oxford Series in: Ecology, and Evolution (R. M. May & P. H. Harvey, eds). Oxford University Press, New York.
  • 28
    Hecht, M.K. & Edwards, J.S. 1976. The determination of parallel or monophyletic relationships. The proteid salamanders – a test case. Amer. Nat. 110: 653 677.
  • 29
    Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, USA.
  • 30
    Hill, C.R. & Camus, J.M. 1986. Evolutionary cladistics of marrattialean ferns. Bull. Brit. Mus. Nat. Hist. (Bot.) 14: 219 300.
  • 31
    Hill, C.R. & Crane, P.R. 1982. Evolutionary cladistics and the origin of angiosperms. In: Problems of Phylogenetic Reconstruction (K. A. Joysey & A. E. Friday, eds), pp. 269–361. Academic Press., London.
  • 32
    Hillis, D.M., Huelsenbeck, J.P., Swofford, D.L. 1994. Consistency: hobgoblin of phylogenetics? Nature 369: 363 364.
  • 33
    Hillis, D.M., Moritz, C., Mable, B.K., eds. 1996. Molecular Systematics. Sinauer., Sunderland, MA.
  • 34
    Hull, D.L. 1967. Certainty and circularity in evolutionary taxonomy. Evolution 21: 174 189.
  • 35
    Hull, D.L. 1988. Science as a Process. University of Chicago Press, Chicago.
  • 36
    Hull, D.L. 1989. The evolution of phylogenetics. In: The Hierarchy of Life (B. Fernholm, K. Bremer & H. Jornwall, eds), pp. 3–15. Elsevier, Amsterdam.
  • 37
    Kemp, T.S. 1985. Models of diversity and phylogenetic reconstruction. Oxford Surv. Evol. Biol. 2: 135 158.
  • 38
    Kemp, T.S. 1988. Haemothermia or Archosauria? : the interrelationships of mammals, birds, and crocodiles. Zool. J. Linn. Soc. 92: 67 104.
  • 39
    Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press., Cambridge, UK.
  • 40
    Kluge, A.G. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81 96.
  • 41
    Lande, R. 1978. Evolutionary mechanisms of limb loss in tetrapods. Evolution 32: 73 92.
  • 42
    Lee, M.S.Y. & Doughty, P. 1997. The relationship between evolutionary theory and phylogenetic analysis. Biol. Rev. 72: 471 495.
  • 43
    Lee, M.S.Y. & Shine, R. 1998. Reptilian viviparity and Dollo’s law. Evolution 52: 1441 1450.
  • 44
    MacNamara, K.J. 1997. Shapes of Time: the Evolution of Growth and Development. Johns Hopkins University Press, Baltimore, USA.
  • 45
    Mayr, E., Linsley E.G., Usinger, R.L. 1953. Methods and Principles of Systematic Zoology. McGraw-Hill, New York.
  • 46
    Muller, H.J. 1939. Reversibility in evolution considered from the standpoint of genetics. Biol. Rev. 14: 261 280.
  • 47
    Naylor, G.J.P. & Brown, W.M. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst. Biol. 47: 61 76.
  • 48
    Neff, N.A. 1986. A rational basis for a priori character weighting. Syst. Zool. 35: 110 123.
  • 49
    Nelson, G. 1978. Ontogeny, phylogeny, and the biogenetic law. Syst. Zool. 27: 324 345.
  • 50
    Nelson, G. & Platnick, N. 1981. Systematics and Biogeography: Cladistics and Vicariance. Columbia University Press, New York.
  • 51
    Omland. 1997. Examining two standard assumptions of ancestral reconstructions: repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51: 1636 1646.
  • 52
    Panchen, A.L. 1992. Classification, Evolution and the Nature of Biology. Cambridge University Press, Cambridge, UK.
  • 53
    Panchen, A.L. & Smithson, T.R. 1987. Character diagnosis, fossils, and the origin of tetrapods. Biol. Rev. 62: 341 438.
  • 54
    Patterson, C. 1980. Cladistics. Biologist 27: 234 240.
  • 55
    Patterson, C. 1988. The impact of evolutionary theories on systematics. In: Prospects in Systematics (D. L. Hawksworth, ed.), pp. 59–91. Clarendon Press, Oxford, UK.
  • 56
    Patterson, C. 1994. Null or minimal models. In: Models in Phylogeny Reconstruction (R. W. Scotland, D. J. Siebert & D. M. Williams, eds), pp. 173–193. Clarendon Press, Oxford, UK.
  • 57
    Patterson, C. 1996. Comments on Mabee’s ‘empirical rejection of the ontogenetic polarity criterion’. Cladistics 12: 147 167.
  • 58
    Penny, D., Lockhart, P.J., Steel, M.A., Hendy, M.D. 1994. The role of models in reconstructing evolutionary trees. In: Models in Phylogeny Reconstruction (R. W. Scotland, D. J. Siebert, & D. M. Williams, eds), pp. 211–230. Clarendon Press, Oxford, UK.
  • 59
    Philippe, H., Lecointre, G., Le H.L.V., Guyander, H. 1996. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol. Biol. Evol. 13: 1174 1186.
  • 60
    De Pinna, M. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7: 367 394.
  • 61
    Platnick, N.I. 1979. Philosophy and the transformation of cladists. Syst. Zool. 28: 537 546.
  • 62
    De Queiroz, K. 1988. Systematics and the Darwinian revolution. Philos. Sci. 55: 238 259.
  • 63
    De Queiroz, K. 1996. Including the characters of interest during tree reconstruction and the problems of circularity and bias in studies of character evolution. Amer. Nat. 148: 700 708.
  • 64
    De Queiroz, K. & Donoghue, M.J. 1988. Phylogenetic systematics and the species problem. Cladistics 4: 317 338.
  • 65
    De Queiroz, K. & Donoghue, M.J. 1990. Phylogenetic systematics or Nelson’s, Version of cladistics? Cladistics 6: 61 75.
  • 66
    Ridley, M. 1986. Evolution and Classification: the Reformation of Cladism. Longman Press, London, UK.
  • 67
    Rieppel, O. 1988. Fundamentals of Comparative Biology. Birkhäuser-Verlag, Basel, Switzerland.
  • 68
    Rieppel, O. & Grande, L. 1994. Summary and Comments on systematic pattern and the evolutionary process. In: Interpreting the Hierarchy of Nature: from Systematic Patterns to Evolutionary Process Theories (L. Grande & O. Rieppel, eds), pp. 227–255. Academic Press, New York.
  • 69
    Rieseberg, L.H. 1997. Hybrid origins of plant species. Annu. Rev. Ecol. Syst. 28: 359 389.
  • 70
    Rosen, D.E. 1984. Hierarchies and history. In: Evolutionary Theory: Paths Into the Future (J. W. Pollard, ed.), pp. 77–97. John Wiley, New York, USA.
  • 71
    De Salle, R. & Brower, A.V.Z. 1997. Process partitions, congruence, and the independence of characters: inferring relationships among closely related Hawaiian Drosophila from multiple gene regions. Syst. Biol. 46: 751 764.
  • 72
    Schoch, R.M. 1986. Phylogeny Reconstruction in Paleontology. Van Nostrand Reinhold, New York.
  • 73
    Scott-Ram, N.R. 1990. Transformed Cladistics, Taxonomy, and Evolution. Cambridge University Press, Cambridge, UK.
  • 74
    Shaffer, H.B. 1986. Utility of quantitative genetic parameters in character weighting. Syst. Zool. 35: 124 134.
  • 75
    Siddall, M.E. & Kluge, A.G. 1997. Probabilism and phylogenetic inference. Cladistics 13: 313 336.
  • 76
    Smith, A.B. 1994. Systematics and the Fossil Record: Documenting Evolutionary Patterns. Blackwell Scientific Publications, Oxford, UK.
  • 77
    Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution and Inference. MIT Press, Cambridge, USA.
  • 78
    Sober, E. 1989. Systematics and circularity. In: What the Philosophy of Biology Is. (M. Ruse, ed.), pp. 263–273. Kluwer Academic Publishers, Dordrecht.
  • 79
    Stevens, P.F. 1991. Character states, morphological variation, and phylogenetic analysis: a review. Syst. Bot. 16: 553 583.
  • 80
    Swofford, D.L. 1999. PAUP* Phylogenetic Analysis Using Parsimony (and other methods). Laboratory of Molecular Systematics, Smithsonian Institution, Washington DC.
  • 81
    Swofford, D.L. & Maddison, W.P. 1992. Parsimony, character-state reconstructions, and evolutionary inferences. In: Systematics, Historical Ecology, and North American Freshwater Fishes (R. C. Mayden, ed.), pp. 186–223. Stanford University Press, Palo Alto.
  • 82
    Szalay, F.S. 1981. Functional analysis and the practice of the phylogenetic method as reflected by some mammalian studies. Amer. Zool. 21: 37 45.
  • 83
    Szalay, F.S. & Bock, W.J. 1991. Evolutionary theory and systematics: relationships between process and patterns. Zeit. Zool. Syst. Evolutionsforsch. 29: 1 40.
  • 84
    Wheeler, W.H. 1994. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44: 321 331.
  • 85
    Wiley, E.O. 1981. Phylogenetics: the Theory and Practice of Phylogenetic Systematics. Wiley, New York.
  • 86
    Williams, P.L. & Fitch, W.M. 1990. Phylogeny determination using dynamically weighted parsimony method. Methods Enzymol. 183: 615 626.
  • 87
    Wilson, E.O. 1998. Consilience: The Unity of Knowledge. Little, Brown and Co., London.
  • 88
    Yang, Z. 1996. Phylogenetic analysis using parsimony and likelihood models. J. Mol. Evol. 42: 294 307.
  • 89
    Yang, Z., Goldman N., Friday, A. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44: 384 399.