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5 - Are we all cladists?

Published online by Cambridge University Press:  05 July 2016

By
Andrew V.Z. Brower
Edited by
David Williams ,
Michael Schmitt  and
Quentin Wheeler
David Williams
Affiliation:
Natural History Museum, London
Michael Schmitt
Affiliation:
Ernst-Moritz-Arndt-Universität Greifswald, Germany
Quentin Wheeler
Affiliation:
State University of New York
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The Future of Phylogenetic Systematics
The Legacy of Willi Hennig
 , pp. 88 - 114
Publisher: Cambridge University Press
Print publication year: 2016

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References

Akaiki, H. (1974). Information theory as an extension of the maximum likelihood principle. In Second International Symposium on Information Theory, ed. Petrov, B. and Csaki, F.. Budapest: Akademiai Kiado, pp. 267–281.Google Scholar
Amundson, R. (2005). The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Anisimova, M., Liberles, D.A., Philippe, H., et al. (2013). State of the art methodologies dictate new standards for phylogenetic analysis. BMC Evolutionary Biology, 13, 161.CrossRefGoogle ScholarPubMed
Assis, L.C.S. (2009). Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics. Cladistics, 25, 528–544.CrossRefGoogle ScholarPubMed
Barry, M. (1837). Further observations on the unity of structure in the animal kingdom, and on congenital anomalies, including “hermaphrodites”; with some remarks on embryology, as facilitating animal nomenclature, classification, and the study of comparative anatomy. Edinburgh New Philosophical Journal, 22, 345–364.Google Scholar
Baum, D.A. and Smith, S.D. (2013). Tree Thinking: an Introduction to Phylogenetic Biology. Greenwood Village, CO: Roberts and Co.Google Scholar
Baum, D.A., Smith, S.D. and Donovan, S.S.S. (2005). The tree-thinking challenge. Science, 310, 979–980.CrossRefGoogle ScholarPubMed
Bergsten, J. (2005). A review of long-branch attraction. Cladistics, 21, 163–193.CrossRefGoogle ScholarPubMed
Bicheno, J.E. (1827). On systems and methods. Transactions of the Linnean Society of London, 15, 479–496.CrossRefGoogle Scholar
Blackburn, S. (1994). The Oxford Dictionary of Philosophy. Oxford: Oxford University Press.Google Scholar
Brady, R.H. (1985). On the independence of systematics. Cladistics, 1, 113–126.CrossRefGoogle ScholarPubMed
Bridgman, P.W. (1927). The Logic of Modern Physics. New York: Macmillan.Google Scholar
Brower, A.V.Z. (2000a). Homology and the inference of systematic relationships: some historical and philosophical perspectives. In Homology and Systematics: Coding Characters for Phylogenetic Analysis, ed. Scotland, R.W. and Pennington, R.T.. London: Taylor and Francis, pp. 10–21.Google Scholar
Brower, A.V.Z. (2000b). Evolution is not an assumption of cladistics. Cladistics, 16, 143–154.CrossRefGoogle Scholar
Brower, A.V.Z. (2002). Cladistics, phylogeny, evidence and explanation – a reply to Lee. Zoologica Scripta, 31, 221–223.CrossRefGoogle Scholar
Brower, A.V.Z. and de Pinna, M.C.C. (2012). Homology and errors. Cladistics, 28, 529–538.CrossRefGoogle ScholarPubMed
Brower, A.V.Z. and de Pinna, M.C.C. (2014). About nothing. Cladistics, 30, 330–336.CrossRefGoogle ScholarPubMed
Brower, A.V.Z. and Rindal, E. (2013). Reality check: a reply to Smith. Cladistics, 29, 464–465.CrossRefGoogle Scholar
Chang, H. (2009). Operationalism. In The Stanford Encyclopedia of Philosophy (Fall 2009 Edition), ed. E.N. Zalta, http://plato.stanford.edu/archives/fall2009/entries/operationalism/.Google Scholar
Christenson, C.M. (1997). The Innovator’s Dilemma. Boston, MA: Harvard Business Press.Google Scholar
Darwin, C. (1859). On the Origin of Species. London: John Murray.Google Scholar
Doolittle, W.F. (2009). The practice of classification and the theory of evolution, and what the demise of Charles Darwin’s tree of life hypothesis means for both of them. Philosophical Transactions- Royal Society of London, Series B Biological Sciences, 364, 2221–2228.CrossRefGoogle ScholarPubMed
Efron, B. (2013). Bayes’ Theorem in the 21st Century. Science, 340, 1177–1178.CrossRefGoogle Scholar
Farris, J.S. (1969). A successive approximations approach to character weighting. Systematic Zoology, 18, 374–385.CrossRefGoogle Scholar
Farris, J.S. (1970). Methods for computing Wagner trees. Systematic Zoology, 19, 83–92.CrossRefGoogle Scholar
Farris, J.S. (1982). Simplicity and informativeness in systematics and phylogeny. Systematic Zoology, 31, 413–444.CrossRefGoogle Scholar
Farris, J.S. (1983). The logical basis of phylogenetic analysis. In Advances in Cladistics, 2, ed. Platnick, N.I. and Funk, V.A.. New York: Columbia University Press, pp. 7–36.Google Scholar
Farris, J.S. (1986). On the boundaries of phylogenetic systematics. Cladistics, 2, 14–27.Google Scholar
Farris, J.S. (1999). Likelihood and inconsistency. Cladistics, 15, 199–204.Google ScholarPubMed
Farris, J.S. (2008). Parsimony and explanatory power. Cladistics, 24, 825–847.CrossRefGoogle Scholar
Farris, J.S. (2011). Systemic foundering. Cladistics, 27, 207–221.CrossRefGoogle Scholar
Farris, J.S. (2012). Counterfeit cladistics. Cladistics, 28, 227–228.CrossRefGoogle ScholarPubMed
Farris, J.S. (2014). “Taxic homology” is neither. Cladistics, 30, 113–115.CrossRefGoogle Scholar
Farris, J.S., Källersjö, M. and De Laet, J.E. (2001). Branch lengths do not indicate support – even in maximum likelihood. Cladistics, 17, 298–299.CrossRefGoogle Scholar
Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology, 27, 401–410.CrossRefGoogle Scholar
Felsenstein, J. (2004). Inferring Phylogenies. Sunderland, MA: Sinauer Associates.Google Scholar
Futuyma, D.J. (1986). Evolutionary Biology. Sunderland, MA: Sinauer Associates.Google ScholarPubMed
Ghiselin, M.T. (1997). Metaphysics and the Origin of Species. Albany, NY: State University of New York Press.Google Scholar
Goloboff, P.A. (2003). Parsimony, likelihood, and simplicity. Cladistics, 19, 91–103.CrossRefGoogle Scholar
Goloboff, P.A., Farris, J.S. and Nixon, K.C. (2008). TNT a free program for phylogenetic analysis. Cladistics, 24, 774–786.CrossRefGoogle Scholar
Goloboff, P.A. and Pol, D. (2005). Parsimony and Bayesian phylogenetics. In Parsimony, Phylogeny, and Genomics, ed. Albert, V.A.. Oxford: Oxford University Press, pp. 148–159.Google Scholar
Günther, K. (1956). Systematik und Stammesgeschichte der Tiere 1939–1953. Fortschrift Zoology, (N. F.) 10, 33–278.Google Scholar
Haas, O. and Simpson, G.G. (1946). Analysis of some phylogenetic terms, with attempts at redefinition. Proceedings of the American Philosophical Society, 90, 319–349.Google ScholarPubMed
Hendy, M.D. and Penny, D. (1989). A framework for the quantitative study of evolutionary trees. Systematic Zoology, 38, 297–309.CrossRefGoogle Scholar
Hennig, W. (1953). Kritische Bemerkungen zum phylogenetischen System der Insekten. Beiträge zur Entomologie, 3, 1–85.Google Scholar
Hennig, W. (1965). Phylogenetic systematics. Annual Reviews of Entomology, 10, 97–116.CrossRefGoogle Scholar
Hennig, W. (1966). Phylogenetic Systematics. Urbana, IL: University of Illinois Press.Google Scholar
Hennig, W. (1975). “Cladistic analysis or cladistic classification?”: a reply to Ernst Mayr. Systematic Zoology, 24, 244–256.CrossRefGoogle Scholar
Huelsenbeck, J.P. (1995). Performance of phylogenetic methods in simulation. Systematic Biology, 44, 17–48.CrossRefGoogle Scholar
Huelsenbeck, J.P., Alfaro, M.E. and Suchard, M.A. (2011). Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Systematic Biology, 60, 225–233.CrossRefGoogle ScholarPubMed
Huelsenbeck, J.P. and Hillis, D.M. (1993). Success of phylogenetic methods in the four-taxon case. Systematic Biology, 42, 247–264.CrossRefGoogle Scholar
Hugall, A.F. and Lee, M.S.Y. (2007). The likelihood node density effect and consequences for evolutionary studies of molecular evolution. Evolution, 61, 2293–2307.CrossRefGoogle Scholar
Hull, D.L. (1968). The operational imperative – sense and nonsense in operationalism. Systematic Zoology, 17, 438–457.CrossRefGoogle Scholar
Kearney, M. and Rieppel, O. (2006). Rejecting the “given” in systematics. Cladistics, 22, 369–377.CrossRefGoogle Scholar
Kluge, A.G. (1976). Phylogenetic relationships in the lizard family Pygopodidae: an evaluation of theory, method and data. Miscellaneous Publications of the Museum of Zoology, University of Michigan, 152, 1–72.Google Scholar
Kluge, A.G. (1997). Testability and the refutation and corroboration of cladistic hypotheses. Cladistics, 13, 81–96.CrossRefGoogle ScholarPubMed
Kluge, A.G. (2001). Parsimony with and without scientific justification. Cladistics, 17, 199–210.CrossRefGoogle ScholarPubMed
Kluge, A.G. and Farris, J.S. (1999). Taxic homology = overall similarity. Cladistics, 15, 205–212.Google ScholarPubMed
Kuhn, T.S. (1970). The Structure of Scientific Revolutions. Chicago, IL: University of Chicago Press.Google Scholar
Lee, M.S.Y. (2002). Divergent evolution, hierarchy, and cladistics. Zoologica Scripta, 31, 217–219.CrossRefGoogle Scholar
Lepore, J. (2014). The disruption machine. The New Yorker, 23 June.Google Scholar
Linnaeus, C. (1758). Systema Naturae, (10th edition, facsimile reprint, 1956). London: British Museum (Natural History).Google Scholar
MacLeay, W.S. (1819). Horae Entomologicae: or Essays on the Annulose Animals. London: S. Bagster.CrossRefGoogle Scholar
MacLeay, W.S. (1830). On the dying struggle of the dichotomous system. Philosophical Magazine, 7, 431–445; 8, 53–57, 134–140, 200–207.Google Scholar
Mayr, E. (1982). The Growth of Biological Thought. Cambridge, MA: Belknap Press.Google Scholar
Mishler, B.D. (2009). Three centuries of paradigm changes in biological classification: Is the end in sight? Taxon, 58, 61–67.CrossRefGoogle Scholar
Morrison, D.A. (2014). Is the Tree of Life the best metaphor, model, or heuristic for phylogenetics? Systematic Biology, 63, 628–638.CrossRefGoogle ScholarPubMed
Nixon, K.C. and Carpenter, J.M. (2012a). On homology. Cladistics, 28, 160–169.CrossRefGoogle ScholarPubMed
Nixon, K.C. and Carpenter, J.M. (2012b). More on errors. Cladistics, 28, 539–544.CrossRefGoogle ScholarPubMed
Oldroyd, D. (1986). The Arch of Knowledge: an Introductory Study of the History of the Philosophy and Methodology of Science. New York: Methuen.Google Scholar
Page, R.D.M. and Holmes, E.C. (1998). Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Science.Google Scholar
Pickett, K.M. and Randle, C.P. (2005). Strange Bayes indeed: uniform topological priors imply non-uniform clade priors. Molecular Phylogenetics and Evolution, 34, 203–211.CrossRefGoogle ScholarPubMed
Platnick, N.I. (1979). Philosophy and the transformation of cladistics. Systematic Zoology, 28, 537–546.CrossRefGoogle Scholar
Popper, K.R. (1965). Conjectures and Refutations: the Growth of Scientific Knowledge. New York: Harper Torchbooks (1968 reissue).Google Scholar
Popper, K.R. (1974). Darwinism as a metaphysical research programme. In The philosophy of Karl Popper, ed. Schilpp, P.A.. La Salle, IL: Open Court, pp. 133–143.Google Scholar
Popper, K.R. (1979). Objective Knowledge: An Evolutionary Approach. Oxford: Clarendon Press.Google Scholar
Popper, K.R. (1983). Realism and the Aim of Science. New York: Routledge.Google Scholar
Rieppel, O. (2005a). The philosophy of total evidence and its relevance for phylogenetic influence. Papeis Avulsos de Zoologia, 45, 77–89.Google Scholar
Rieppel, O. (2005b). A skeptical look at justification. Cladistics, 21, 203–207.CrossRefGoogle Scholar
Rieppel, O. (2005c). Monophyly, paraphyly, and natural kinds. Biology and Philosophy, 20, 465–487.CrossRefGoogle Scholar
Rieppel, O. (2005d). A note on reality, ontology, and pattern cladism. Neues Jahrbuch für Geologie und Palaontologie-Monatshefte, 3, 142–150.CrossRefGoogle Scholar
Rieppel, O. (2007a). The nature of parsimony and instrumentalism in systematics. Journal of Zoological Systematics and Evolutionary Research, 45, 177–183.CrossRefGoogle Scholar
Rieppel, O. (2007b). Parsimony, likelihood, and instrumentalism in systematics. Biology and Philosophy, 22, 141–144.CrossRefGoogle Scholar
Rieppel, O. and Kearney, M. (2007). The poverty of taxonomic characters. Biology and Philosophy, 22, 95–113.CrossRefGoogle Scholar
Rindal, E. and Brower, A.V.Z. (2011). Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data. Cladistics, 27, 331–334.CrossRefGoogle ScholarPubMed
Ripplinger, J. and Sullivan, J. (2008). Does choice in model selection affect maximum likelihood analysis? Systematic Biology, 57, 76–85.CrossRefGoogle ScholarPubMed
Sanderson, M.J. (1990). Estimating rates of speciation and evolution: a bias due to homoplasy. Cladistics, 6, 387–391.CrossRefGoogle ScholarPubMed
Schlee, D. (1975). Numerical phyletics: an analysis from the viewpoint of phylogenetic systematics. Entomologica Scandinavica, 6, 193–208.CrossRefGoogle Scholar
Schuh, R.T. and Brower, A.V.Z. (2009). Biological Systematics: Principles and Applications, 2nd edition. Ithaca, NY: Cornell University Press.Google Scholar
Schwarz, G. (1978). Estimating the dimensions of a model. Annals of Statistics, 6, 461–464.CrossRefGoogle Scholar
Siddall, M.E. and Kluge, A.G. (1997). Probabilism and phylogenetic inference. Cladistics, 13, 313–336.CrossRefGoogle ScholarPubMed
Smith, M.R. (2013). Likelihood and parsimony diverge at high taxonomic levels. Cladistics, 29, 463.CrossRefGoogle ScholarPubMed
Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy. San Francisco: W.H. Freeman.Google Scholar
Sober, E. (1988). Reconstructing the Past: Parsimony, Evolution and Inference. Cambridge, MA: MIT Press.Google Scholar
Sober, E. (2008). Empiricism. In The Routledge Companion to the Philosophy of Science, ed. Psillos, S. and Curd, M.. London: Routledge, pp. 129–138.Google Scholar
Sober, E. (2009). Parsimony and models of animal minds. In The Philosophy of Animal Minds, ed. Lurz, R.. Cambridge: Cambridge University Press, pp. 237–257.CrossRefGoogle Scholar
Steel, M. (2002). Some statistical aspects of the maximum parsimony method. In Molecular Systematics and Evolution: Theory and Practice, ed. DeSalle, R., Giribet, G. and Wheeler, W.. Basel, Switzerland: Birkhäuser Verlag, pp. 125–139.CrossRefGoogle Scholar
Strickland, H.E. (1841). On the true method of discovering the natural system in zoology and botany. Annals and Magazine of Natural History, (1st ser.) 6, 184–194.CrossRefGoogle Scholar
Sullivan, J. and Joyce, P. (2005). Model selection in phylogenetics. Annual Reviews in Ecology and Systematics, 36, 445–466.Google Scholar
Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996). Phylogenetic inference. In Molecular Systematics, ed. Hillis, D.M., Mable, B.K. and Moritz, C.. Sunderland, MA: Sinauer Associates, pp. 407–514.Google Scholar
Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., et al. (2001). Bias in phylogenetic estimation and its relevance to choice between parsimony and likelihood methods. Systematic Biology, 50, 525–539.CrossRefGoogle ScholarPubMed
Van Fraassen, B.C. (1980). The Scientific Image. New York: Oxford University Press.CrossRefGoogle Scholar
Vergara-Silva, F. (2009). Pattern cladistics and the ‘realism-antirealism debate’ in the philosophy of biology. Acta Biotheoretica, 57, 269–294.CrossRefGoogle ScholarPubMed
Von Baer, K.E. (1828). Über Entwickelungsgeschiichte der Thiere: Beobachtung und Reflexion. Königsberg: Börntrager.Google Scholar
Wägele, J.-W. (2005). Foundations of Phylogenetic Systematics. Munich: Verlag Dr. Friedrich Pfeil.Google Scholar
Wheeler, Q.D. (1995). The “old systematics”: classification and phylogeny. In Biology, Phylogeny and Classification of Coleoptera: Papers Celebrating the 80th Birthday of Roy A. Crowson, ed. Pakaluk, J. and Slipinski, S.A.. Warszawa: Muzeum i Instytut Zoologii PAN, pp. 31–62.Google Scholar
Wheeler, W.C. (2012). Systematics: A Course of Lectures. Chichester: Wiley-Blackwell.CrossRefGoogle Scholar
Wiley, E.O. and Lieberman, B.S. (2011). Phylogenetics: Theory and Practice of Phylogenetic Systematics. Hoboken, NJ: John A. Wiley and Sons.CrossRefGoogle Scholar
Wilkins, J.S. and Ebach, M.C. (2014). The Nature of Classification: Relationships and Kinds in the Natural Sciences. Basingstoke, New York: Palgrave Macmillan.CrossRefGoogle Scholar
Williams, D.M., Ebach, M.C. and Wheeler, Q.D. (2010). Beyond belief: the steady resurrection of phenetics. In Beyond Cladistics: the Branching of a Paradigm, ed. Williams, D.M. and Knapp, S.. Berkeley, CA: University of California Press, pp. 169–195.Google Scholar
Winsor, M.P. (2009). Taxonomy was the foundation of Darwin’s evolution. Taxon, 58, 43–49.CrossRefGoogle Scholar

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