Abstract
The emphasis on testing phylogenetic hypotheses has been prominent since the English language introductions of Willi Hennig’s Phylogenetic Systematics (1966) and Karl Popper’s (1959) Logic of Scientific Discovery. While the mechanics of hypothesis and theory testing are well established in other fields of science, adherence to those prescriptions in biological systematics has rarely been formally recognized. The consequence has been the development of potentially contradictory approaches to empirically evaluating phylogenetic hypotheses under the guise of testing. In his brief review of the topic, Assis (Cladistics, 30:240–242, 2014) identified five different views on phylogenetic hypothesis testing: (1) total evidence, (2) taxonomic congruence, (3) reciprocal illumination, (4) homology assessment, and (5) taxa sampling. The present paper examines the validity of these views against the actual inferential steps required to infer hypotheses and subsequently engage in testing, i.e., abduction, deduction, and induction (sensu stricto), respectively. It is shown that none of the tests discussed by Assis are valid, and while it is straightforward to outline what is required to properly test phylogenetic hypotheses, the feasibility of accomplishing such tests is operationally impractical in most instances.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Notes
In those instances in which a common cause theory is not used in lieu of substitution rates factored into the theoretical make up of an abductive inference, one would have to take into account all additional instances of novel character origin/fixation “along branches.” This would necessitate considering the individual testing of each and every hypothesis of events making up such “branch lengths,” which is likely to be operationally unfeasible given what is required to properly test those hypotheses.
This presupposition is often violated when sequence data are considered because rates of substitution are introduced as part of the phylogenetic theory. This is an instance of interjecting background knowledge at the incorrect juncture in inquiry. Consideration of rates of substitution would have to be applied at the point one considers their observation statements. What might appear to be shared characters would require reinterpretation per the assumption that evolutionary rates can obfuscate perceptions. Once those corrections are made, revised observation statements of shared similarities would lead to why-questions that are again answered by use of a common-cause theory similar to that shown in [4].
For the remainder of this section, references to the testing of “homology” will be replaced with what is the appropriate term, homologue, to avoid perpetuating conflation of the two terms.
References
Achinstein, P. (1970). Inference to scientific laws. In R. H. Stuewer (Ed.), Volume V: historical and philosophical perspectives of science. Minnesota Studies in the Philosophy of Science (pp. 87–111). Minneapolis: University of Minnesota Press.
Achinstein, P. (2001). The Book of Evidence. New York: Oxford University Press.
Aliseda, A. (2006). Abductive reasoning: logical investigations into discovery and explanation. Dordrecht: Springer.
Ariew, A. (2003). Ernst Mayr’s ‘ultimate/proximate’ distinction reconsidered and reconstructed. Biology and Philosophy, 18, 553–565.
Assis, L. C. S. (2014). Testing evolutionary hypotheses: from Willi Hennig to Angiosperm Phylogeny Group. Cladistics, 30, 240–242.
Baker, V. R. (1996). Hypotheses and geomorphological reasoning. In B. L. Rhoads & C. E. Thorn (Eds.), The Scientific Nature of Geomorphology: Proceedings of the 27th Binghamton Symposium in Geomorphology held 27–29 September 1996 (pp. 57–85). New York: John Wiley & Sons.
Barker, S. F. (1957). Induction and Hypothesis. New York: Cornell University Press.
Barnes, E. (1994). Why P rather than Q? The curiosities of fact and foil. Philosophical Studies, 73, 35–53.
Beatty, J. (1994). The proximate/ultimate distinction in the multiple careers of Ernst Mayr. Biology and Philosophy, 9, 333–356.
Ben-Menahem, Y. (1990). The inference to the best explanation. Erkenntnis, 33, 319–344.
Bremer, K. (1988). The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution, 42, 795–803.
Bremer, K. (1994). Branch support and tree stability. Cladistics, 10, 295–304.
Bromberger, S. (1966). Why-questions. In R. G. Colodny (Ed.), Mind and cosmos: essays in contemporary science and philosophy. University of Pittsburgh Series in the Philosophy of Science, 3 (pp. 86–111). University of Pittsburgh Press.
Brower, A. V. Z., & de Pinna, M. C. C. (2012). Homology and errors. Cladistics, 28, 529–538.
Brower, A. V. Z., & Schawaroch, V. (1996). Three steps of homology assessment. Cladistics, 12, 265–272.
Burton, R. B. (2000). The problem of control in abduction. Transactions of the Charles S. Peirce Society, 36, 149–156.
Carnap, R. (1950). Logical Foundations of Probability. University of Chicago Press.
Cleland, C. E. (2001). Historical science, experimental science, and the scientific method. Geology, 29, 987–990.
Cleland, C. E. (2002). Methodological and epistemic differences between historical science and experimental science. Philosophy of Science, 69, 474–496.
Cleland, C. E. (2009). Philosophical issues in natural history and historiography. In A. Tucker (Ed.), A Companion to the Philosophy of History and Historiography (pp. 44–62). Malden: Wiley-Blackwell.
Cleland, C. E. (2011). Prediction and explanation in historical natural science. British Journal for the Philosophy of Science, 62, 551–582.
Cleland, C. E. (2013). Common cause explanation and the search for a smoking gun. The Geological Society of America Special Papers, 502, 1–9.
Copi, I. M., & Cohen, C. (1998). Logic. PrenticeHall: Upper Saddle River.
Curd, M. V. (1980). The logic of discovery: an analysis of three approaches. In T. Nickles (Ed.), Scientific Discovery, Logic and Rationality (pp. 201–219). Dordrecht: D. Reidel Publishing.
Davis, J. I. (1995). A phylogenetic structure for the monocotyledons, as inferred from chloroplast DNA restriction site variation, and a comparison of measures of clade support. Systematic Botany, 20, 503–527.
Dawid, R. (2013). String Theory and the Scientific Method. New York: Cambridge University Press.
de Pinna, M. C. C. (1991). Concepts and tests of homology in the cladistic paradigm. Cladistics, 7, 367–394.
de Queiroz, K. (2014). Popperian corroboration and phylogenetics. Systematic Biology, 63, 1018–1022.
de Queiroz, K., & Poe, S. (2001). Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper’s writings on corroboration. Systematic Biology, 50, 305–321.
de Queiroz, K., & Poe, S. (2003). Failed refutations: further comments on parsimony and likelihood methods and their relation-ship to Popper’s degree of corroboration. Systematic Biology, 52, 322–330.
de Regt, H. W., & Dieks, D. (2005). A contextual approach to scientific understanding. Synthese, 144, 137–170.
de Regt, H. W., Leonelli, S., & Eigner, K. (2009). Focusing on scientific understanding. In H. de Regt, S. Leonelli, & K. Eigner (Eds.), Scientific understanding: philosophical perspectives (pp. 1–17). Pittsburgh: University of Pittsburgh Press.
Desper, R., & Gascuel, O. (2002). Fast and accurate phylogeny reconstruction algorithms based on the minimum- evolution principle. Journal of Computational Biology, 9, 687–705.
Douven, I. (2002). Testing inference to the best explanation. Synthese, 130, 355–377.
Efron, B. (1979). Bootstrap methods: another look at the jackknife. Annals of Statistics, 7, 1–26.
Efron, B., & Tibshirani, R. J. (1993). An Introduction to the Bootstrap. New York: Chapman & Hall.
Efron, B., Halloran, E., & Holmes, S. (1996). Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences, 93, 7085–7090.
Egan, M. G. (2006). Support versus corroboration. Journal of Biomedical Informatics, 39, 72–85.
Eldredge, N., & Cracraft, J. (1980). Phylogenetic patterns and the evolutionary process: method and theory in comparative biology. New York: Columbia University Press.
Faith, D. P. (2004). From species to supertrees: Popperian corroboration and some current controversies in systematics. Australian Systematic Botany, 17, 1–16.
Faith, D. P. (2006). Science and philosophy for molecular systematics: which is the cart and which is the horse? Molecular Phylogenetics and Evolution, 38, 553–557.
Faith, D. P., & Cranston, P. S. (1992). Probability, parsimony, and Popper. Systematic Biology, 41, 252–257.
Faith, D. P., & Trueman, J. W. H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology, 50, 331–350.
Faith, D. P., Köhler, F., Puslednik, L., & Ballard, J. W. O. (2011). Phylogenies with corroboration assessment. Zootaxa, 2946, 52–56.
Fann, K. T. (1970). Peirce’s Theory of Abduction. The Hague: Martinus Nijhoff.
Farris, J. S. (1983). The logical basis of phylogenetic analysis. In N. I. Platnick & V. A. Funk (Eds.), Advances in Cladistics. Volume 2. Proceedings of the Second Meeting of the Willi Hennig Society (pp. 7–36). New York: Columbia University Press.
Farris, J. S., Albert, V. A., Källersjö, M., Lipscomb, D., & Kluge, A. G. (1996). Parsimony jackknifing outperforms neighbor-joining. Cladistics, 12, 99–124.
Farris, J. S., Kluge, A. G., & Carpenter, J. M. (2001). Popper and likelihood versus “Popper*.”. Systematic Biology, 50, 438–444.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.
Felsenstein, J. (1988). Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics, 22, 521–565.
Felsenstein, J. (2004). Inferring Phylogenies. Sunderland: Sinauer Associates.
Fetzer, J. H. (1993). Philosophy of Science. New York: Paragon House.
Fetzer, J. H., & Almeder, R. F. (1993). Glossary of Epistemology/Philosophy of Science. New York: Paragon House.
Fitzhugh, K. (2005a). Les bases philosophiques de l’inférence phylogénétique: une vue d’ensemble. Biosystema, 24, 83–105.
Fitzhugh, K. (2005b). The inferential basis of species hypotheses: the solution to defining the term ‘species.’. Marine Ecology, 26, 155–165.
Fitzhugh, K. (2006a). The abduction of phylogenetic hypotheses. Zootaxa, 1145, 1–110.
Fitzhugh, K. (2006b). The ‘requirement of total evidence’ and its role in phylogenetic systematics. Biology and Philosophy, 21, 309–351.
Fitzhugh, K. (2006c). The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zoologica Scripta, 35, 261–286.
Fitzhugh, K. (2008a). Fact, theory, test and evolution. Zoologica Scripta, 37, 109–113.
Fitzhugh, K. (2008b). Abductive inference: implications for ‘Linnean’ and ‘phylogenetic’ approaches for representing biological systematization. Evolutionary Biology, 35, 52–82.
Fitzhugh, K. (2008c). Clarifying the role of character loss in phylogenetic inference. Zoologica Scripta, 37, 561–569.
Fitzhugh, K. (2009). Species as explanatory hypotheses: refinements and implications. Acta Biotheoretica, 57, 201–248.
Fitzhugh, K. (2010). Evidence for evolution versus evidence for intelligent design: parallel confusions. Evolutionary Biology, 37, 68–92.
Fitzhugh, K. (2012). The limits of understanding in biological systematics. Zootaxa, 3435, 40–67.
Fitzhugh, K. (2013). Defining ‘species’, ‘biodiversity’, and ‘conservation’ by their transitive relations. In I. Y. Pavlinov (Ed.), The Species Problem – Ongoing Problems (pp. 93–130). New York: InTech.
Fitzhugh, K. (2014). Character mapping and cladogram comparison versus the requirement of total evidence: does it matter for polychaete systematics? Memoirs of Museum Victoria, 71, 67–78.
Fitzhugh, K. (2015). What are species? Or, on asking the wrong question. The Festivus, 47, 229–239.
Fitzhugh, K. (2016). Sequence data, phylogenetic inference, and implications of downward causation. Acta Biotheoretica (in press).
Franz, N. M. (2005). Outline of an explanatory account of cladistic practice. Biology and Philosophy, 20, 489–515.
Gaffney, E. S. (1979). An introduction to the logic of phylogeny reconstruction. In J. Cracraft & N. Eldredge (Eds.), Phylogenetic Analysis and Paleontology. New York: Columbia University Press.
Godfrey-Smith, P. (2003). Theory and reality: an introduction to the philosophy of science. University of Chicago Press.
Grandcolas, P., Deleporte, P., & Desutter-Grandcolas, L. (1997). Testing evolutionary processes with phylogenetic patterns: test power and test limitations. In P. Grandcolas (Ed.), The Origin of Biodiversity in Insects: Phylogenetic Tests of Evolutionary Scenarios. Mémoires du Muséum National d’Histoire Naturelle, 173, 53–71.
Grant, T., & Kluge, A. G. (2008). Clade support measures and their adequacy. Cladistics, 24, 1051–1064.
Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696–704.
Hacking, I. (2001). An Introduction to Probability and Inductive Logic. New York: Cambridge University Press.
Hanson, N. R. (1958). Patterns of discovery: an inquiry into the conceptual foundations of science. New York: Cambridge University Press.
Harman, G. H. (1965). Inference to the best explanation. The Philosophical Review, 74, 88–95.
Hausman, D. M. (1998). Causal Asymmetries. New York: Cambridge University Press.
Hawkins, J. A., Hughes, C. E., & Scotland, R. W. (1997). Primary homology assessment, characters and character states. Cladistics, 13, 275–283.
Heath, T. A., Hedtke, S. M., & Hillis, D. M. (2008). Taxon sampling and the accuracy of phylogenetic analysis. Journal of Systematics and Evolution, 46, 239–257.
Helfenbein, G. K., & DeSalle, R. (2005). Falsifications and corroborations: Karl Popper’s influence on systematics. Molecular Phylogenetics and Evolution, 35, 271–280.
Hempel, C. G. (1962). Deductive nomological vs. statistical explanation. In H. Feigl & G. Maxwell (Eds.), Minnesota Studies in the Philosophy of Science, Volume 3 (pp. 98–169). Minneapolis: University of Minnesota Press.
Hempel, C. G. (1965). Aspects of Scientific Explanation and Other Essays in the Philosophy of Science. New York: The Free Press.
Hempel, C. G. (1966). Recent problems of induction. In R. G. Colodny (Ed.), Mind and Cosmos (pp. 112–134). Pittsburgh: University of Pittsburgh Press.
Hempel, C. G. (2001). The philosophy of Carl G. Hempel: studies in science, explanation, and rationality. In J. H. Fetzer (Ed.). New York: Oxford University Press.
Hennig, W. (1966). Phylogenetic Systematics. Urbana: University of Illinois Press.
Hillis, D. M. (1995). Approaches for assessing phylogenetic accuracy. Systematic Biology, 44, 3–16.
Hoffmann, M. (1999). Problems with Peirce’s concept of abduction. Foundations of Science, 4, 271–305.
Holmes, S. (2003). Bootstrapping phylogenetic trees: theory and methods. Statistical Science, 18, 241–255.
Hoyningen-Huene, P. (2013). Systematicity: the nature of science. New York: Oxford University Press.
Hull, D. L. (1974). Philosophy of Biological Science. Englewood Cliffs: Prentice-Hall.
Jeffares, B. (2008). Testing times: regularities in the historical sciences. Studies in History and Philosophy of Biological and Biomedical Sciences, 39, 469–475.
Josephson, J. R., & Josephson, S. G. (Eds.). (1994). Abductive inference: computation, philosophy, technology. New York: Cambridge University Press.
Kelly, T. (2008). Common sense as evidence: against revisionary ontology and skepticism. Midwest Studies in Philosophy, 32, 53–78.
Kim, J. (1993). Improving the accuracy of phylogenetic estimation by combining different methods. Systematic Biology, 42, 331–340.
Kluge, A. G. (1989). A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology, 38, 7–25.
Kluge, A. G. (1997a). Sophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematics. Zoologica Scripta, 26, 349–360.
Kluge, A. G. (1997b). Testability and the refutation and corroboration of cladistic hypotheses. Cladistics, 13, 81–96.
Kluge, A. G. (1998). Total evidence or taxonomic congruence: cladistics or consensus classification. Cladistics, 14, 151–158.
Kluge, A. G. (1999). The science of phylogenetic systematics: explanation, prediction, and test. Cladistics, 15, 429–436.
Kluge, A. G. (2001). Philosophical conjectures and their refutation. Systematic Biology, 50, 322–330.
Laland, K. N., Sterelny, K., Odling-Smee, J., Hoppitt, W., & Uller, T. (2011). Cause and effect in biology revisited: is Mayr’s proximate-ultimate dichotomy still useful? Science, 334, 1512–1516.
Lankester, E. R. (1870). II. – On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements. Annals and Magazine of Natural History, Series, 4(6), 34–43.
Laubichler, M. D. (2014). Homology as a bridge between evolutionary morphology, developmental evolution, and phylogenetic systematics. In A. Hamilton (Ed.), The Evolution of Phylogenetic Systematics (pp. 63–85). Los Angeles: University of California Press.
Lavelle, J. S., Botterill, G., & Lock, S. (2013). Contrastive explanation and the many absences problem. Synthese, 190, 3495–3510.
Lipton, P. (2004). Inference to the Best Explanation. New York: Routledge.
Lipton, P. (2005). Testing hypotheses: prediction and prejudice. Science, 307, 219–221.
Longino, H. E. (1979). Evidence and hypothesis: an analysis of evidential relations. Philosophy of Science, 46, 35–56.
Magnani, L. (2001). Abduction, reason, and science: processes of discovery and explanation. New York: Kluwer Academic.
Mahner, M., & Bunge, M. (1997). Foundations of Biophilosophy. New York: Springer.
Marwick, P. (1999). Interrogatives and contrasts in explanation theory. Philosophical Studies, 96, 183–204.
Mayo, D. G. (1991). Novel evidence and severe tests. Philosophy of Science, 58, 523–552.
Mayo, D. G. (1996). Error and the Growth of Experimental Knowledge. Chicago: The University of Chicago Press.
Mayo, D. G. (2005). Peircean induction and the error-correcting thesis. Transactions of the Charles S Peirce Society, 41, 299–319.
Mayr, E. (1961). Cause and effect in biology. Science, 131, 1501–1506.
Mayr, E. (1982). The growth of biological thought: diversity, evolution, and inheritance. Cambridge: Harvard University Press.
Mayr, E. (1993). Proximate and ultimate causation. Biology and Philosophy, 8, 95–98.
Mayr, E. (1994). Response to John Beatty. Biology and Philosophy, 9, 359–371.
McLaughlin, A. (1970). Rationality and total evidence. Philosophy of Science, 37, 271–278.
McMullin, E. (1995). The Inference That Makes Science. Milwaukee: Marquette University Press.
Miller, J. A. (2003). Assessing progress in systematics with continuous jackknife function analysis. Systematic Biology, 52, 55–65.
Minelli, A. (1994). Biological systematics: the state of the art. New York: Chapman & Hall.
Moritz, C., & Hillis, D. M. (1996). Molecular systematics: context and controversies. In D. M. Hillis, C. Moritz, & B. K. Mable (Eds.), Molecular Systematics (pp. 1–13). Sunderland: Sinauer Associates.
Nabhan, A. R., & Sarkar, I. N. (2011). The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Briefings in Bioinformatics, 13, 122–134.
Neta, R. (2008). What evidence do you have? The British Journal for the Philosophy of Science, 59, 89–119.
Nickles, T. (1980). Introductory essay: scientific discovery and the future of philosophy of science. In T. Nickles (Ed.), Scientific Discovery, Logic and Rationality (pp. 1–59). Dordrecht: D. Reidel Publishing Company.
Niiniluoto, I. (1999). Defending abduction. Philosophy of Science, 66, S436–S451.
Nixon, K. C., & Carpenter, J. M. (2012). On homology. Cladistics, 28, 160–169.
Nola, R., & Sankey, H. (2007). Theories of scientific method: an introduction. Ithaca: McGill–Queen’s University Press.
Norton, J. D. (2003). A material theory of induction. Philosophy of Science, 70, 647–670.
Owen, R. (1843). Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals, Delivered at the Royal College of Surgeons, in 1843. London: Longman, Brown, Green, and Longmans.
Owen, R. (1847). Report on the archetype and homologies of the vertebrate skeleton. Report of the British Association of the Advancement of Science for, 1846, 169–340.
Owen, R. (1848). On the Archetype and Homologies of the Vertebrate Skeleton. London: Richard and John E. Taylor.
Owen, R. (1849). On the Nature of Limbs. A Discourse Delivered on Friday, February 9, at an Evening Meeting of the Royal Institution of Great Britain. London: John Van Voorst.
Owen, R. (2007). On the Nature of Limbs. A Discourse. The University of Chicago Press.
Paavola, S. (2012). On the origin of ideas: an abductionist approach to discovery. Saarbrücken: Lap Lambert Academic Publishing.
Patterson, C. (1982). Morphological characters and homology. In K. A. Joysey & A. E. Friday (Eds.), Problems of Phylogenetic Reconstruction (pp. 21–74). London: Academic Press.
Peirce, C. S. (1878). Illustrations of the logic of science. Sixth paper.—Deduction, induction, and hypothesis. Popular Science Monthly, 13, 470–482.
Peirce, C. S. (1883). A theory of probable inference. In C. S. Peirce (Ed.), The Johns Hopkins Studies in Logic (pp. 126–181). Boston: Little Brown and Co.
Peirce, C. S. (1902). Reasoning. In J. M. Baldwin & B. Rand (Eds.), Dictionary of Philosophy and Psychology: Prefatory Note. Text, Le-Z. Addenda: Indices. I. Greek Terms. II. Latin Terms. III. German Terms. IV. French Terms. V. Italian Terms (pp. 426–428). New York: The Macmillan Company.
Peirce, C. S. (1931). Collected Papers of Charles Sanders Peirce, Volume 1, Principles of Philosophy. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1932). Collected Papers of Charles Sanders Peirce, Volume 2, Elements of Logic. In C. Hartshorne, P. Weiss & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1933a). Collected Papers of Charles Sanders Peirce, Volume 3, Exact Logic. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1933b). Collected Papers of Charles Sanders Peirce, Volume 4, the Simplest Mathematics. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1934). Collected Papers of Charles Sanders Peirce, Volume 5, Pragmatism and Pragmaticism. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1935). Collected Papers of Charles Sanders Peirce, Volume 6, Scientific Metaphysics. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1958a). Collected Papers of Charles Sanders Peirce, Volume 7, Science and Philosophy. In C. Hartshorne, P. Weiss, & A. Burks (Eds.). Cambridge: Harvard University Press.
Peirce, C. S. (1958b). Collected Papers of Charles Sanders Peirce, Volume 8, Correspondence and Bibliography. In A. Burks (Ed.). Cambridge: Harvard University Press.
Poe, S. (2003). Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Systematic Biology, 52, 423–428.
Popper, K. R. (1959). The logic of scientific discovery. New York: Basic Books.
Popper, K. R. (1962). Conjectures and refutations: the growth of scientific knowledge. New York: Basic Books.
Popper, K. R. (1971). The Open Society and its Enemies. Volume 2: Hegel and Marx. Princeton University Press.
Popper, K. R. (1983). Objective knowledge: an evolutionary approach. New York: Oxford University Press.
Popper, K. R. (1988). The Poverty of Historicism. New York: Routledge.
Popper, K. R. (1992). Realism and the Aim of Science. New York: Routledge.
Psillos, S. (2002). Simply the best: a case for abduction. In A. C. Kakas & F. Sadri (Eds.), Computational logic: logic programming and beyond (pp. 605–625). New York: Springer.
Psillos, S. (2007). Philosophy of Science A–Z. Edinburgh: University Press.
Psillos, S. (2011). An explorer upon untrodden ground: peirce on abduction. In D. Gabbay, S. Hartmann, & J. Woods (Eds.), The Handbook of the History of Logic. Volume 10: Inductive Logic (pp. 117–151). Oxford: Elsevier B. V.
Rannala, B., Huelsenbeck, J. P., Yang, Z., & Nielsen, R. (1998). Taxon sampling and the accuracy of large phylogenies. Systematic Biology, 47, 702–710.
Reilly, F. E. (1970). Charles Peirce’s Theory of Scientific Method. New York: Fordham University Press.
Rescher, N. (1970). Scientific Explanation. New York: The Free Press.
Rescher, N. (1978). Peirce’s philosophy of science: critical studies in his theory of induction and scientific method. University of Notre Dame Press.
Reynolds, P. D. (1971). A Primer in Theory Construction. Indianapolis: ITT Bobbs-Merrill Educational Publishing Company.
Rieppel, O. (1988). Fundamentals of Comparative Biology. Boston: Birkhäuser Verlag.
Rieppel, O. (2007). The performance of morphological characters in broad-scale phylogenetic analyses. Biological Journal of the Linnean Society, 92, 297–308.
Salmon, W. C. (1967). The Foundations of Scientific Inference. University of Pittsburgh Press.
Salmon, W. C. (1984a). Scientific Explanation and the Causal Structure of the World. Princeton University Press.
Salmon, W. C. (1984b). Logic. Englewood Cliffs: Prentice-Hall, Inc.
Salmon, W. C. (1989). Four decades of scientific explanation. In P. Kitcher & W. C. Salmon (Eds.), Scientific Explanation. Minnesota Studies in the Philosophy of Science, Volume XIII (pp. 3–219). Minneapolis: University of Minnesota Press.
Salmon, W. C. (1998). Causality and Explanation. New York: Oxford University Press.
Schuh, R. T. (2000). Biological systematics: principles and applications. Ithaca: Cornell University Press.
Schuh, R. T., & Brower, A. V. Z. (2009). Biological systematics: principles and applications (2nd ed.). Ithaca: Cornell University Press.
Schurz, G. (2005). Explanations in science and the logic of why-questions: discussion of the Halonen–Hintikka—approach and alternative proposal. Synthese, 143, 149–178.
Schurz, G. (2008). Patterns of abduction. Synthese, 164, 201–234.
Siddall, M. E., & Kluge, A. G. (1997). Probabilism and phylogenetic inference. Cladistics, 13, 313–336.
Sintonen, M. (2004). Reasoning to hypotheses: where do questions come? Foundation of Science, 9, 249–266.
Sober, E. (1975). Simplicity. New York: Oxford University Press.
Sober, E. (1984). The nature of selection: evolutionary theory in philosophical focus. Cambridge: The MIT Press.
Sober, E. (1986). Explanatory presupposition. Australasian Journal of Philosophy, 64, 143–149.
Sober, E. (1988). Reconstructing the past: parsimony, evolution, and inference. Cambridge: The MIT Press.
Sober, E. (1994). From a biological point of view: essays in evolutionary biology. New York: Cambridge University Press.
Soltis, P. S., & Soltis, D. E. (2003). Applying the bootstrap in phylogeny reconstruction. Statistical Science, 18, 256–267.
Strahler, A. N. (1992). Understanding science: an introduction to concepts and issues. Buffalo: Prometheus Books.
Thagard, P. (1988). Computational Philosophy of Science. Cambridge: The MIT Press.
Thagard, P. (2004). Rationality and science. In A. Mele & P. Rawlings (Eds.), Handbook of Rationality (pp. 363–379). Oxford University Press.
Tucker, A. (2004). Our knowledge of the past: a philosophy of historiography. New York: Cambridge University Press.
Tucker, A. (2011). Historical science, over- and underdetermined: a study of Darwin’s inference of origins. British Journal for the Philosophy of Science, 62, 805–829.
Turner, D. (2007). Making prehistory: historical science and the scientific realism debate. New York: Cambridge University Press.
Van Fraassen, B. C. (1990). The Scientific Image. New York: Clarendon Press.
Walton, D. (2004). Abductive Reasoning. Tuscaloosa: The University of Alabama Press.
Wenzel, J. W. (1997). When is a phylogenetic test good enough? In: P. Grandcolas (Ed.), The Origin of Biodiversity in Insects: Phylogenetic Tests of Evolutionary Scenarios. Mémoires du Muséum National d’Histoire Naturelle, 173, 31–45.
Wheeler, Q. D. (2004). Taxonomic triage and the poverty of phylogeny. Philosophical Transactions of the Royal Society B, 359, 571–583.
Wheeler, Q. D. (2010). Do we need to describe, name, and classify all species? In D. M. Williams & S. Knapp (Eds.), Beyond cladistics: the branching of a paradigm (pp. 67–75). Berkeley: University of California Press.
Wheeler, W. C. (2012). Systematics: a course of lectures. Oxford: Wiley–Blackwell.
Wheeler, Q., & Hamilton, A. (2014). The new systematics, the new taxonomy, and the future of biodiversity studies. In A. Hamilton (Ed.), The Evolution of Phylogenetic Systematics (pp. 287–301). Los Angeles: University of California Press.
Wiens, J. J., & Servedio, M. R. (1997). Accuracy of phylogenetic analysis including and excluding polymorphic characters. Systematic Biology, 46, 332–345.
Wiley, E. O. (1975). Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Systematic Zoology, 24, 233–243.
Wiley, E. O., & Lieberman, B. S. (2011). Phylogenetics: theory and practice of phylogenetic systematics. Oxford: Wiley-Blackwell.
Williams, D. M., & Ebach, M. C. (2008). Foundations of Systematics and Biogeography. New York: Springer.
Williams, D. M., & Ebach, M. C. (2012). Confusing homologs as homologies: a reply to “On homology.”. Cladistics, 28, 223–224.
Worrall, J. (1989). Fresnel, Poisson and the white spot: the role of successful predictions in the acceptance of scientific theories. In D. Gooding, T. Pinch, & S. Schaffer (Eds.), The Uses of Experiment: Studies in the Natural Sciences (pp. 135–157). Cambridge University Press.
Zwickl, D. J., & Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology, 51, 588–598.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fitzhugh, K. Dispelling five myths about hypothesis testing in biological systematics. Org Divers Evol 16, 443–465 (2016). https://doi.org/10.1007/s13127-016-0274-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13127-016-0274-6