Skip to main content Skip to main navigation menu Skip to site footer
Type: Articles
Published: 2011-07-08
Page range: 7–16
Abstract views: 51
PDF downloaded: 23

Will the real phylogeneticists please stand up?

Department of Ecology and Evolutionary Biology and Biodiversity Research Center, University of Kansas, Lawrence, KS, U.S.A.
Museum of Natural Science, Louisiana State University, Baton Rouge, LA, U.S.A.
Department of Marine Sciences, University of Puerto Rico, Mayagüez, Puerto Rico, 00681, U.S.A.
Museum of Natural Science, Louisiana State University, Baton Rouge, LA, U.S.A.
Johnson County Community College, Overland Park, KS 66210-1299, U.S.A.
Saint Louis University, Department of Biology, Laclede Ave., St. Louis, MO, U.S.A.
Department of Zoology, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, U.S.A.

Abstract

In a recently published commentary, Mooi & Gill asserted that there is a crisis brewing in systematic ichthyology caused by a failure of investigators to apply the basic tenets of outgroup comparison to recover clades based solely on shared apomorphic characters. The result, they claim, is that many recent analyses disregard real synapomorphies and discover clades by phenetic rather than phylogenetic principles. We take the opportunity to refute this claim and assert that matrix-based analyses, whether parametric or nonparametric, satisfy the basic tenets of Hennig’s methods, resulting in monophyletic groups confirmed by synapomorphies.

References

  1. Ebach, M.C., Morrone, J.J. & Williams, D.M. (2008) A new cladistics of cladists. Biological Philosophy, 23, 153–156.

    Efron, B., Halloran, E. & Holmes, S. (1996) Bootstrap confidence levels for phylogentic analysis. Proceedings of the National Academy of Sciences USA, 93, 7085–7090.

    Erixon, P., Svennblad, B., Britton, T. & Oxelman, B. (2003) Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Systematic Biology, 52, 665–673.

    Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783–791.

    Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates, Sunderland, Mass.

    Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworth, C.J., Campbell, J.A., Blotto, B., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M. & Wheeler, W.C. (2006) The amphibian tree of life. Bulletin of the American Museum of Natural History, 297, 1–370.

    Gauthier, J.A., Kluge, A. & Rowe, T. (1988) Amniote phylogeny and the importance of fossils. Cladistics, 4, 105–209.

    Goloboff, P.A. (2003) Parsimony, likelihood, and simplicity. Cladistics, 19, 91–103.

    Hennig, W. (1966) Phylogenetic Systematics. University of Illinois Press, Urbana, Illinois.

    Huelsenbeck, J.P., Rannala, B. & Yang, Z. (1997) Statistical test of host-parasite cospeciation. Evolution, 51, 410–419.

    Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17, 754–755.

    Johnson, G.D. & Patternson, C. (1993) Percomorph phylogeny: A survey of acanthomorphs and a new proposal. Bulletin of Marine Science, 52, 554–626.

    Källersjö, M., Albert, V.A. & Farris, J.S. (1999) Homoplasy increases phylogenetic structure. Cladistics, 15, 91–93.

    Kawahara, R, Miya, M., Mabuchi, K., Lavoué S., Inoue, J.G., Satoh, T.P., Kawaguchi, A. & Nishida, M. (2008) Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts. Molecular Phylogenetics and Evolution, 46, 224–236.

    Lewis, P.O. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50, 913–925.

    Maddison, W.P. & Maddison, D.R. (2009) Mesquite: a modular system for evolutionary analysis. Version 2.72 http://mesquiteproject.org

    Miya, M., Holcroft, N.I., Satoh, T.P., Yamaguchi, M., Nishida, M. & Wiley, E.O. (2007) Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae). Ichthyological Research, 54, 323–332.

    Miya, M., Takeshima, H., Endo, H., Ishiguro, N.B., Inoue, J.G., Mukai, T., Satoh, T.P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. & Nishida, M. (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 26, 121–138.

    Mooi, R.D. & Gill, A.C. (2004) Notograptidae, sister to Acanthoplesiops Regan (Teleostei: Plesiopidae: Acanthoclininae), with comments on biogeography, diet and morphological convergence with Congrogadinae (Teleostei: Pseudochromidae). Zoological Journal of the Linnean Society, 141, 179–205.

    Mooi, R.D. & Gill, A.C. (2010) Phylogenetics without synapomorphies — A crisis in fish systematics: time to show some character. Zootaxa, 2450, 26–40.

    Pagel, M. (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology, 48, 612–622.

    Patterson, C. (1982) Morphological characters and homology, p. 21–74. In: Problems of Phylogenetic Reconstruction. K. A. 16 · Zootaxa 2946 © 2011 WILEY ET AL. Magnolia Press Joysey and A. E. Friday (eds.). Systematic Association Special Volume Number 25. Academic Press, London.

    Patterson, C. (1988) Homology in classical and molecular biology. Molecular Biology and Evolution, 5, 603–625.

    dePinna, M.G.G. (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics, 7, 367–394.

    Remane, A. (1956) Die Grundlagen des natürlichen Systems der vergleichenden Anatomie und Phylogenetik 2. Auflage, Geest und Portig K. G. Leipzig, Germany.

    Schluter, D., Price, T., Mooers, A.O. & Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699–1711.

    Shimodaira, H. (2002) An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51, 492–508.

    Smith, W.L. & Craig, M.T. (2007) Casting the percomorph net widely: the importance of broad taxonomic sampling in the search for the placement of serranid and percid fishes. Copeia, 2007, 35–55.

    Sober, E. (1988) Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press. Cambridge, MA.

    Sokal, R.R. & Sneath, P.H.A. (1963) Principles of numerical taxonomy. W. H. Freeman, San Francisco.

    Sparks, J.S. & Smith, W.L. (2004) Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics, 20, 501–517.

    Sukumaran, J. & Holder, M.T. (2010) DendroPY: A python library for phylogenetic computing. Bioinformatics, advanced access, 25 April, 2010. (http://bioinformatics.oxfordjournals.org/cgi/reprint/btq228v1)

    Swofford, D.L. (2002) PAUP*: Phylogenetic analysis using parsimony (and other methods), Sinauer Associates, Sunderland, Mass.

    Thacker, C.E. (2009) Phylogeny of Gobioidei and placement within Acanthomorpha with a new classification and investigation of diversification and character evolution. Copeia, 2009, 93–104.

    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. (1976) The phylogeny and biogeography of fossil and recent gars (Actinoptergii: Lepisosteidae). Miscellaneous Publications, Museum of Natural History, University of Kansas, 64, 1–111.

    Wiley, E.O. (1981) Phylogenetics. The Theory and Practice of Phylogenetic Systematics. Wiley-Interscience, New York.

    Wiley, E.O. (2008) Homology, identity and transformation, p. 9--21. IN: Mesozoic Fishes 4 – Homology and Phylogeny. G. Arratia and H.-P. Schultze (eds.). Verlag Dr. Friedrich Pfeil, München, Germany.

    Wiley, E.O., Dimminck, W. & Johnson, G.D. (2000) The interrelationships of acanthomorph fishes: a total evidence approach using molecular and morphological data. Biochemical Systematics and Ecology, 28, 319–350.

    Wiley, E.O. & Johnson, G.D. (2010) A teleost classification based on monophyletic groups, p. 123–182. IN: Origin and Phylogenetic Interrelationships of Teleosts. J.S. Nelson, H.-P. Schultze, and M.V.H. Wilson (eds.). Verlag Dr. Friedrich Pfeil, München, Germany.

    Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A. (1991) The compleat cladist: A primer of phylogenetic procedures. The University of Kansas Museum of Natural History Special Publication, 19, 1–158.