On the Other “Phylogenetic Systematics”
Kevin C. Nixon
Bailey Hortorium, Cornell University, Ithaca, New York, 14853
Search for more papers by this authorJames M. Carpenter
Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024
Search for more papers by this authorKevin C. Nixon
Bailey Hortorium, Cornell University, Ithaca, New York, 14853
Search for more papers by this authorJames M. Carpenter
Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024
Search for more papers by this authorAbstract
De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor “widely held belief” systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new “Phylogenetic Systematics”—instead we have been presented with a vague and sketchy manifesto based upon the assertion that “clades are individuals” and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for “node pointing,” yet even their own examples show that the opposite is true, and their node pointing system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the node pointing system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.
References
- Ax, P. (1987). “ The Phylogenetic System: The Systematization of Organisms on the Basis of Their Phylogenesis”. Wiley, Chichester . [Translation of 1984 publication].
- Baum, D. A. (1998). Individuality and the existence of species through time. Syst. Biol. 47, 641–653.
- Baum, D. A., Alverson, W. S., and Nyffeler, R. (1998). A durian by any other name: Taxonomy and nomenclature of the core Malvales. Harv. Pap. Bot. 3, 315–330.
- Baum, D. A., and Donoghue, M. J. (1995). Choosing among alternative “phylogenetic” species concepts. Syst. Bot. 20, 560–573.
- Bremer, K., Chase, M. W., and Stevens, P. F. (under the pseudonym “The Angiosperm Phylogeny Group”). (1998). An ordinal classification for the flowering plants. Ann. Missouri Bot. Gard. 85, 531–553.
- Bryant, H. N. (1996). Explicitness, stability, and universality in the phylogenetic definition and usage of taxon names: A case study of the phylogenetic taxonomy of the Carnivora (Mammalia). Syst. Biol. 45, 174–189.
- Cantino, P. D. (2000). Phylogenetic nomenclature: Addressing some concerns. Taxon 49, 85–93.
- Cantino, P. D., Bryant, H. N., de Queiroz, K., Donoghue, M. J., Eriksson, T., Hillis, D. M., and Lee, M. S. Y. (1999). Species names in phylogenetic nomenclature. Syst. Biol. 48, 790–807.
- Cantino, P. D., Olmstead, R. G., and Wagstaff, S. J. (1997). A comparison of phylogenetic nomenclature with the current system: A botanical case study. Syst. Biol. 46, 313–331.
- Carpenter, J. M. (1987). Cladistics of cladists. Cladistics 3, 363–375.
10.1111/j.1096-0031.1987.tb00899.x Google Scholar
- Crepet, W. L., and Nixon, K. C. (1998). Two new fossil flowers of magnoliid affinity from the Late Cretaceous of New Jersey. Am. J. Bot. 85, 1273–1288.
- Cunningham, C. W. (1997). Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46, 464–478.
- Davis, J. (1997). Evolution, evidence, and the role of species concepts in phylogenetics. Syst. Bot. 22, 373–403.
- de Queiroz, K. (1988). Systematics and the Darwinian revolution. Philos. Sci. 55, 238–259.
- de Queiroz, K. (1992a). Phylogenetic relationships and rates of allozyme evolution among the lineages of sceloporine sand lizards. Biol. J. Linn. Soc. 45, 333–362.
- de Queiroz, K. (1992b). Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7, 295–313.
- de Queiroz, K. (1994). Replacement of an essentialistic perspective on taxonomic definitions as exemplified by the definition of “Mammalia.”Syst. Biol. 43, 497–510.
- de Queiroz, K. (1997). Misunderstandings about the phylogenetic approach to biological nomenclature: A reply to Liden and Oxelman. Zool. Scr. 26, 67–70.
- de Queiroz, K., and Donoghue, M. J. (1988). Phylogenetic systematics and the species problem. Cladistics 4, 317–338.
- de Queiroz, K., and Gauthier, J. (1990). Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39, 307–322.
- de Queiroz, K., and Gauthier, J. (1992). Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23, 449–480.
10.1146/annurev.es.23.110192.002313 Google Scholar
- de Queiroz, K., and Gauthier, J. (1994). Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9, 27–31.
- de Queiroz, K., and Gauthier, J. (1995). Translating phylogenies into classifications: Basic principles. Am. J. Bot. 82(Suppl.), 108.
- Dominguez, E., and Wheeler, Q. D. (1997). Taxonomic stability is ignorance. Cladistics 13, 367–372.
- Donoghue, M. J. (1995). Phylogeny and phylogenetic taxonomy of Dipsacales. Am. J. Bot. 82(Suppl.), 108.
- Donoghue, M. J., and Doyle, J. A. (1989a). Phylogenetic analysis of angiosperms and the relationships of Hamamelidae. In “ Evolution, Systematics, and Fossil History of the Hamamelidae 1” ( P. R. Crane and S. Blackmore, Eds.), Syst. Assoc. Spec. Vol. 40A, pp. 17–45. Clarendon, Oxford .
- Donoghue, M. J., and Doyle, J. A. (1989b). Phylogenetic studies of seed plants and angiosperms based on morphological characters. In “ The Hierarchy of Life” ( B. Fernholm, K. Bremer, and H. Jornvall, Eds.), pp. 181–193. Elsevier, Amsterdam .
- Doyle, J. A., Donoghue, M. J., and Zimmer, E. A. (1994). Integration of morphological and ribosomal RNA data on the origin of angiosperms. Ann. Missouri Bot. Gard 81, 419–450.
- Farris, J. S. (1979). The information content of the phylogenetic system. Syst. Zool. 28, 483–519.
- Farris, J. S. (1985). The pattern of cladistics. Cladistics 1, 190–201.
10.1111/j.1096-0031.1985.tb00422.x Google Scholar
- Frost, D. R., and Kluge, A. G. (1994). A consideration of epistemology in systematic biology, with special reference to species. Cladistics 10, 259–294.
- Gauthier, J., Estes, R., and de Queiroz, K. (1988). A phylogenetic analysis of Lepidosauromorpha. In “ Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp” ( R. Estes and G. Pregill, Eds.), pp. 15–98. Stanford Univ. Press, Stanford .
- Ghiselin, M. T. (1966). An application of the theory of definitions to systematic principles. Syst. Zool. 15, 127–130.
10.2307/2411630 Google Scholar
- Ghiselin, M. T. (1969). “ The Triumph of the Darwinian Method”. Univ. of California Press, Berkeley .
- Ghiselin, M. T. (1974). A radical solution to the species problem. Syst. Zool. 23, 536–554.
- Ghiselin, M. T. (1984a). Narrow approaches to phylogeny: A review of nine books on cladism. Oxford Surv. Evol. Biol. 1, 209–222.
- Ghiselin, M. T. (1987). Hierarchies and their components. Paleobiology 13, 108–111.
- Ghiselin, M. T. (1984b). “Definition”, “character”, and other equivocal terms. Syst. Zool. 33, 104–110.
- Ghiselin, M. T. (1995). Ostensive definitions of the names of species and clades. Biol. Philos. 10, 219–222.
- Goloboff, P. A. (1998). NONA, version 1.8. Program and documentation. Fundación e Instituto Miguel Lillo, Tucumán , Argentina .
- Graybeal, A. (1995). Naming species. Syst. Biol. 44, 237–250.
- Griffiths, G. C. D. (1973). Some fundamental problems in biological classification. Syst. Zool. 22, 338–343.
- Griffiths, G. C. D. (1974). On the foundations of biological systematics. Acta Biotheor. 23, 85–131.
10.1007/BF01556343 Google Scholar
- Griffiths, G. C. D. (1976). The future of Linnaean nomenclature. Syst. Zool. 25, 168–173.
- Haeckel, E. (1866). “ Generelle Morphologie der Organismen.” G. Reiner, Berlin .
10.1515/9783110848281 Google Scholar
- Hennig, W. (1966). “ Phylogenetic Systematics.” Univ. of Illinois Press, Urbana .
- Hillis, D. (1996). Inferring complex phylogenies. Nature 383, 130–131.
- Hull, D. L. (1965). The effect of essentialism on taxonomy: Two thousand years of stasis. Br. J. Philos. Sci. 15, 314–326; 16, 1–18.
- Hull, D. L. (1978). A matter of individuality. Philos. Sci. 45, 335–360.
- Jefferies, R. S. P. (1979). The origin of the chordates–A methodological essay. In “The Origin of Major Invertebrate Groups” ( M. R. House, Ed.), Syst. Assoc. Spec. Vol. 12, pp. 443–477.
- Judd, W. S., and Manchester, S. R. (1995). Circumscription of Malvaceae (Malvales) as determined by preliminary cladistic analyses employing morphological and chemical characters. Am. J. Bot. 82(Suppl.), 138.
- Lee, M. S. Y. (1996). The phylogenetic approach to biological taxonomy: Practical aspects. Zool. Scr. 25, 187–190.
- Lee, M. S. Y. (1999). Stability of higher taxa in phylogenetic nomenclature–Some comments on Moore. Zool. Scr. 28, 361–366.
- Lidén, M., and Oxelman, B. (1996). Do we need “phylogenetic taxonomy” Zool. Scr. 25, 183–185.
- Lidén, M., Oxelman, B., Backlund, A., Andersson, L., Bremer, B., Eriksson, R., Moberg, R., Nordal, I., Persson, K., Thulin, M., and Zimmer, B. (1997). Charlie is our darling. Taxon 46, 735–738.
- Luckow, M. (1995). Species concepts: Assumptions, methods, and applications. Syst. Bot. 20, 589–605.
- Mayr, E. (1969). “ Principles of Systematic Zoology.” McGraw-Hill, New York .
- Mishler, B. D. (1985). The morphological, developmental and phylogenetic basis of species concepts in bryophytes. Bryologist 88, 207–214.
- Moore, G. (1998). A comparison of traditional and phylogenetic nomenclature. Taxon 47, 561–579.
- Nixon, K. C. (1996). Paleobotany in cladistics and cladistics in paleobotany: Enlightenment and uncertainty. Rev. Palaeobot. Palynol. 90, 361–373.
- Nixon, K. C. (1999). The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407–414.
- Nixon, K. C., and Carpenter, J. M. (1996a). On simultaneous analysis. Cladistics 12, 221–241.
- Nixon, K. C., and Carpenter, J. M. (1996b). On consensus, collapsibility, and clade concordance. Cladistics 12, 305–321.
- Nixon, K. C, and Wheeler, Q. D. (1990). An amplification of the phylogenetic species concept. Cladistics 6, 211–223.
- Pennisi, E. (1996). Evolutionary and systematic biologists converge. Science 273, 181.
- Pleijel, F. (1999). Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Syst. Biol. 48, 755–789.
- Schander, C. (1999). Types, emendations and names–A reply to Lidén et al. Taxon 47, 401–406.
- Schander, C., and Thollesson, M. (1995). Phylogenetic taxonomy—Some comments. Zool. Scr. 24, 263–268.
- Sereno, P. C. (1999). Definitions in phylogenetic taxonomy: Critique and rationale. Syst. Biol. 48, 329–351.
- Soltis, D. E., Soltis, P. S., Nickrent, D. L., Johnson, L. A., Hahn, W. J., Hoot, S. B., Sweere, J. A., Kuzoff, R. A., Kron, K. A., Chase, M. W., Swensen, S. M., Zimmer, E. A., Chaw, S., Gillespie, L. J., Kress, W. J., and Sytsma, K. J. (1997). Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann. Missouri Bot. Gard. 84, 1–49.
- Soltis, D. E., Soltis, P. S., Chase, M. W., Mort, M. E., Albach, D. C., Zanis, M., Savolainen, V., Hahn, W. J., Hoot, S. B., Fay, M. F., Axtell, M., Swensen, S. M., Nixon, K. C, and Farris, J. S. Angiosperm phylogeny inferred from a combined data set of 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc, in press.
- Sundberg, P., and Pleijel, F. (1994). Phylogenetic classification and the definition of taxon names. Zool. Scr. 23, 19–25.
- Swofford, D. L. (1989). Paup, version 3.0. Program and documentation. Illinois Natural History Survey, Champaign .
- Takhtajan, A. (1997). “ Diversity and Classification of Flowering Plants.” Columbia Univ. Press, New York .
- 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” ( J. Pakaluk and S. A. Slipinksi, Eds.), pp. 31–62. Muz. Inst. Zool. PAN, Warsaw , Poland .
- Whitehead, A. N., and Russell, B. (1962). “ Principia Mathematica to *56.” Cambridge Univ. Press, Cambridge .
- Wiley, E. O. (1979). An annotated Linnaean hierarchy, with comments on natural taxa and competing systems. Syst. Zool. 28, 308–337.
- Wyss, A. R., and Meng, J. (1996). Application of phylogenetic taxonomy to poorly resolved crown clades: A stem-modified node-based definition of Rodentia. Syst. Biol. 45, 559–568.