Literature on Phylogenetic Nomenclature



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Literature on Phylogenetic Nomenclature

P. Cantino and K. de Queiroz


The following is a list of publications dealing with phylogenetic nomenclature, which is intended to provide access to the literature on that subject. The list is divided into categories emphasizing particular aspects of phylogenetic nomenclature. Because these categories are not always mutually exclusive, some papers are listed under more than one category. The list is undoubtedly incomplete (particularly in the category "Other Applications of Phylogenetic Nomenclature") but should provide a good starting point for anyone wishing to explore the subject.
Because we had to draw the line somewhere, a number of related papers have been excluded. For example, we did not list all papers that used widely known names for crown clades (a convention commonly associated with phylogenetic nomenclature that is neither a necessary component of the approach nor supported by some of its advocates); instead, we only included those papers if they also used explicit phylogenetic definitions. In general, the list contains papers in which explicit phylogenetic definitions are either used or discussed.
We intend to update the list as new information becomes available. If you notice omissions or feel that a paper has been assigned to the wrong category (or should be listed under additional categories), please contact Phil Cantino (cantino@ohio.edu) or Kevin de Queiroz (dequeirk@si.edu).
Last revision: August 23, 2006
News Reports and Overviews:

CANTINO, P. D. 2001. Nomenclature, phylogenetic. Pp. 242-244 in McGraw-Hill Yearbook of Science & Technology 2002. New York: McGraw-Hill.

FOER, J. 2005. Pushing PhyloCode. Discover (April 2005): 46-51.

HÄRLIN, M. 2004. Classification nomenclature. Pp. 52-54 in McGraw-Hill Yearbook of Science & Technology 2004. New York: McGraw-Hill.

HARRIS, R. 2005. Attacks on taxonomy. Amer. Scientist 93: 311-312.

HOLMES, B. 2004. Time for Linnaeus to leave the stage. New Scientist (11 Sept. 2004): 12-13.

LAURIN, M., and P. D. CANTINO. 2004. First International Phylogenetic Nomenclature Meeting: a report. Zool. Scripta 33: 475-479.

LAURIN, M., and A. DE RICQLÈS. 2004. Compte rendu sur le premier congrès international de nomenclature phylogénétique: 6-9 juillet 2004, MNHN, Paris. Bull. Soc. Française Syst. 32: 9-10.

MILIUS, S. 1999. Should we junk Linnaeus? Science News 156: 268-270.

Nyffeler, R. 1999. A new ordinal classification of the flowering plants. Trends Ecol. Evol. 14: 168-170.

PLEIJEL, F. 2000. Nomenclature linnéenne et nomenclature phylogénétique. Bull. Soc. Fran. Syst. 24: 25-28.

PLEIJEL, F. and B. DAYRAT. 2000. De l'évolution dans la nomenclature? La Recherche 333: 48-50.

PENNISI, E. 2001. Linnaeus's last stand? Science 291:2304-2307.

SOARES, C. 2004. What's in a name? Scientific American (Nov. 2004): 36-37.

SPOONER, D., W. L. A. HETTERSCHEID, R. G. VAN DEN BERG, and W. BRANDENBURG. 2003. Plant nomenclature and taxonomy: an horticultural and agronomic perspective. Horticultural Reviews 28: 1-60.

WITHGOTT, J. 2000. Is it "So long, Linnaeus"? BioScience 50: 646-651.
Formative Early Publications

DE QUEIROZ, K. 1988. Systematics and the Darwinian revolution. Philos. Sci. 55: 238-259.

DE QUEIROZ, K., and J. GAUTHIER. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39: 307-322.

DE QUEIROZ, K., and J. GAUTHIER. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23: 449-480.

DE QUEIROZ, K., and J. GAUTHIER. 1994. Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9: 27-31.

ESTES, R., K. DE QUEIROZ, and J. GAUTHIER. 1988. Phylogenetic relationships within Squamata. Pp. 119-281 in R. Estes and G. K. Pregill (eds.), Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford Calif.: Stanford Univ. Press.

GAUTHIER, J., R. ESTES, and K. DE QUEIROZ. 1988. A phylogenetic analysis of Lepidosauromorpha. Pp. 15-98 in R. Estes and G. K. Pregill (eds.), Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford Calif.: Stanford Univ. Press.

GHISELIN, M. T. 1984. "Definition," "character," and other equivocal terms. Syst. Zool. 33: 104-110.

ROWE, T. 1987. Definition and diagnosis in the phylogenetic system. Syst. Zool. 36: 208-211.
Other Publications on the Theory and Practice of Phylogenetic Nomenclature:

ANDERSON, J. S. 2002. Use of well-known names in phylogenetic nomenclature: a reply to Laurin. Syst. Biol. 51: 822-827.

BROCHU, C. A., and C. D. SUMRALL. 2001. Phylogenetic nomenclature and paleontology. J. Paleont. 75: 754-757.

BRYANT, H. N. 1994. Comments on the phylogenetic definition of taxon names and conventions regarding the naming of crown clades. Syst. Biol. 43: 124-130.

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.

BRYANT, H. N. 1997. Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names. Biol. J. Linn. Soc. 62: 495-503.

BRYANT, H. N., and P. D. CANTINO. 2002. A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue? Biol. Rev. 77: 39-55.

CANTINO, P. D. 2000. Phylogenetic nomenclature: addressing some concerns. Taxon 49: 85-93.

CANTINO, P. D. 2004. Classifying species versus naming clades. Taxon 53: 795-798.

CANTINO, P. D., R. G. OLMSTEAD, and S. J. WAGSTAFF. 1997. A comparison of phylogenetic nomenclature with the current system: a botanical case study. Syst. Biol. 46: 313-331.

CHRISTOFFERSEN, M. L. 1995. Cladistic taxonomy, phylogenetic systematics, and evolutionary ranking. Syst. Biol. 44: 440-454.

de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biol. Phil. 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. 1997a. The Linnaean hierarchy and the evolutionization of taxonomy, with emphasis on the problem of nomenclature. Aliso 15: 125-144.

De Queiroz, K. 2005. Linnaean, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa. Symb. Bot. Ups. 33: 127-140.

DE QUEIROZ, K. 2006. The PhyloCode and the distinction between taxonomy and nomenclature. Syst. Biol. 55: 160-162.

DE QUEIROZ, K., and P. D. CANTINO. 2001a. Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nom. 58: 254-271.

DONOGHUE, M. J. 2004. Immeasurable progress on the tree of life. Pp. 548-552 in J. Cracraft and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford: Oxford University Press.

DONOGHUE, P. C. J. 2005. Saving the stem group—a contradiction in terms? Paleobiology 31: 553-558.

ERESHEFSKY, M. 1997. The evolution of the Linnaean hierarchy. Biol. Phil. 12: 493-519.

ERESHEFSKY, M. 2001. The Poverty of the Linnaean Hierarchy: a Philosophical Study of Biological Taxonomy. Cambridge: Cambridge University Press.

GAUTHIER, J., and K. DE QUEIROZ. 2001. Feathered dinosaurs, flying dinosaurs, crown dinosaurs, and the name "Aves". Pp. 7-41 in J. Gauthier and L. F. Gall (eds.), New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom. New Haven: Peabody Mus. Nat. Hist., Yale University.

HÄRLIN, M. 1996. Tree-thinking and nemertean systematics. Ph.D. thesis, Göteborg University.

HÄRLIN, M. 1998. Taxonomic names and phylogenetic trees. Zool. Scr. 27: 381-390.

HÄRLIN, M. 1999. The logical priority of the tree over characters and some of its consequences for taxonomy. Biol. J. Linn. Soc. 68: 497-503.

HÄRLIN, M. 1999. Phylogenetic approaches to nomenclature: a comparison based on a nemertean case study. Proc. Royal Soc. London, Ser. B 266: 2201-2207.



Härlin, M. 2001. Towards a new biological taxonomy—let us give up the Linnean hierarchy! [Review of Ereshefsky, M. 2001. The poverty of the Linnean hierarchy.] Zool. Scr. 30: 337-339.

HÄRLIN, M. 2003a. Taxon names as paradigms: the structure of nomenclatural revolutions. Cladistics 19: 138-143.

HÄRLIN, M. 2003b. On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature. Cladistics 19: 144-147.

HÄRLIN, M. 2005. Definitions and phylogenetic nomenclature. Proc. California Acad. Sci. 56: 216-224.

HÄRLIN, M., and P. SUNDBERG. 1998. Taxonomy and philosophy of names. Biol. and Philos. 13: 233-244.

HÄRLIN, M., and M. THOLLESSON. 2005. Fundamentals of phylogenetic nomenclatures: an exchange of views. Symbolae Botanicae Upsalienses 33: 141-151.

HIBBETT, D. S., and M. J. DONOGHUE. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90: 347-356.

HIBBETT, D. S., R. H. NILSSON, M. SNYDER, M. FONSECA, J. COSTANZO, and M. SHONFELD. 2005. Automated phylogenetic taxonomy: an example in the Homobasidiomcetes (mushroom-forming fungi). Syst. Biol. 54: 660-668.

JOYCE, W. G., J. F. PARHAM, and J. A. GAUTHIER. 2004. Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles. J. Paleontol. 78: 989-1013.

KRON, K. A. 1997. Exploring alternative systems of classification. Aliso 15: 105-112.

LANGER, M. C. 2001. Linnaeus and the PhyloCode: where are the differences? Taxon 50: 1091-1096.

LaPorte, J. 2004. Natural kinds and conceptual change. Cambridge: Cambridge University Press.

LAURIN, M. 2001. L'utilisation de la taxonomie phylogénétique en paléontologie: avatages et inconvénients. Biosystema 19 – Systématique et Paléontologie: 197-211.

LAURIN, M. 2002. Tetrapod phylogeny, amphibian origins, and the definition of the name Tetrapoda. Syst. Biol. 51: 364-369.

LAURIN, M. 2005. The advantages of phylogenetic nomenclature over Linnean nomenclature. Pp. 67-97 in A. Minelli, G. Ortalli, and G. Sanga (eds), Animal Names. Venice, Italy: Instituto Veneto di Scienze, Lettere ed Arti.

LAURIN, M., and J. S. ANDERSON. 2004. Meaning of the name Tetrapoda in the scientific literature: an exchange. Syst. Biol. 53: 68-80.

LEE, M. S. Y. 1996a. The phylogenetic approach to biological taxonomy: practical aspects. Zool. Scr. 25: 187-190.

LEE, M. S. Y. 1996b. Stability in meaning and content of taxon names: an evaluation of crown-clade definitions. Proc. R. Soc. Lond. B. Biol. Sci. 263: 1103-1109.

LEE, M. S. Y. 1998a. Phylogenetic uncertainty, molecular sequences, and the definition of taxon names. Syst. Biol. 47: 719-726.

LEE, M. S. Y. 1998b. Ancestors and taxonomy. Trends Ecol. Evol. 13: 26.

LEE, M. S. Y. 1999a. Reference taxa and phylogenetic nomenclature. Taxon 48: 31-34.

LEE, M. S. Y. 1999b. Stability of higher taxa in phylogenetic nomenclature—some comments on Moore (1998). Zool. Scr. 28: 361-366.

LEE, M. S. Y. 2001. On recent arguments for phylogenetic nomenclature. Taxon 50: 175-180.

LEE, M. S. Y. 2005. Choosing reference taxa in phylogenetic nomenclature. Zool. Scripta 34: 329-331.

LUCAS, S. G. 1992. Extinction and the definition of class Mammalia. Syst. Biol. 41: 370-371.



Minelli, A. 1995. The changing paradigms of biological systematics: new challenges to the principles and practice of biological nomenclature. Bull. Zool. Nomen. 52: 303-309.

MOORE, G. 1998. A comparison of traditional and phylogenetic nomenclature. Taxon 47: 561-579.

PLEIJEL, F. and M. HäRLIN. 2004. Phylogenetic nomenclature is compatible with diverse philosophical perspectives. Zool. Scripta 33: 587-591.

PLEIJEL, F. and G. W. ROUSE. 2003. Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature. J. Zool. Syst. Evol. Research 41: 162-174.

ROWE, T., and J. GAUTHIER. 1992. Ancestry, paleontology and definition of the name Mammalia. Syst. Biol. 41: 372-378.

SCHANDER, C. 1998b. Mandatory categories and impossible hierarchies — a reply to Sosef. Taxon 47: 407-410.

SCHANDER, C., and M. THOLLESSON. 1995. Phylogenetic taxonomy — some comments. Zool. Scr. 24: 263-268.

SERENO, P. C. 1998. A rationale for phylogenetic definitions, with application to the higher-level taxonomy of Dinosauria. N. Jb. Geol. Paläont. Abh. 210: 41-83.

SERENO, P. C. 1999. Definitions in phylogenetic taxonomy: critique and rationale. Syst. Biol. 48: 329-351.

SERENO, P. C. 2005. The logical basis of phylogenetic taxonomy. Syst. Biol. 54: 595-619.

STEVENS, P. F. 2002. Why do we name organisms? Some reminders from the past. Taxon 51: 11-26.

SUNDBERG, P., and F. PLEIJEL. 1994. Phylogenetic classification and the definition of taxon names. Zool. Scr. 23: 19-25.

WILKINSON, M. 2006. Identifying stable reference taxa for phylogenetic nomenclature. Zool. Scr. 35: 109-112.

WYSS, A. R., and J. MENG. 1996. Application of phylogenetic taxonomy to poorly resolved crown clades: a stem-modified node-based definition of Rodentia. Syst. Biol. 45: 559-568.


Phylogenetic Nomenclature of Species (or applying specific epithets to small clades that others view as species):

ARTOIS, T. 2001. Phylogenetic nomenclature: the end of binomial nomenclature? Belg. J. Zool. 131: 87-89.



Brandley, M. C., and K. de Queiroz. 2004. Phylogeny, ecomorphological evolution, and historical biogeography of the Anolis cristatellus series. Herpetol. Monogr. 18: 90-126.

CANTINO, P. D. 1998. Binomials, hyphenated uninomials, and phylogenetic nomenclature. Taxon 47: 425-429.

CANTINO, P. D., H. N. BRYANT, K. DE QUEIROZ, M. J. DONOGHUE, T. ERIKSSON, D. M. HILLIS, and M. S. Y. LEE. 1999. Species names in phylogenetic nomenclature. Syst. Biol. 48: 790-807.

CANTINO, P. D., S. J. WAGSTAFF, and R. G. OLMSTEAD. 1999. Caryopteris (Lamiaceae) and the conflict between phylogenetic and pragmatic considerations in botanical nomenclature. Syst. Bot. 23: 369-386.



Clarke, J. A. 2004. The Morphology, phylogenetic taxonomy and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae). Bull. Am. Mus. Nat. Hist. 286: 1-179.

DE QUEIROZ, K., and J. GAUTHIER. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23: 449-480.



de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biol. Phil. 7: 295-313.

De Queiroz, K. 1995. The definitions of species and clade names: A reply to Ghiselin. Biol. Phil. 10: 223-228.

DAYRAT, B., C. SCHANDER and K. D. ANGIELCZYK. 2004. Suggestions for a new species nomenclature. Taxon 53: 485-591.

DAYRAT, B. 2005. Advantages of naming species under the PhyloCode: an example of how a new species of Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) may be named. Marine Biol. Res. 1: 216-232.

DAYRAT, B. and T. M. GOSLINER. 2005. Species names and metaphyly: a case study in Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina). Zool. Scripta 34: 199-224.

FISHER, K. 2006. Rank-free monography: a practical example from the moss clade Leucophanella (Calymperaceae). Syst. Bot. 31: 13-30.

Ghiselin, M. T. 1995. Ostensive definitions of the names of species and clades. Biol. Phil. 10: 219-222.

HILLIS, D. M., D. A. CHAMBERLAIN, T. P. WILCOX, and P. T. CHIPPINDALE. 2001. A new species of subterranean blind salamander (Plethodontidae: Hemidactyliini: Eurycea: Typhlomolge) from Austin, Texas, and a systematic revision of central Texas paedomorphic salamanders. Herpetologica 57: 266-280.



Nicholson, K. E. 2002. Phylogenetic analysis and a test of the current infrageneric classification of Norops (beta Anolis). Herpetol. Monogr. 16: 93-120.

LEE, M. S. Y. 2002. Species and phylogenetic nomenclature. Taxon 51: 507-510.

MISHLER, B. D. 1999. Getting rid of species? Pp. 307-315 in R. Wilson (ed.), Species: New Interdisciplinary Essays. Cambridge, Massachusetts: M.I.T. Press.

PLEIJEL, F. 1999. Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Syst. Biol. 48: 755-789.

PLEIJEL, F., and G. W. ROUSE. 2000. Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proc. R. Soc. London B 267: 627-630.

PLEIJEL, F., and G. W. ROUSE. 2000. A new taxon, capricornia (Hesionidae, Polychaeta), illustrating the LITU ('least-inclusive taxonomic unit') concept. Zool. Scripta 29: 157-168.

SPANGLER, R. E. 2003. Taxonomy of Sarga, Sorghum and Vacoparis (Poaceae: Andropogoneae). Australian Syst. Bot. 16: 279-299.
Other Applications of Phylogenetic Nomenclature:

Aguinaldo, A. M., J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, and J. S. Lake. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387: 489-493.

ALVERSON, W. S., B. A. WHITLOCK, R. NYFFELER, C. BAYER, and D. A. BAUM. 1999. Phylogeny of the core Malvales: evidence from ndhF sequence data. Amer. J. Bot. 86: 1474-1486.



Archibald, J. D. 1996. Fossil evidence for a Late Cretaceous origin of "hoofed" mammals. Science 272: 1150-1153.

BAUM, D. A., W. S. ALVERSON, and R. NYFFELER. 1998. A durian by any other name: taxonomy and nomenclature of the core Malvales. Harv. Pap. Bot. 3:315-330.



Berta, A. 1994. What is a whale? Science 263: 180-181.

BREMER, K. 2000. Phylogenetic nomenclature and the new ordinal system of the angiosperms. Pp. 125-133 in B. Nordenstam, G. El-Ghazaly, and M. Kassas (eds.), Plant Systematics for the 21st Century. London: Portland Press.

BROCHU, C. A. 1997. Synonymy, redundancy, and the name of the crocodile stem-group. J. Vertebrate Paleontology 17: 448-449.

BROCHU, C. A. 1999. Phylogenetics, taxonomy, and historical biogeography of Alligatoroidea. J. Vert. Paleontol. 19 (suppl. to no. 2): 9-100.

BROCHU, C. A. 2003. Phylogenetic approaches toward crocodylian history. Annu. Rev. Earth Planet Sci. 31: 357-397.

Bryant, J. D., and M. C. McKenna. 1995. Cranial anatomy and phylogenetic position of Tsaganomys altaicus (Mammalia: Rodentia) from the Hsanda Gol Formation (Oligocene), Mongolia. Am. Mus. Novit. 3156: 1-42.

Cannatella, D. C., and D. M. Hillis. 1993. Amphibian relationships: phylogenetic analysis of morphology and molecules. Herpetol. Monogr. 7:1-7.

Caterino, M. S. 1998. A phylogenetic revision of Spilodiscus Lewis (Coleoptera: Histeridae). J. Nat. Hist. 32: 1129-1168.

CHIAPPE, L. M., J. Shu'an, J. Qiang, and M. Norell. 1999. Anatomy and systematics of the Confuciusornithidae (Theropoda: Aves) from the Late Mesozoic of northeastern China. Bull. Am. Mus. Nat. Hist. 242: 1-89.

COCHRANE, S. J. 2003. Snowflakes and feather-dusters: some challenges for fanworm systematics. Hydrobiologia 496: 49-62.



Deméré, T. A. 1994. The family Odobenidae: A phylogenetic analysis of fossil and living taxa. Proc. San Diego Soc. Nat. Hist. 29: 99-123.

DE QUEIROZ, K. 1985. Phylogenetic Systematics of Iguanine Lizards: A Comparative Osteological Study. Master's thesis, San Diego State University.

DE QUEIROZ, K. 1987. Phylogenetic systematics of iguanine lizards. A comparative osteological study. Univ. Calif. Publ. Zool. 118: 1-203.

Dilkes, D. W. 1998. The Early Triassic rhynchosaur Mesochchus browni and the interrelationships of basal archosauromorph reptiles. Phil. Trans. R. Soc. London B 353: 501-541.

DONOGHUE, M. J., T. ERIKSSON, P. A. REEVES, and R. G. OLMSTEAD. 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Pap. Bot. 6: 459-479.

DOYLE, J. A., and M. J. DONOGHUE. 1993. Phylogenies and angiosperm diversification. Paleobiology 19: 141-167.

ERIKSSON, T., M. J. DONOGHUE, and M. S. HIBBS. 1998. Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae (Rosaceae). Plant Syst. Evol. 211: 155-179.

ESTES, R., K. DE QUEIROZ, and J. GAUTHIER. 1988. Phylogenetic relationships within Squamata. Pp. 119-281 in R. Estes and G. K. Pregill (eds.), Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford, Calif.: Stanford Univ. Press.

Ford, L. S., and D. C. Cannatella. 1993 The major clades of frogs. Herpetol. Monogr. 7: 94-117.

Flynn, J. J., J. M. Parrish, B. Rakotosamimanana, W. F. Simpson, and A. R. Wyss. 1999. A Middle Jurassic mammal from Madagascar. Nature 401: 57-60.

Flynn, J. J., J. M. Parrish, B. Rakotosamimanana, W. F. Simpson, R. L. Whatley, and A. R. Wyss. 1999. A Triassic fauna from Madagascar, including early dinosaurs. Science 286: 763-765.

GAUTHIER, J. 1984. A Cladistic Analysis of the Higher Systematic Categories of the Diapsida. Ph.D. dissertation, University of California at Berkeley.

GAUTHIER, J. 1986. Saurischian monophyly and the origin of birds. Pp. 1-55 in K. Padian (ed.), The Origin of Birds and the Evolution of Flight. San Francisco: California Academy of Sciences.

GAUTHIER, J., R. ESTES, and K. DE QUEIROZ. 1988. A phylogenetic analysis of Lepidosauromorpha. Pp. 15-98 in R. Estes and G. K. Pregill (eds.), Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford Calif.: Stanford Univ. Press.

GAUTHIER, J. A., A. KLUGE, and T. ROWE. 1988. The early evolution of Amniota. Pp. 15-98 in M. J. Benton (ed.), The Phylogeny and Classification of the Tetrapods: Volume 1: Amphibians, Reptiles, Birds. Oxford: Clarendon Press.

Gauthier J., A. G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4: 105-209.

GAUTHIER, J., and K. PADIAN. 1985. Phylogenetic, functional, and aerodynamic analyses of the origin of birds and their flight. Pp. 185-197 in M. K. Hecht, J. H. Ostrom, G. Viohl., and P. Wellnhofer (eds.), The Beginnings of Birds. Eichstatt, Germany: Freude des Jura-Museums.

GOOD, D. A. 1988. The phylogenetic position of fossils assigned to the Gerrhonotinae (Squamata: Anguidae). J. Vert. Paleontol. 8: 188-195.

Härlin, M. 1998. Tree-thinking and nemertean systematics, with a systematization of the eureptantic nemerteans. Hydrobiologia 365: 33-46.

Härlin, M., and C. Härlin. 2001. Phylogeny of the eureptantic nemerteans revisited. Zool. Scr. 30: 49-58.

Hollingsworth, B. D. 1998. The systematics of chuckwallas (Sauromalus) with a phylogenetic analysis of other iguanid lizards. Herpetol. Monogr. 12: 38-191.

HOLTZ, T. R. 1994. The phylogenetic position of the Tyrannosauridae: Implications for theropod systematics. J. Paleontol. 68: 1100-1117.

HOLTZ, T. R. 1996. Phylogenetic taxonomy of the Coelurosauria (Dinosauria: Theropoda). J. Paleontol. 70: 536-538.

Jondelius, U., and M. Thollesson. 1993. Phylogeny of the Rhabdocoela (Platyhelminthes): a working hypothesis. Can. Jo. Zool. 71: 298-308.

JUDD, W. S., R. W. SANDERS, and M. J. DONOGHUE. 1994. Angiosperm family pairs: preliminary phylogenetic analyses. Harvard Pap. Bot. 5: 1-51.

JUDD, W. S., W. L. STERN, and V. I. CHEADLE. 1993. Phylogenetic position of Apostasia and Neuwiedia (Orchidaceae). Bot. J. Linn. Soc. 113: 87-94.

Kay, R. F., and B. A. Williams. 1994. Cladistics, computers, and character analysis. [Review of W. P. Maddison and D. R. Maddison. 1992. MacClade, version 3.] Evol. Anthropol. 3: 32-35.

Laurin, M. 1991. The osteology of a Lower Permian eosuchian from Texas and a review of diapsid phylogeny. Zool. Jo. Linn. Soc. 101: 59-95.

LAURIN, M. 1996. A redescription of the cranial anatomy of Seymouria baylorensis, the best known seymouriamorph (Vertebrata: Seymouriamorpha).  PaleoBios 17: 1-16.

LAURIN, M. 1998. The importance of global parsimony and historical bias in understanding tetrapod evolution. Part I-systematics, middle ear evolution, and jaw suspension.  Annales de Sciences Naturelles, Zoologie, 13ème Série 19: 1-42.

LAURIN, M. 1998. A reevaluation of the origin of pentadactyly.  Evolution 52: 1476-1482.

LAURIN, M. 2000. Travaux récents sur l'évolution et la paléoécologie des stégocéphales. Bull. Soc. Herp. France 96: 25-37.

LAURIN, M., M. GIRONDOT, and A. DE RICQLÈS. 2000. Early tetrapod evolution. Trends Ecol. Evol. 15: 118-123.

LAURIN, M., M. GIRONDOT, and A. DE RICQLÈS. 2000. Reply from M. Laurin, M. Girondot and A. de Ricqlès. Trends Ecol. Evol. 15: 328.

LAURIN, M., and R. R. REISZ. 1995. A reevaluation of early amniote phylogeny.  Zool. J. of the Linn. Soc. 113: 165-223.

LAURIN, M., and R. R. REISZ. 1996. The osteology and relationships of Tetraceratops insignis, the oldest known therapsid.  J. Vert. Paleontol. 16: 95-102.

LAURIN, M., and R. R. REISZ. 1997. A new perspective on tetrapod phylogeny. Pp. 9-59 in S. Sumida and K. Martin (eds), Amniote Origins: Completing the Transition to Land. London: Academic Press.

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Critiques of Phylogenetic Nomenclature:

BARKLEY, T. M., P. DEPRIEST, V. FUNK, R. W. KIGER, W. J. KRESS, and G. MOORE. 2004. Linnaean nomenclature in the 21st Century: a report from a workshop on integrating traditional nomenclature and phylogenetic classification. Taxon 53: 153-158.

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BERRY, P. E. 2002. Biological inventories and the PhyloCode. Taxon 51: 27-29.

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CARPENTER, J. M. 2003. Critique of pure folly. Bot. Rev. 69: 79-92.

DOMINGUEZ, E. and Q. D. WHEELER. 1997. Taxonomic stability is ignorance. Cladistics 13: 367-372.

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Dyke, G. J. 2002. Should paleontologists use "phylogenetic" nomenclature? J. Paleontol. 76: 793-796.

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FOREY, P. L. 2002. PhyloCode—pain, no gain. Taxon 51: 43-54.

Gao, K. Q., and Y. L. Sun. 2003. Is the PhyloCode better than Linnaean system? New development and debate on biological nomenclatural issues. Chinese Sci. Bull. 48: 308-312.

Ghiselin, M. T. 1995. Ostensive definitions of the names of species and clades. Biol. Phil. 10: 219-222.

Greuter, W. 2004. Recent developments in international biological nomenclature. Turk. Jo. Bot. 28: 17-26.

JANOVEC, J. P., L. G. CLARK, and S. A. MORI. 2003. Is the neotropical flora ready for the PhyloCode? Bot. Rev. 69: 22-43.

JØRGENSEN, P. M. 2002. Two nomenclatural systems? Taxon 51: 737.

JØRGENSEN, P. M. 2004. Rankless names in the Code? Taxon 53: 162.

KELLER, R. A., R. N. BOYD, and Q. D. WHEELER. 2003. The illogical basis of phylogenetic nomenclature. Bot. Rev. 69: 93-110.

KOJIMA, J. 2003. Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication. Bot. Rev. 69: 44-58.

LIDéN, M. and B. OXELMAN. 1996. Do we need phylogenetic taxonomy? Zool. Scripta 25: 183-185.

LIDéN, M., B. OXELMAN, A. BACKLUND, L. ANDERSSON, B. BREMER, R. ERIKSSON, R. MOBERG, I. NORDAL, K. PERSSON, M. THULIN, and B. ZIMMER. 1997. Charlie is our darling. Taxon 46: 735-738.

LOBL, I. 2001. Les nomenclatures "linéenne" et "phylogénetique", et d'autres problèmes artificiels. Bull. Soc. Fr. Syst. 26: 16-21.

Monsch, K. A. 2003. The use of apomorphies in taxonomic defining. Taxon 52: 105-107.

MOORE, G. 2003. Should taxon names be explicitly defined? Bot. Rev. 69: 2-21.

NIXON, K. C., and J. M. CARPENTER. 2000. On the other "phylogenetic systematics". Cladistics 16:298-318.

NIXON, K. C., J. M. CARPENTER, and D. W. STEVENSON. 2003. The PhyloCode is fatally flawed, and the "Linnaean" system can easily be fixed. Bot. Rev. 69: 111-120.

PICKETT, K. M. 2005. The new and improved PhyloCode, now with types, ranks, and even polyphyly: a conference report from the First International Phylogenetic Nomenclature Meeting. Cladistics 21: 79-82.

POLASZEK, A. and E. O. WILSON. 2005. Sense and stability in animal names. Trends Ecol. Evol. 20: 421-422.

RIEPPEL, O. 2006. The PhyloCode: a critical discussion of its theoretical foundation. Cladistics 22: 186-197.

SCHUH, R. T. 2003. The Linnaean system and its 250-year persistence. Bot. Rev. 69: 59-78.

SLUYS, R., K. Martens, and F. R. SCHRAM. 2004. The PhyloCode: naming of biodiversity at a crossroads. Trends Ecol. Evol. 19: 280-281.

STEVENS, P. F. 2006. An end to all things?—plants and their names. Australian Syst. Bot. 19: 115-133.

STUESSY, T. F. 2000. Taxon names are not defined. Taxon 49: 231-233.

STUESSY, T. F. 2001. Taxon names are still not defined. Taxon 50: 185-186.

TANG, Y.-C., and A.-M. MING. 2005. Paraphyletic group, PhyloCode and phylogenetic species—the current debate and a preliminary commentary. Acta Phytotax. Sin. 43: 403-419.

WENZEL, J. W., K. C. NIXON, and G. CUCCODORO. 2004. Dites non au PhyloCode! Bull. Soc. Fr. Syst. 31: 19-23.


Replies to Critiques:

BERTRAND, Y. and F. PLEIJEL. 2003. Nomenclature phylogénétique: une reponse. Bull. Soc. Fr. Syst. 29: 25-28.

BRYANT, H. N., and P. D. CANTINO. 2002. A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue? Biol. Rev. 77: 39-55.

CANTINO, P. D. 2000. Phylogenetic nomenclature: addressing some concerns. Taxon 49: 85-93.

CANTINO, P. D. 2004. Classifying species versus naming clades. Taxon 53: 795-798.

De Queiroz, K. 1995. The definitions of species and clade names: A reply to Ghiselin. Biol. Phil. 10: 223-228.

DE QUEIROZ, K. 1997. Misunderstandings about the phylogenetic approach to biological nomenclature: a reply to Lidén and Oxelman. Zool. Scr. 26: 67-70.

DE QUEIROZ, K. 2000. The definitions of taxon names: a reply to Stuessy. Taxon 49:533-536.

DE QUEIROZ, K. 2006. The PhyloCode and the distinction between taxonomy and nomenclature. Syst. Biol. 55: 160-162.

DE QUEIROZ, K., and P. D. CANTINO. 2001. Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nom. 58: 254-271.

DE QUEIROZ, K., and P. D. CANTINO. 2001. Taxon names, not taxa, are defined. Taxon 50: 821-826.

DONOGHUE, M. J. and J. A. GAUTHIER. 2004. Implementing the PhyloCode. Trends Ecol. Evol. 19: 281-282.

LAURIN, M. 2005. Dites oui au PhyloCode. Bull. Soc. Fr. Syst. 34: 25-31.

LAURIN, M., K. DE QUEIROZ, P. CANTINO, N. CELLINESE, and R. OLMSTEAD. 2005. The PhyloCode, types, ranks, and monophyly: a response to Pickett. Cladistics 21: 605-607.

LAURIN, M., K. DE QUEIROZ, and P. D. CANTINO. 2006. Sense and stability of taxon names. Zool. Scr. 35: 113-114.

LEE, M. S. Y. 1996a. The phylogenetic approach to biological taxonomy: practical aspects. Zool. Scr. 25: 187-190.

LEE, M. S. Y. 2001. On recent arguments for phylogenetic nomenclature. Taxon 50: 175-180.



SCHANDER, C. 1998. Types, emendations and names — a reply to Lidén et al. Taxon 47: 401-406.


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