Literature on Phylogenetic Nomenclature
Philip D. Cantino and Kevin 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 () or Kevin de Queiroz ().

News Reports and Overviews

  • CANTINO, P. D. (2001). Nomenclature, phylogenetic. Pages 242–244 in McGraw-Hill Yearbook of Science and Technology 2002. New York: McGraw-Hill.
  • FOER, J. (2005). Pushing PhyloCode. Discover (April 2005): 46–51.
  • HÄRLIN, M. (2004). Classification nomenclature. Pages 52–54 in McGraw-Hill Yearbook of Science and 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 Sep 2004): 12–13.
  • LAURIN, M., & H. N. BRYANT (2009). Third meeting of the International Society for Phylogenetic Nomenclature: a report. Zool. Scr. 38: 333–337.
  • LAURIN, M., & 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.
  • LAURIN, M., & P. D. CANTINO (2006). Second Congrès International de la Société de Nomenclature Phylogénétique: 28 juin–2 juillet, 2006, Université de Yale, USA. Journal de l'Association Paléontologique Française 50: 18–21.
  • LAURIN, M., & P. D. CANTINO (2007). Second meeting of the International Society for Phylogenetic Nomenclature: a report. Zool. Scr. 36: 109–117.
  • LAURIN, M., & P. D. CANTINO (2004). First International Phylogenetic Nomenclature Meeting: a report. Zool. Scr. 33: 475–479.
  • 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.
  • PENNISI, E. (2001). Linnaeus's last stand? Science 291: 2304–2307.
  • PLEIJEL, F. (2000). Nomenclature linnéenne et nomenclature phylogénétique. Bull. Soc. Fran. Syst. 24: 25–28.
  • PLEIJEL, F., & B. DAYRAT (2000). De l'évolution dans la nomenclature? La Recherche 333: 48–50.
  • 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, & 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., & J. GAUTHIER (1990). Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39: 307–322.
  • DE QUEIROZ, K., & J. GAUTHIER (1992). Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23: 449–480.
  • DE QUEIROZ, K., & J. GAUTHIER (1994). Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9: 27–31.
  • ESTES, R., K. DE QUEIROZ, & J. GAUTHIER (1988). Phylogenetic relationships within Squamata. Pages 119–281 in R. Estes & G. K. Pregill (eds.) Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford, Calif.: Stanford Univ. Press.
  • GAUTHIER, J., K. DE QUEIROZ, & R. ESTES (1988). A phylogenetic analysis of Lepidosauromorpha. Pages 15–98 in R. Estes & 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.
  • BERTRAND, Y., & M. HÄRLIN (2006). Stability and universality in the application of taxon names in phylogenetic nomenclature. Syst. Biol. 55: 848–858.
  • BROCHU, C. A., & 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, & 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., & 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 (2008). Application of phylogenetically defined names does not require that every specifier be present on a tree. Syst. Biol. 57: 157–160.
  • CANTINO, P. D., R. G. OLMSTEAD, & S. J. WAGSTAFF. (1997). A comparison of phylogenetic nomenclature with the current system: a botanical case study. Syst. Biol. 46: 313–331.
  • CHRISTOFFERSON, M. L. (1995). Cladistic taxonomy, phylogenetic systematics, & 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. (1997). 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, & 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. (2007). Toward an integrated system of clade names. Syst. Biol. 56: 956–974.
  • DE QUEIROZ, K. (2009). [Untitled]. Pages 199–203 in S. Knapp & Q. Wheeler (eds.) Letters to Linnaeus. London: Linnean Society of London.
  • DE QUEIROZ, K., & P. D. CANTINO (2001). Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nom. 58: 254–271.
  • DONOGHUE, M. J. (2004). Immeasurable progress on the tree of life. Pages 548–552 in J. Cracraft & 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.
  • ERESHEFSKY, M. (2002). Linnaean ranks: vestiges of a bygone era. Philos. Sci. 69: S305–S315.
  • ERESHEFSKY, M. (2007). Foundational issues concerning taxa and taxon names. Syst. Biol. 56: 295–301.
  • GAUTHIER, J., & K. DE QUEIROZ (2001). Feathered dinosaurs, flying dinosaurs, crown dinosaurs, & the name "Aves". Pages 7–41 in J. Gauthier & 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). Phylogenetic approaches to nomenclature: a comparison based on a nemertean case study. Proc. Royal Soc. London, Ser. B 266: 2201–2207.
  • 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. (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. (2003). Taxon names as paradigms: the structure of nomenclatural revolutions. Cladistics 19: 138–143.
  • HÄRLIN, M. (2003). 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., & M. THOLLESSON (2005). Fundamentals of phylogenetic nomenclatures: an exchange of views. Symb. Bot. Ups. 33: 141–151.
  • HÄRLIN, M., & P. SUNDBERG (1998). Taxonomy and philosophy of names. Biol. & Philos. 13: 233–244.
  • HIBBETT, D. S., & 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, & M. SHONFELD (2005). Automated phylogenetic taxonomy: an example in the Homobasidiomycetes (mushroom-forming fungi). Syst. Biol. 54: 660–668.
  • JOYCE, W. G., J. F. PARHAM, & 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.
  • KEESEY, T. M. (2007). A mathematical approach to defining clade names, with potential applications to computer storage and processing. Zool. Scr. 36: 607–621.
  • KRON, K. A. (1997). Exploring alternative systems of classification. Aliso 15: 105–112.
  • KUNTNER, M. AND I. AGNARSSON (2006). Are the Linnean and phylogenetic nomenclatural systems combinable? Recommendations for biological nomenclature. Syst. Biol. 55: 774–784.
  • 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: avantages et inconvénients. Biosystema (Systématique et Paléontologie) 19: 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. Pages 67–97 in A. Minelli, G. Ortalli, & G. Sanga (eds.) Animal Names. Venice, Italy: Instituto Veneto di Scienze, Lettere ed Arti.
  • LAURIN, M. (2008). The splendid isolation of biological nomenclature. Zool. Scr. 37: 223–233.
  • LAURIN, M. (2008). Le PhyloCode. Pages 411–420 in D. Prat, A. Raynal-Roques, & A. Roguenant (eds.) Peut-on Classer le Vivant? Linné et la Systématique Aujourd'hui. Paris: Editions Berlin.
  • LAURIN, M. (2009). La nomenclature biologique aujourd’hui: que reste-t-il de Linné? Pages 1–16 in Roche, C. (ed.) TOTh 2009. Annecy, France: Institut Porphyre. [http://www.porphyre.org/toth/actes]
  • LAURIN, M. (2010). The subjective nature of Linnaean categories and its impact in evolutionary biology and biodiversity studies. Contributions to Zoology 79: 131–146.
  • LAURIN, M., & J. S. ANDERSON. (2004). Meaning of the name Tetrapoda in the scientific literature: an exchange. Syst. Biol. 53: 68–80.
  • LEE, M. S. Y. (1996). The phylogenetic approach to biological taxonomy: practical aspects. Zool. Scr. 25: 187–190.
  • LEE, M. S. Y. (1996). 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. (1998). Phylogenetic uncertainty, molecular sequences, and the definition of taxon names. Syst. Biol. 47: 719–726.
  • LEE, M. S. Y. (1998). Ancestors and taxonomy. Trends Ecol. Evol. 13: 26.
  • LEE, M. S. Y. (1999). Reference taxa and phylogenetic nomenclature. Taxon 48: 31–34.
  • LEE, M. S. Y. (1999). 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. Scr. 34: 329–331.
  • LEE, M. S. Y., & A. SKINNER (2007). Stability, ranks, and the PhyloCode. Acta Palaeontol. Pol. 52: 643–650.
  • LEE, M. S. Y., & A. SKINNER (2008). Hierarchy and clade definitions in phylogenetic taxonomy. Organisms, Diversity & Evol. 8: 17–20.
  • 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., & G. W. ROUSE (2003). Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature. J. Zool. Syst. Evol. Research 41: 162–174.
  • PLEIJEL, F., & M. HÄRLIN (2004). Phylogenetic nomenclature is compatible with diverse philosophical perspectives. Zool. Scr. 33: 587–591.
  • ROWE, T., & J. GAUTHIER (1992). Ancestry, paleontology and definition of the name Mammalia. Syst. Biol. 41: 372–378.
  • SCHANDER, C. (1998). Mandatory categories and impossible hierarchies—a reply to Sosef. Taxon 47: 407–410.
  • SCHANDER, C., & 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? Taxon 51: 11–26.
  • SUNDBERG, P., & F. PLEIJEL. (1994). Phylogenetic classification and the definition of taxon names. Zool. Scr. 23: 19–25.
  • TAYLOR, M. P. (2007). Phylogenetic definitions in the pre-PhyloCode era; implications for naming clades under the PhyloCode. PaleoBios 27: 1–6.
  • WILKINSON, M. (2006). Identifying stable reference taxa for phylogenetic nomenclature. Zool. Scr. 35: 109–112.
  • WYSS, A. R., & 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

  • ARTOIS, T. (2001). Phylogenetic nomenclature: the end of binomial nomenclature? Belg. J. Zool. 131: 87–89.
  • BETHOUX, O. (2008). Revision and phylogenetic affinities of the Lobeattid species bronsoni Dana, 1864 and silvatica Laurentiaux & Laurentiaux-Vieira, 1980 (Pennsylvanian: Archaeorthoptera). Arthropod Systematics & Phylogeny 66: 145–163.
  • BETHOUX, O., R. DE LA HORRA, M. I. BENITO, J. F. BARRENECHEA, A. B. GALAN, & J. LOPEZ-GOMEZ (2009). A new triadotypomorphan insect from the Anisian (Middle Triassic), Buntsandstein facies, Spain. J. Iberian Geol. 35: 179–184.
  • BRANDLEY, M. C., & 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, & M. S. Y. LEE (1999). Species names in phylogenetic nomenclature. Syst. Biol. 48: 790–807.
  • CANTINO, P. D., S. J. WAGSTAFF, & 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.
  • 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., & T. M. GOSLINER (2005). Species names and metaphyly: a case study in Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina). Zool. Scr. 34: 199–224.
  • DAYRAT, B., C. SCHANDER, & K. D. ANGIELCZYK (2004). Suggestions for a new species nomenclature. Taxon 53: 485–591.
  • 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.
  • DE QUEIROZ, K., & J. GAUTHIER (1992). Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23: 449–480.
  • 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, & 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.
  • LEE, M. S. Y. (2002). Species and phylogenetic nomenclature. Taxon 51: 507–510.
  • MISHLER, B. D. (1999). Getting rid of species? Pages 307–315 in R. Wilson (ed.) Species: New Interdisciplinary Essays. Cambridge, Mass.: MIT Press.
  • NICHOLSON, K. E. (2002). Phylogenetic analysis and a test of the current infrageneric classification of Norops (beta Anolis). Herpetol. Monogr. 16: 93–120.
  • PLEIJEL, F. (1999). Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Syst. Biol. 48: 755–789.
  • PLEIJEL, F., & G. W. ROUSE (2000). A new taxon, capricornia (Hesionidae, Polychaeta), illustrating the LITU ('least-inclusive taxonomic unit') concept. Zool. Scr. 29: 157–168.
  • PLEIJEL, F., & G. W. ROUSE (2000). Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proc. R. Soc. London B 267: 627–630.
  • SPANGLER, R. E. (2003). Taxonomy of Sarga, Sorghum and Vacoparis (Poaceae: Andropogoneae). Australian Syst. Bot. 16: 279–299.
  • WOLSAN, M. (2007). Naming species in phylogenetic nomenclature. Syst. Biol. 56: 1011–1021.
  • WOLSAN, M. (2007). Impracticality and instability of species names under Lanham's method. Taxon 56: 292–294.
  • WOLSAN, M. (2007). Naming species in phylogenetic nomenclature. Syst. Biol. 56: 1011–1021.

Other Applications of Phylogenetic Nomenclature

  • AGUINALDO, A. M., J. M. TURBEVILLE, L. S. LINFORD, M. C. RIVERA, J. R. GAREY, R. A. RAF., & 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, & 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, & 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. Pages 125–133 in B. Nordenstam, G. El-Ghazaly, & 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: 9–100.
  • BROCHU, C. A. (2003). Phylogenetic approaches toward crocodylian history. Annu. Rev. Earth Planet Sci. 31: 357–397.
  • BRYANT, J. D., & 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., & D. M. HILLIS. (1993). Amphibian relationships: phylogenetic analysis of morphology and molecules. Herpetol. Monogr. 7: 1–7.
  • CANTINO, P. D., J. A. DOYLE, S. W. GRAHAM, W. S. JUDD, R. G. OLMSTEAD, D. E. SOLTIS, P. A. SOLTIS, & M. J. DONOGHUE (2007). Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56: 822–846.
  • 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, & 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.
  • 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.
  • DEMÉRÉ, T. A. (1994). The family Odobenidae: A phylogenetic analysis of fossil and living taxa. Proc. San Diego Soc. Nat. Hist. 29: 99–123.
  • DILKES, D. W. (1998). The Early Triassic rhynchosaur Mesosuchus 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, & 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., & M. J. DONOGHUE (1993). Phylogenies and angiosperm diversification. Paleobiology 19: 141–167.
  • ERIKSSON, T., M. J. DONOGHUE, & 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, & J. GAUTHIER (1988). Phylogenetic relationships within Squamata. Pages 119–281 in R. Estes & G. K. Pregill (eds.) Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford, Calif.: Stanford Univ. Press..
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Critiques of Phylogenetic Nomenclature

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  • BERRY, P. E. (2002). Biological inventories and the PhyloCode. Taxon 51: 27–29.
  • CARPENTER, J. M. (2003). Critique of pure folly. Bot. Rev. 69: 79–92.
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  • DUBOIS, A. (2007). Naming taxa from cladograms: a cautionary tale. Molec. Phyl. Evol. 42: 317–330.
  • DYKE, G. J. (2002). Should paleontologists use "phylogenetic" nomenclature? J. Paleontol. 76: 793–796.
  • FOREY, P. L. (2001). The PhyloCode: description and commentary. Bull. Zool. Nom. 58: 81–96.
  • FOREY, P. L. (2002). PhyloCode—pain, no gain. Taxon 51: 43–54.
  • GAO, K. Q., & 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.
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  • JÖRGENSEN, P. M. (2002). Two nomenclatural systems? Taxon 51: 737.
  • JÖRGENSEN, P. M. (2004). Rankless names in the Code? Taxon 53: 162.
  • KELLER, R. A., R. N. BOYD, & 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., & B. OXELMAN (1996). Do we need phylogenetic taxonomy? Zool. Scr. 25: 183–185.
  • LIDÉN, M., B. OXELMAN, A. BACKLUND, L. ANDERSSON, B. BREMER, R. ERIKSSON, R. MOBERG, I. NORDAL, K. PERSSON, M. THULIN, & 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.
  • MONSCH, K. A. (2006). The PhyloCode, or alternative nomenclature: why it is not beneficial to palaeontology, either. Acta Palaeontol. Pol. 51: 521–524.
  • MOORE, G. (2003). Should taxon names be explicitly defined? Bot. Rev. 69: 2–21.
  • NIXON, K. C., & J. M. CARPENTER (2000). On the other "phylogenetic systematics". Cladistics 16: 298–318.
  • NIXON, K. C., J. M. CARPENTER, & 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., & 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, & 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., & A.-M. LU (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, & G. CUCCODORO (2004). Dites non au PhyloCode! Bull. Soc. Fr. Syst. 31: 19–23.

Replies to Critiques

  • BERTRAND, Y., & F. PLEIJEL (2003). Nomenclature phylogénétique: une reponse. Bull. Soc. Fr. Syst. 29: 25–28.
  • BRYANT, H. N., & 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., & M. J. DONOGHUE (2011). Phylogenetic nomenclature, three-taxon statements, and unnecessary name changes. Systematic Biology 60: 887–892.
  • DE QUEIROZ, K., & P. D. CANTINO (2001). Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nom. 58: 254–271.
  • DE QUEIROZ, K., & P. D. CANTINO (2001). Taxon names, not taxa, are defined. Taxon 50: 821–826.
  • DONOGHUE, M. J., & J. A. GAUTHIER (2004). Implementing the PhyloCode. Trends Ecol. Evol. 19: 281–282.
  • HILLIS, D. M. (2007). Constraints in naming parts of the tree of life. Molec. Phyl. Evol. 42: 331–338.
  • LAURIN, M. (2005). Dites oui au PhyloCode. Bull. Soc. Fr. Syst. 34: 25–31.
  • LAURIN, M., K. DE QUEIROZ, & P. D. CANTINO (2006). Sense and stability of taxon names. Zool. Scr. 35: 113–114.
  • LAURIN, M., K. DE QUEIROZ, P. CANTINO, N. CELLINESE, & R. OLMSTEAD (2005). The PhyloCode, types, ranks, and monophyly: a response to Pickett. Cladistics 21: 605–607.
  • LEE, M. S. Y. (1996). 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.
  • LEE, M. S. Y., & A. SKINNER (2007). Stability, ranks, and the PhyloCode. Acta Palaeontol. Pol. 52: 643–650.
  • SCHANDER, C. (1998). Types, emendations and names—a reply to Lidén et al. Taxon 47: 401–406.