Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a diagnosis, a statement intended to supply characters that differentiate the taxon from others with which it is likely to be confused. Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified.
Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and all its descendants. These groups can equivalently be called monophyletic. There are slightly different ways of specifying the ancestor, which are discussed below. Once the ancestor is specified, the meaning of the name is fixed: the ancestor and all organisms which are its descendants are included in the named taxon. Listing all these organisms (i.e. providing a full circumscription) requires the full phylogenetic tree to be known. In practice, there are only one or more hypotheses as to the correct tree. Different hypotheses lead to different organisms being thought to be included in the named taxon, but do not affect what organisms the name actually applies to. In this sense the name is independent of theory revision.
Phylogenetic definitions of clade names 
Phylogenetic nomenclature ties names to clades, creating taxa consisting solely of an ancestor and all its descendants. This can be done in different ways, as explained in Article 9 of the PhyloCode.
1) The ancestor can be indicated by its relation to two or more specifiers that are mentioned explicitly. This can be done in three ways, which are shown in the diagram:
- A node-based definition could read: "the last common ancestor of A and B, and all descendants of that ancestor". Thus, the entire line below the junction of A and B does not belong to the clade to which the name with this definition refers.
- A branch-based definition, often called a stem-based definition, could read: "the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor". Thus, the entire line below the junction of A and B does belong to the clade to which the name with this definition refers.
- An apomorphy-based definition could read: "the first ancestor of A to possess derived trait M as inherited by A, and all descendants of that ancestor". In the diagram, M evolves at the intersection of the horizontal line with the tree. Thus, the clade to which the name with this definition refers contains that part of the line below the last common ancestor of A and B which corresponds to ancestors possessing the apomorphy M. The rest of the line is excluded.
2) The ancestor can be indicated by its relation to two or more specifiers that are not mentioned explicitly, but described as members of another taxon that fulfill a certain criterion. Such definitions first describe an unnamed clade and then use its extant members as specifiers for a node-based definition. Examples are:
- A branch-modified node-based definition could read: "the last common ancestor of all extant specimens/populations/species that share a more recent common ancestor with A than with C".
- An apomorphy-modified node-based definition could read: "the last common ancestor of all extant specimens/populations/species that possess derived trait M as inherited by A".
Other forms of phylogenetic definition are possible as well.
Ancestry-based definitions of the names of paraphyletic and polyphyletic taxa 
In the PhyloCode, only a clade can receive a "phylogenetic definition", and this restriction is observed in the present article. However, it is also possible to create definitions for the names of other groups that are phylogenetic in the sense that they use only ancestral relations anchored on species or specimens. For example, assuming Mammalia and Aves (birds) are defined in this manner, Reptilia could be defined as "the most recent common ancestor of Mammalia and Aves and all its descendants except Mammalia and Aves". This is an example of a paraphyletic group, a clade minus one or more subordinate clades. Names of polyphyletic groups, characterized by a trait that evolved convergently in two or more subgroups, can similarly be defined as the sum of multiple clades.
Under the traditional nomenclature codes, such as the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants, taxa that are not explicitly associated with a rank cannot be formally named, because the application of a name to a taxon is based on both a type and a rank. The requirement for a rank is a major difference between traditional and phylogenetic nomenclature. It has several consequences: it limits the number of nested levels at which names can be applied; it causes the endings of names to change if a group has its rank changed, even if it has precisely the same members (i.e. the same circumscription); and it is logically inconsistent with all taxa being monophyletic.
Especially in recent decades (due to advances in phylogenetics), taxonomists have named many "nested" taxa (i.e. taxa which are contained inside other taxa). No system of nomenclature attempts to name every clade; this would be particularly difficult in traditional nomenclature since every named taxon must be given a lower rank than any named taxon in which it is nested, so the number of names that can be assigned in a nested set of taxa can be no greater than the number of generally recognized ranks. Gauthier et al. (1988) suggested that, if Reptilia is assigned its traditional rank of class, then a phylogenetic classification has to assign the rank of genus to Aves. In such a classification, all ~12,000 known species of extant and extinct birds would then have to be incorporated into this genus.
Various solutions have been proposed while keeping the rank-based nomenclature codes. Patterson and Rosen (1977) suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997) introduced a large array of new ranks in order to cope with the diversity of Mammalia; these have not been widely adopted. In botany, the Angiosperm Phylogeny Group, responsible for the currently most widely used classification of flowering plants, chose a different approach. They retained the traditional ranks of family and order, considering them to be of value in teaching and in studying relationships between taxa, but also introduced named clades without formal ranks.
The current codes also have rules stating that names must have certain endings depending on the rank of the taxa to which they are applied. When a group has a different rank in different classifications, its name must have a different suffix. Ereshefsky (1997:512) gave an example. He noted that Simpson in 1963 and Wiley in 1981 agreed that the same group of genera, which included the genus Homo, should be placed together in a taxon. Simpson treated this taxon as a family, and so gave it the name "Hominidae": "Homin-" from "Homo" and "-idae" as the family ending under the zoological code. Wiley considered it to be at the rank of tribe, and so gave it the name "Hominini", "-ini" being the tribe ending. Wiley's tribe Hominini formed only part of a family which he called "Hominidae". Thus, under the zoological code, two groups with precisely the same circumscription were given different names (Simpson's Hominidae and Wiley's Hominini) and two groups with the same name had different circumscriptions (Simpson's Hominidae and Wiley's Hominidae).
In phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g. Gauthier (1994) and the PhyloCode). Ranks are, however, not altogether forbidden in phylogenetic nomenclature. They are merely decoupled from nomenclature: they do not influence which names can be used, which taxa are associated with which names, and which names can refer to nested taxa.
The principles of traditional rank-based nomenclature are logically incompatible with all taxa being strictly monophyletic. Every organism must belong to a genus, for example, so there would have to be a genus for every common ancestor of the mammals and the birds. For such a genus to be monophyletic, it would have to include both the class Mammalia and the class Aves. In rank-based nomenclature, however, classes must include genera, not the other way around.
The conflict between phylogenetic and traditional nomenclature reflects differing views of the metaphysics of taxa. For the advocates of phylogenetic nomenclature, a taxon is an individual, an entity that gains and loses attributes as time passes. Just as a person does not become somebody else when his or her properties change through maturation, senility, or more radical changes like amnesia, the loss of a limb, or a change in sex, so a taxon remains the same entity whatever characteristics are gained or lost.
For any individual, there has to be something that connects its temporal stages in virtue of which it remains the same thing. For a person, the spatiotemporal continuity of the body provides the relevant connection; from infancy to old age, the body traces a continuous path through the world and it is this path, rather than any characteristics of the individual, that connects the baby and the octogenarian. For a taxon, if characteristics are not relevant, it can only be ancestral relations that connect the Devonian Rhyniognatha hirsti with the modern monarch butterfly as representatives, separated by 400 million years, of the taxon Insecta.
If ancestry is sufficient for the continuity of a taxon, however, then all descendants of a taxon member will also be included in the taxon, so all bona fide taxa are monophyletic; the names of paraphyletic groups do not merit formal recognition. As "Pelycosauria" refers to a paraphyletic group that includes some Permian tetrapods but not their extant descendants, it cannot be admitted as a valid taxon name.
To the adherent of traditional nomenclature, on the other hand, taxa are sets or classes. Unlike individuals, they are constituted by similarities, characteristics shared among their members. Monophlyletic groups are particularly worthy of attention and naming primarily because they often share properties of interest. Since many paraphyletic groups also share such properties, plesiomorphies in their case, providing them with names is also conducive to productive research. Such naming is strongly defended by some scientists; in a 2005 letter to the editors of the journal Taxon, 150 biologists from around the world joined in defense of paraphyletic taxa. For Darwin, they pointed out, evolution involved descent and modification, not just descent. Taxa, for them, are sets of organisms united by similarity; when the similarity is too weak, descendants are not in all of their ancestors' taxa.
Ultimately, phylogenetic nomenclature is a result of the general acceptance of branching in the course of evolution, represented in the diagrams of Jean-Baptiste Lamarck and later writers like Charles Darwin and Ernst Haeckel. In 1866, Haeckel for the first time constructed a single tree of all life (see figure) and immediately proceeded to translate it into a classification. This classification was rank-based, as was usual at the time, but did not contain taxa that Haeckel considered polyphyletic In it, Haeckel introduced the rank of phylum which carries a connotation of monophyly in its name (literally meaning "stem").
Ever since, it has been debated in which ways and to what extent the phylogeny of life should be used as a basis for its classification, with views ranging from "numerical taxonomy" (phenetics) over "evolutionary taxonomy" (gradistics) to "phylogenetic systematics". From the 1960s onwards, rankless classifications were occasionally proposed, but in general the principles of rank-based nomenclature were used by all three schools of thought.
Most of the basic tenets of phylogenetic nomenclature (lack of obligatory ranks, and something close to phylogenetic definitions) can, however, be traced to 1916, when Edwin Goodrich interpreted the name Sauropsida, erected 40 years earlier by T. H. Huxley, to include the birds (Aves) as well as part of Reptilia, and coined the new name Theropsida to include the mammals as well as another part of Reptilia. Goodrich did not give them ranks, and treated them exactly as if they had phylogenetic definitions, using neither contents nor diagnostic characters to decide whether a given animal should belong to Theropsida, Sauropsida, or something else once its phylogenetic position was agreed upon. Goodrich also opined that the name Reptilia should be abandoned once the phylogeny of the reptiles would be better known.
The principle that only clades should be formally named became popular in some circles in the second half of the 20th century. It spread together with the methods for discovering clades (cladistics) and is an integral part of phylogenetic systematics (see above). At the same time, it became apparent that the obligatory ranks that are part of the traditional systems of nomenclature produced problems. Some authors suggested abandoning them altogether, starting with Willi Hennig's abandonment of his earlier proposal to define ranks as geological age classes.
The first use of phylogenetic nomenclature in a publication can be dated to 1986. Theoretical papers outlining the principles of phylogenetic nomenclature, as well as further publications containing applications of phylogenetic nomenclature (mostly to vertebrates), soon followed (see Literature section).
In an attempt to avoid a schism in the biologist community, "Gauthier suggested to two members of the ICZN to apply formal taxonomic names ruled by the zoological code only to clades (at least for supraspecific taxa) and to abandon Linnean ranks, but these two members promptly rejected these ideas" (Laurin, 2008: 224). This led Kevin de Queiroz and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature.
Willi Hennig's pioneering work provoked a spirited debate about the relative merits of phylogenetic nomenclature versus Linnaean taxonomy, or the related approach of evolutionary taxonomy, which has continued down to the present. Some of the debates in which the cladists were engaged had been running since the 19th century. While Hennig insisted that different classification schemes were useful for different purposes, he gave primacy to his own, claiming that the categories of his system had "individuality and reality" in contrast to the "timeless abstractions" of morphology-based classifications.
Formal classifications based on cladistic reasoning are said to emphasize ancestry at the expense of descriptive characteristics, and thus ignore biologically sensible, clearly defined groups which are not clades (e.g. reptiles as traditionally defined, or prokaryotes). Nonetheless, most taxonomists today avoid paraphyletic groups whenever they think it is possible within Linnaean taxonomy; polyphyletic taxa have long fallen out of fashion.
The International Code of Phylogenetic Nomenclature 
The ICPN, or PhyloCode, is a draft code of rules and recommendations for phylogenetic nomenclature.
- The ICPN will only regulate clade names. Names for para- or polyphyletic taxa, and names for species (which may or may not be clades), will not be considered, at least not at first. This means that the regulation of species names will be left, for the time being, to the rank-based codes of nomenclature.
- The Principle of Priority will be introduced for names and for definitions. The starting point for priority will be the publication date of the ICPN.
- Definitions for existing names, and new names along with their definitions, will have to be published in peer-reviewed works (on or after the starting date) and will have to be registered in an online database in order to be valid.
The number of supporters for widespread adoption of the PhyloCode is still small, and it is uncertain (as of May 2013) when the code will be implemented and how widely it will be followed.
- Franz, Nico M. (2005), "On the lack of good scientific reasons for the growing phylogeny/classification gap", Cladistics 21 (5): 495–500, doi:10.1111/j.1096-0031.2005.00080.x
- International Commission on Zoological Nomenclature (1999), "Glossary", International Code of Zoological Nomenclature (4th ed.), ISBN 0-85301-006-4
- Cantino, Philip D. & de Queiroz, Kevin (2010), "Article 9. General Requirements for Establishment of Clade Names", International Code of Phylogenetic Nomenclature, Version 4c
- de Queiroz, K.; Gauthier, J. (1990). "Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names". Systematic Zoology 39 (4): 307–322. doi:10.2307/2992353.
- Gauthier, J., Estes, R. & de Queiroz, K. 1988. A Phylogenetic Analysis of Lepidosauromorpha. Pp. 15–98 in R. Estes & G. Pregill (eds): Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford University Press. ISBN 978-0-8047-1435-8
- Ereshefsky, M. (1997). "The Evolution of the Linnaean Hierarchy". Biology and Philosophy 12 (4): 493–519. doi:10.1023/A:1006556627052.
- Patterson, C. & Rosen, D. 1977 Review of ichthyodectiform and other Mesozoic teleost fishes and the theory and practice of classifying fossils. Bulletin of the American Museum of Natural History 158: 81–172.
- McKenna, M. C. & Bell, S. K. 1997. Classification of Mammals Above the Species Level. Columbia University Press. ISBN 0-231-11012-X
- Angiosperm Phylogeny Group (1998), "An ordinal classification for the families of flowering plants", Annals of the Missouri Botanical Garden 85 (4): 531–553, doi:10.2307/2992015, JSTOR 2992015
- Gauthier, J. A. 1994. The diversification of the amniotes. Pp. 129–159 in: D. R. Prothero & Rainer R. Schoch (eds): Major features of vertebrate evolution. Paleontological Society.
- de Queiroz, K.; Gauthier, J. (1992). "Phylogenetic taxonomy [sic]". Ann. Rev. Ecol. Syst. 23: 449–480.
- Cantino, P. D. (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon 49 (1): 85–93. doi:10.2307/1223935.
- Bryant, H. N.; Cantino, P. D. (2002). "A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?". Biol. Rev. 77 (1): 39–55. doi:10.1017/S1464793101005802. PMID 11911373.
- Kazlev, M. A. "Cladistic and Linnaean systems — incompatible or complementary?". (palaeos.com). Retrieved September 30, 2012.
- Assis, L. C. S.; Brigandt, I. (2009), "Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution", Evolutionary Biology 36 (2): 248–255, doi:10.1007/s11692-009-9054-y
- Rowe, Timothy (1988), "Definition, diagnosis, and origin of Mammalia", Journal of Vertebrate Paleontology 8 (3): 241–264, doi:10.1080/02724634.1988.10011708
- Wiggins, David (1967), Identity and Spatio-temporal Continuity, Oxford University Press, ISBN 0631103708
- Entry for "taxon" in: International Commission on Zoological Nomenclature (1999), "Glossary", International Code of Zoological Nomenclature (4th ed.), ISBN 0-85301-006-4
- Nordal, Inger & Stedje, Brita, coordinators (2005), "Paraphyletic taxa should be accepted", Taxon 54 (1): 5–8, doi:10.2307/25065296
- Haeckel, E. H. Ph. A. 1866. Generelle Morphologie der Organismen. Georg Reimer.
- Ragan, Mark A. (2009), "Trees and networks before and after Darwin", Biology Direct 4 (43): 43, doi:10.1186/1745-6150-4-43, PMC 2793248, PMID 19917100
- Goodrich, E. S. (1916). "On the classification of the Reptilia". Proc. R. Soc. Lond. B 89 (615): 261–276. doi:10.1098/rspb.1916.0012.
- Hennig, W. 1969. Die Stammesgeschichte der Insekten. Waldemar Kramer.
- Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag.
- Hennig, W. (1965). "Phylogenetic Systematics". Annual Review of Entomology 10: 97–116. doi:10.1146/annurev.en.10.010165.000525.
- 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. Memoir 8 of the California Academy of Sciences.
- Laurin, M. (2008). "The splendid isolation of biological nomenclature". Zoologica Scripta 37 (2): 223–233. doi:10.1111/j.1463-6409.2007.00318.x.
- Wheeler, Quentin (2000), Species Concepts and Phylogenetic Theory: A Debate, Columbia University Press, ISBN 978-0-231-10143-1
- Benton, M. J. (2000), "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?", Biological Reviews 75 (4): 633–648, doi:10.1111/j.1469-185X.2000.tb00055.x, PMID 11117201
- Hull, David (1988), Science as a Process, University of Chicago Press, pp. 232–276, ISBN 978-0-226-36051-5
- Hennig, Willi (1966), Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl), Urbana, IL: Univ. of Illinois Press (reprinted 1979 and 1999), p. 9, ISBN 0-252-06814-9
- Hennig 1966, p. 81
Further reading 
A few seminal publications not cited in the references are cited here. An exhaustive list of publications about phylogenetic nomenclature can be found on the website of the International Society for Phylogenetic Nomenclature.
- Bryant, Harold N. (1994). "Comments on the phylogenetic definition of taxon names and conventions regarding the naming of crown clades". Syst. Biol. 43: 124–129.
- Cantino, Philip D.; Olmstead, Richard G. (2008). "Application of phylogenetically defined names does not require that every specifier be present on a tree". Syst. Biol. 57: 157–160.
- de Queiroz, Kevin (1992). Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7:295–313.
- Gauthier, Jacques A., Arnold G. Kluge, and Timothy Rowe (1988). The early evolution of the Amniota. Pages 103–155 in Michael J. Benton (ed.): The Phylogeny and Classification of the Tetrapods, Volume 1: Amphibians, Reptiles, Birds. Syst. Ass. Spec. Vol. 35A. Clarendon Press, Oxford.
- Gauthier, Jacques, David Cannatella, Kevin de Queiroz, Arnold G. Kluge, and Timothy Rowe (1989). Tetrapod phylogeny. Pages 337–353 in B. Fernholm, K. Bremer, and H. Jörnvall (eds.): The Hierarchy of Life. Elsevier Science B. V. (Biomedical Division), New York.
- Ghiselin, M. T. (1984). "Definition," "character," and other equivocal terms". Syst. Zool. 33: 104–110.
- Keesey, T. Michael (2007). "A mathematical approach to defining clade names, with potential applications to computer storage and processing". Zool. Scr. 36: 607–621.
- Laurin, Michel (2005). The advantages of phylogenetic nomenclature over Linnean nomenclature. Pages 67–97 in A. Minelli, G. Ortalli, and G. Sanga (eds): Animal Names. Instituto Veneto di Scienze, Lettere ed Arti; Venice.
- Lee, Michael S. Y. (2005). "Choosing reference taxa in phylogenetic nomenclature". Zool. Scr. 34: 329–331.
- Rowe, Timothy (1987). "Definition and diagnosis in the phylogenetic system". Syst. Zool. 36: 208–211.
- Rowe, Timothy; Gauthier, Jacques (1992). "Ancestry, paleontology and definition of the name Mammalia". Syst. Biol. 41: 372–378.
- Sereno, Paul 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, Paul C. (1999). "Definitions in phylogenetic taxonomy: critique and rationale". Syst. Biol. 48: 329–351.
- Sereno, Paul C. (2005). "The Logical Basis of Phylogenetic Taxonomy [sic]". Syst. Biol. 54: 595–619.
- Taylor, Michael P. (2007). "Phylogenetic definitions in the pre-PhyloCode era; implications for naming clades under the PhyloCode". PaleoBios 27: 1–6.
- Wilkinson, Mark (2006). "Identifying stable reference taxa for phylogenetic nomenclature". Zool. Scr. 35: 109–112.
- Wyss, A. R.; 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.