Phylogenetic nomenclature

Phylogenetic nomenclature (PN) or phylogenetic taxonomy is an alternative to rank-based nomenclature, applying definitions from cladistics (or phylogenetic systematics). Its two defining features are the use of phylogenetic definitions of biological taxon names, and the lack of obligatory ranks. It is currently not regulated, but the PhyloCode (International Code of Phylogenetic Nomenclature) is intended to regulate it once implemented.

The terms cladism and cladist were first introduced by Ernst W. Mayr in 1965. They sometimes refer to cladistics as a whole.^{[citation needed]}

Definitions

For types of phylogenetic definitions, see Phylogenetic definitions of a clade

Under the rank-based codes of biological nomenclature, names themselves do not have definitions, but are instead usually linked to a type. Some biologists have claimed that this is unsatisfactory and that instability in nomenclature should only reflect instability of our knowledge of phylogeny, not instability in subjective opinions about which ranks should be given to which groups.^[1][2][3] Phylogenetic nomenclature, on the other hand, uses phylogenetic definitions to tie a name to a clade, a group consisting solely of a species and all its descendants, in such a manner that the meaning of the name is objective under any phylogenetic hypothesis. This prevents splitting and lumping (unless definitions are changed in the process, which will be allowed under the PhyloCode only under carefully restricted circumstances).^{[citation needed]}

Traditionally, groups named in phylogenetic nomenclature are usually monophyletic-that is, they define a natural group made up of all descendants of a single common ancestor. However, it is also possible to create phylogenetic definitions for the names of paraphyletic taxa .^[4] Assuming Mammalia and Aves are defined, Reptilia could be defined as "the most recent common ancestor of birds and mammals and all its descendants except birds and mammals". This includes taxa that are not currently named and even taxa that cannot be named under the rank-based codes without seriously disrupting existing classifications, such as "all organisms that share a more recent common ancestor with Homo sapiens than with birds and plesiomorphically keep laying eggs". Names of polyphyletic taxa could be defined by referring to the sum of two or more clades or paraphyletic taxa .^[4]

Philosophy

Rank-based and phylogenetic nomenclature differ in philosophical outlook. This manifests itself, particularly, in different approaches to the definitions of taxonomic terms. In providing the definition of "mammal," for example, users of rank-based nomenclature will start with the extension of the term that they want to define, perhaps the collection consisting of all animals with hair and mammary glands, and then formulate a definition satisfied by exactly these animals; users of phylogenetic nomenclature, rather, will formulate a definition, perhaps "the least inclusive clade containing brown bears and short-beaked echidnas," and stipulate that it defines the word "mammal."^[5]

Put another way, users of a rank-based system name species and classify them into higher taxa, only some of which are clades, while proponents of phylogenetic nomenclature focus on clades and name them as entities that are of interest in their own right.^[6]

The analogy with chemistry

Proponents of phylogenetic nomenclature claim that, as rank-based nomenclature does not delimit taxa precisely, its definitions will need to change as the science of biology advances. They see their approach as preferable in that their definitions are not susceptible to this kind of instability.^[7] It is a disputed matter whether such changes are characteristic of sciences outside of biology and whether, if so, biology should follow the example of such sciences. Chemistry has been used as an example.

Michel Laurin, one of the foremost advocates of phylogenetic nomenclature, considers that the concept of a chemical element has been stable ever since Dmitri Mendeleev put forth the periodic table in 1869.^[7] Biology should, on Laurin’s view, follow the example of chemistry and define its terms as precisely as possible.

The historian and philosopher Thomas Kuhn argued that changing the meaning of established concepts is central to significant advances in science.^[8] Prior to John Dalton’s work, he pointed out, the criteria for something’s being a chemical compound were such as to include salt water; by new criteria adopted afterwards, this fluid was excluded.^[9]

Michael Benton, a prominent defender of rank-based nomenclature, regards biology as an endeavor very different from chemistry. Chemical classification, as he sees it, circumscribes entities in terms of properties that enter into knowable laws; biology, lacking such laws, must look to the usefulness of classifications. From this perspective, he argues, it is less important that the definition of a term classifying organisms remain constant than it is that the term continue to apply to most of the same organisms. As he views phylogenetic nomenclature as seeking the former kind of stability and rank-based nomenclature as seeking the latter, he considers rank-based nomenclature to be preferable.^[10]

Lack of ranks

The current codes of biological nomenclature stipulate that taxa cannot be given a valid name without being given a rank.^{[citation needed]} However, the number of generally recognized ranks is limited. Gauthier et al. (1988)^[11] claimed that a classification which uses the common array of ranks, while including Aves within Reptilia and keeping Reptilia at its traditional rank of class, is forced to demote Aves substantially, perhaps to the rank of genus. This despite the ~ 12,000 known species of extant and extinct birds that would have to be incorporated into such a genus. To reduce this problem, Patterson and Rosen (1977)^[12] suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997)^[13] introduced a large array of new ranks in order to cope with the diversity of Mammalia.

The current codes also each have rules saying that names must have certain endings if they are applied to taxa that have certain ranks. When a taxon changes rank from one classification to another, its name must change its suffix. Ereshefsky (1997:512)^[14] stated:

The Linnaean rule of assigning rank-specific suffices [sic] gives rise to even more confusing cases. Simpson (1963, 29–30) and Wiley (1981, 238) agree that the genus Homo belongs to a particular taxon. They disagree, however, on that taxon's rank. Acting in accord with the Linnaean system, they attach different suffixes to the root Homini [actually Homin-] and give the taxon in question different names: Wiley calls it 'Hominini' [tribe rank] and Simpson calls it 'Hominidae' [family rank]. Their disagreement does not stop there. Wiley believes that the taxon just cited is a part of a more inclusive taxon which is a family. Using the root Homini, and following the rules of the Linnaean system [more precisely, the zoological code], he names the more inclusive taxon 'Hominidae.' So for Wiley and Simpson, the name 'Hominidae' refers to two different taxa. In brief, the Linnaean system causes Wiley and Simpson to assign different names to what they agree is the same taxon, and it causes them to give the same name to what they agree are different taxa.

In phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g.;^[15] see also 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 (e.g.^[16][17][18]).

History

"Monophyletic tree of organisms". Ernst Haeckel: Generelle Morphologie der Organismen, etc. Berlin, 1866.

Ultimately, phylogenetic nomenclature is a result of Darwin's discovery that the diversity and history of life is best represented in tree-shaped diagrams. This discovery immediately led to changes in the existing classifications. For example, John Hogg proposed the term Protoctista in 1860 for organisms that did not seem closely related to either animals or plants. In 1866, the controversial biologist Ernst Haeckel for the first time reconstructed a single tree of all life (see figure) and immediately proceeded to translate it into a classification. This classification was rank-based, in accordance with the only code of biological nomenclature that existed 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.

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" (cladistics – today, the term "cladistics" is only used for the method of phylogeny reconstruction, but its inventor, Willi Hennig,^[19] regarded this method as a mere tool for the purpose of classification). 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^[20] interpreted the name Sauropsida, erected 40 years earlier by 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, but 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 lack of compatibility of his scheme with the existing rank-based classifications (despite agreement on the phylogeny in all but details), and the lack of a method of phylogenetics at this time, are the most likely reasons why Goodrich's suggestions were largely ignored.

The principle that only clades (monophyletic taxa – an ancestor plus all its descendants) should be formally named became popular 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^[21] of his earlier proposal to define ranks as geological age classes.^[19][22]

The origin of phylogenetic nomenclature can be dated to 1986, when Jacques Gauthier used phylogenetic definitions for the first time in a published work.^[23] 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).^[7] This led him, Kevin de Queiroz, and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature.

References

1. ^ Michel Laurin and Philip D. Cantino (2004). "First International Phylogenetic Nomenclature Meeting: a report". Zoologica Scripta 33 (5): 475–479. doi:10.1111/j.0300-3256.2004.00176.x. 
2. ^ Michel Laurin and Philip 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. 
3. ^ Michel Laurin and Philip D. Cantino (2007). "Second meeting of the International Society for Phylogenetic Nomenclature: A report". Zoologica Scripta 36: 109–117. doi:10.1111/j.1463-6409.2006.00268.x. 
4. ^ ^{a b} Kevin de Queiroz & Jacques Gauthier (1990). "Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names". Syst. Zool. 39 (4): 307–322. doi:10.2307/2992353. JSTOR 2992353. 
5. ^ Kevin de Queiroz (1994). "Replacement of an essentialistic perspective on taxonomic definitions as exemplified by the definition of "Mammalia"". Syst. Biol. 43 (4): 497–510. doi:10.2307/2413548. JSTOR 2413548. 
6. ^ Philip D. Cantino (2004). "Classifying species versus naming clades". Taxon 53 (3): 795–798. doi:10.2307/4135453. JSTOR 4135453. 
7. ^ ^{a b c} Michel Laurin (2008). "The splendid isolation of biological nomenclature". Zoologica Scripta 37 (2): 223–233. doi:10.1111/j.1463-6409.2007.00318.x. 
8. ^ Thomas S. Kuhn (1962). The Structure of Scientific Revolutions. University of Chicago Press. p. 102. ISBN 226458032. 
9. ^ Thomas S. Kuhn (1998). "Metaphor and theory change". In Andrew Ortony. Metaphor and Thought. Cambridge University Press. p. 539. ISBN 0521227275. 
10. ^ Michael J. Benton (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?". Biological reviews of the Cambridge Philosophical Society 75 (4): 633–648. PMID 11117201. http://palaeo.gly.bris.ac.uk/Benton/reprints/2000phylocode.pdf. 
11. ^ Jacques Gauthier, Richard Estes, and Kevin de Queiroz (1988). A Phylogenetic Analysis of Lepidosauromorpha. In Richard Estes and G. Pregill. . Phylogenetic Relationships of the Lizard Families (Stanford University Press): 15–98. http://si-pddr.si.edu/dspace/bitstream/10088/6458/1/Gauthier_1988.pdf. 
12. ^ C. Patterson & D. Rosen (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. 
13. ^ Malcolm C. McKenna and S. K. Bell (1997). Classification of Mammals Above the Species Level. Columbia University Press. ISBN 023111012X. 
14. ^ Marc Ereshefsky (1997). "The Evolution of the Linnaean Hierarchy". Biology and Philosophy 12 (4): 493–519. doi:10.1023/A:1006556627052. 
15. ^ Jacques A. Gauthier (1994). The diversification of the amniotes. In Donald R. Prothero and Rainer M. Schoch. . Major features of vertebrate evolution (Paleontological Society): 129–159. 
16. ^ Kevin de Queiroz and Jacques Gauthier (1992). "Phylogenetic taxonomy [sic]". Ann. Rev. Ecol. Syst. 23: 449–480. 
17. ^ Philip D. Cantino (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon 49 (1): 85–93. doi:10.2307/1223935. JSTOR 1223935. 
18. ^ H. N. Bryant and Philip D. Cantino (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. 
19. ^ ^{a b} Willi Hennig (1950). Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag. "no" 
20. ^ Edwin S. Goodrich (1916). "On the classification of the Reptilia". Proc. R. Soc. Lond. B 89 (615): 261–276. doi:10.1098/rspb.1916.0012. 
21. ^ Willi Hennig (1969). Die Stammesgeschichte der Insekten. Waldemar Kramer. "no" 
22. ^ Willi Hennig (1965). "Phylogenetic Systematics". Annual Review of Entomology 10: 97–116. doi:10.1146/annurev.en.10.010165.000525. 
23. ^ Jacques Gauthier (1986). Saurischian Monophyly and the Origin of Birds. In Kevin Padian. . The Origin of Birds and the Evolution of Flight. (Mem. Cal. Acad. Sci. 8): 1–55. 

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., and Richard G. Olmstead (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, and Jacques Gauthier (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., 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.