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Should taxon names be explicitly defined?

II. Traditional ("Linnaean") Nomenclature


Under the current codes of biological nomenclature (Lapage et al., 1992; Ride et al., 1999; Greuter et al., 2000), each taxon name is assigned a rank (see Articles 3 and 4 of the current International Code of Botanical Nomenclature). In botanical nomenclature (Greuter et al., 2000) there are seven principal ranks (kingdom, division/phylum, class, order, family, genus, species) and five secondary ranks (tribe, section, series, variety, form). The prefix "sub" can be added to these rank-denoting terms to create additional ranks. Additional ranks are also allowed as long as error or confusion is not introduced. Furthermore, new names or combinations published after 1953 must have a clear indication of rank assignment (Article 35.3), and the sequence of rank-denoting terms must not be altered (Article 33.7; see also Moore, 2001). Similar guidelines for rank assignment are also present in bacteriological (Lapage et al., 1992) and zoological (Ride et al., 1999) nomenclature. Thus, when introducing new taxon names i nto scientific literature, biologists are required to do so within the framework of a hierarchical classification system.

In botanical nomenclature (Greuter et al., 2000), guidelines are established in the formation of taxon names so that one can readily identify a taxon's rank simply through the examination of its name. This allows the name itself (i.e., when used outside the context of a taxonomy or phylogeny) to convey broad information with regard to set exclusivity (Moore, 1998; Nixon & Carpenter, 2000).

The three main codes of nomenclature (Lapage et al., 1992; Ride et al., 1999; Greuter et al., 2000) also provide guidelines for the assignment of nomenclatural types to taxon names. A type is simply that element to which a taxon name is permanently attached. No matter how the circumscription of a taxon may change upon taxonomic revision, the type must be included within the circumscription. It is this mechanism of nomenclatural types that allows nomenclature to remain distinct from taxonomy (Nicolson, 1977; Ride 1988, 1991; Moore, 1998; McNeill, 2000). Thus all taxonomists who choose to use a given taxon name must include the type within the circumscription of that taxon. This agreed-upon type element ensures that when a taxon is delimited differently by taxonomists the different circumscriptions will not be mutually exclusive, since all circumscriptions must include the type element. Thus types are the "ties that bind" taxonomists together with regard to the application of taxon names.

Above the rank of a species, taxon names are typified through classification types (Farber, 1976). A classification type is the type of a name of a subordinate taxon, which typifies the name of a higher taxon. Above the level of genus, the generic name that corresponds to that type will usually serve as the basis for the name of the higher taxon. For example, the family name Scrophulariaceae is typified by the generic name Scrophularia L. and the circumscription of Scrophulariaceae must include Scrophularia. At the rank of genus and below, the classification type is not apparent in the name itself. For example, the type of the genus name Rhynchospora Vahl, R. alba (L.) Vahl, is not apparent from the name Rhynchospora (for discussions of the nomenclatural type method, see Cook, 1898, 1900; Hitchcock, 1905, 1925; Lawrence, 1951; Steam, 1957; Farber, 1976). The nomenclatural type method should not be confused with conceptual type methods adopted by some early biologists (for reviews of conceptual typological met hods in botany, see Stevens, 1984, 1994).

Below the rank of species, taxon names are typified by specimens. For example, the name Johannesteijsmannia magnifica Dransfield is typified by the specimen Dransfield 862 (K). It should be noted that ultimately all names are typified by specimens, since here is a "typification cascade" present that "flows" to a type specimen (Moore, 1998). For example, the circumscription of Amaryllidaceae must include the genus Amaryllis L., Amaryllis must include A. belladona L. (the type), and A. belladona's circumscription must include its type specimen (Herb. Clifford: 135, Amaryllis No. 2 (BM)).


In the recent debate about nomenclature, the current system has been frequently described as "Linnaean." Because this characterization is so widespread (for example, see Pennisi, 1996, 2001; Chui, 1999; Ereshefsky, 1999, 2001; Milius, 1999; Fellman, 2000; Withgott, 2000), it is worth reviewing what aspects of our current system of nomenclature can be attributed to Linnaeus.

Linnaeus did indeed write a set of rules of nomenclature. These can be found in aphorisms 210-324 in his Fundamenta Botanica (1736), and he elaborated on the rules in his Critica Botanica (1737). These aphorisms (210-250 covered generic names; 251-255, classes and natural orders; 256-305, specific names; 306-317, varieties; and 318-324, synonyms) focused heavily on the proper formation of names (e.g., aphorism 226: "generic names ending in-oides are to be banished from the domain of Botany") and most of them (such as aphorism 226) are not incorporated into our current code of botanical nomenclature (Greuter et al., 2000). A few principles put forth by Linnaeus in his aphorisms do occur in our current system of nomenclature (e.g., homonyms should not be permitted; names at the rank of genera and above should consist of single names; see Hill, 1938).

One of the basic components of our current system of nomenclature--the principle of priority--was not followed by Linnaeus. Rather, Linnaeus simply believed that the "best" name should be the accepted name. This is summed up in aphorism 319: "The best synonym should come first" (i.e., be recognized as the accepted name). If the names were equally good, Linnaeus (1737, aphorism 246) believed that the name to be retained should be "the most familiar, the oldest and the one which is in officinal use." Of course, it is difficult to determine what is meant by "best" (I suspect the more a name adhered to Linnaeus's set of aphorisms the "better" it was to him), and this certainly contributed to the formalization of the principle of priority, first in zoology in the Stricklandian Code (Strickland et al., 1843) and then in botany with Candolle's Lois de la nomenclature botanique ... (1867). It should also be noted that Linnaeus was not averse to introducing a new name even when several were available: "I am not induce d to believe that Botanists ought to abstain from making new names in the endeavor to produce better ones" (1737, aphorism 319).

Another basic component of our current nomenclatural system--the nomenclatural type method--was also not followed by Linnaeus (Hitchcock, 1925; Steam, 1957). The nomenclatural type method was perhaps first spelled out formally in the Stricklandian code of zoological nomenclature (Strickland et al., 1843) and was first applied in botanical nomenclature in the American (Brittonian) codes (Fairchild, 1892; Britton, 1893; Swingle, 1893; Arthur et al., 1904, 1907; see also Nicolson, 1991). Indeed, the development of the nomenclatural type method was a critical post-Linnaean development that allowed nomenclature to remain distinct not only from taxonomy but from concepts that link the name to characters (Moore, 1998; McNeill, 2000).

The current sequence of rank-denoting terms is certainly similar to the hierarchy used by Linnaeus in his works (e.g., 1753, 1754, 1758-1759, 1762-1763, 1764). However, it is by no means identical, because Linnaeus recognized only five formal ranks--class, natural order, genus, species, and variety--whereas our current system of botanical nomenclature recognizes seven primary ranks, as well as five secondary ranks.

Our current system does follow Linnaeus in using binary nomenclature for names of species. Binary nomenclature represented a significant shift, because prior to the use of binomials species were designated using descriptive polynomials. Thus, plant names and taxon descriptions were effectively the same thing. Binomials allowed the two components (a species' name and a species' description) to be separate (Moore, 1998; McNeill, 2000).

However, the use of binomials did not begin with Linnaeus (he did not consistently use them until after 1753); earlier workers who used binary nomenclature included Gesner (15 16- 1565) and Bauhin (1560-1624) (see Choate, 1912; Lawrence, 1951; Steam, 1957; Heller, 1964; Vaczy, 1971). Furthermore, Linnaeus's introduction of his binary nomina trivialia was quite accidental and they played no role in his Fundamenta Botanica (1736) or Critica Botanica (1737) (Stafleu, 1971). Although Linnaeus's aphorisms 256-305 did cover species names, these names were his polynomial diagnostic phrase names (nomina specifica), not his binary trivial names (nomina trivialia).

Ereshefsky (1999, 2001) discussed "several motivations" that Linnaeus had for adopting binary nomenclature, such as Linnaeus's belief that "[g]enera display the function of reproduction and that function is responsible for the existence of genera and species" (2001: 204-205). Ereshefsky (2001) then goes on to document how many of Linnaeus's "motivations" for binomials have become "obsolete" in the context of modem biology and to recommend that functional binomials be abandoned (i.e., they could be retained but would not indicate a taxon's rank or position). However, Ereshefsky's (2001) analysis has a major flaw: He cites the aphorisms in the Critica Botanica (1737) as the source of Linnaeus's "motivations" for using binomials. However, Linnaeus's aphorisms on specific names (e.g., aphorisms 256-305) addressed not his binary nomina trivialia but his polynomial nomina specifica. The aphorisms themselves are quite clear on this point (see Hill, 1938; Steam, 1957; Stafleu, 1971). Therefore, any "motivations" pres ent in these aphorisms represent motivations Linnaeus had for using polynomial nomina specifica, not binomial names. Indeed, some of these motivations are outdated, and Linnaeus's polynomial phrase names have been accordingly abandoned.

An amended aphorism 257 in Philosophia Botanica (Linnaeus, 1751) did briefly address the nomnina trivialia: "[t]riviale autem nomen legibus etiamnum caret" (the rules for trivial names have not yet been drawn up) (see Stafleu, 1971). However, Linnaeus never did draft rules for the formation of his binary species names (Stafleu, 1971).

He did provide the following brief guideline in Philosophia Botanica (1751; translation by Heller, 1964: 54): "Trivial names may perhaps be admitted after the fashion I have followed in Pan Suecicus [1749]; they should consist of a single word, a word freely taken from any source." According to Stafleu (1971: 86-87), Linnaeus's trivial names "played a minor role in Linnaeus's thinking until he realized how successful the device had been. It was of little importance to Linnaeus the theoretician, but it suited Linnaeus the practical systematist." Although Linnaeus's "motivations" for using polynomial phrase names have become obsolete, considering the practical aspects of taxonomy--his true motivation for using binary nomenclature--is not something that has become obsolete.

Binary nomenclature is not limited to biological nomenclature. Binomials are commonly used in general language with a noun representing a collective name and an adjective used as distinguisher (e.g., grizzly bear, polar bear). Indeed, binary nomenclature is not limited to taxon names--I used my palmar interosseus and dorsal interosseus muscles to type this manuscript. Most philosophers of language recognize a general class of definition termed "species and genus" in which an expression is applicable to some (i.e., the species) but not all entities of a certain type (i.e., the genus) and inapplicable to all entities not of that type (Yagisawa, 1995).

The most significant convention in botanical nomenclature that links our rules to Linnaeus is the recognition of his first edition of Species Plantarum (1753) as the starting point for most major groups of nonfossil plants (Article 13.1). Similarly, zoological nomenclature (Ride et al., 1999) uses Linnacus's tenth edition of Systema Naturae (1758--1759) as the starting point for zoological nomenclature. More than anything else, these retroactive maneuvers are what link Linnaeus to our current system of nomenclature. Thus, most practicing taxonomists and floristicians frequently consult Linnaeus's Species Plantarum (1753), as well as his later works (e.g., 1754, 1762-1763), while paying less attention to his earlier works (e.g., 1737).

Some have argued that our current nomenclatural system is impoverished by Linaneus's outdated views of biological theory: "The Linnaean system was set up under a creationist world view to reflect a hierarchy of ideas in the eyes of a creator" (Mishler, quoted in Pennisi, 2001: 2304); "Biologists still use the Linnaean hierarchy despite its essentialist and creationist roots" (Ereshefsky, 2001: 47). Although such statements may apply to Linnaeus's taxonomy (no longer in use), they should not be applied to the few nomenclatural conventions (e.g., some rank-denoting terms, binomials) that survive today. Philosophical mountains should not be made out of the few Linnaean molehills that remain.

Unfortunately, many recent popular articles on biological nomenclature have not made the critical distinction between nomenclature and taxonomy and thus give the impression that taxonomists continue to employ Linnaeus's taxonomy. Statements such as "while a phylogenetic tree's arrangement of branches reflects how closely different species are related and which ones share a common ancestor, it does not follow how organisms are grouped and ranked according to Linnaeus" and "phylogenetic studies indicate that, because of their common origins, birds should be included within reptiles but they are not" (Pennisi, 1996: 181) imply that Linnaeus's taxonomy is embedded in our current system of nomenclature and that this prevents the synonymization of Ayes with Reptilia. Such a conclusion is incorrect, because the current system in no way prevents one from treating the names Ayes and Reptilia as synonyms. Pennisi (1996: 181): "[T]axonomists order the living world according to appearances." Pennisi (2001: 2304): "Under the traditional system, a taxonomist begins by assessing the physical characteristics ... then selects the most representative species to be the 'type' for each genus, then the most representative genus to be the type of the family and so forth. Individual specimens are then deposited in a museum to serve as the reference point for that species and genus. Thereafter, as new specimens with similar characteristics are found, they are deemed part of a known species, or even a new genus based on how closely they resemble the type specimen." Such characterizations of our current system paint a picture that the doctrine of phenetics is embedded into our current system. Again this is an inaccurate representation of our current nomenclatural system, which simply assigns a rank and a type to a taxon name, and the type need not be "typical" in any conceptual sense.

De Queiroz's (2000) distinction between Linnaeus's nomenclature and his taxonomy as "a Linnaean system" and "the Linnaean system" is inadequate because it is homonymic, and all good nomenclators, be they traditionalists or phylogenetic, should reject homonyms. In this case it has led to the confusion of Linnaeus's nomenclature with his classification. Ereshefsky (2001) frequently refers to the "Linnaean system" without making it clear whether he is referring to Linnaeus's taxonomy or his nomenclature. In summary, the current system of nomenclature assigns ranks and types to laxon names. Although it does employ some conventions used by Linnaeus (e.g., some rank-denoting terms, binomials) and also uses Linnaean publications as official starting dates for nomenclature, it is also fundamentally different in several ways (e.g., the nomenclatural type method, strict principle of priority, lack of diagnostic phrase names for species) (see also Stuessy, 2000). Ereshefsky (2001) asserts that our current system of nome nclature represents the "Linnaean system" and that, in order to bring nomenclature into a "post-Linnaean" era, taxonomists need to adopt a new system, such as the rankless system he proposes. However, no such change is needed, for our current system already resides in the "post-Linnaean" era.

Characterizing the traditional nomenclature as "Linnaean" makes for interesting headlines: "Biologists Urged to Retire Linnaeus" (Pennisi, 1996); "Should We Junk Linnaeus?" (Milius, 1999); "Is Linnaeus Dead?" (Benton, 2000); "Is It 'So Long Linnaeus'?" (Withgott, 2000); "The Poverty of the Linnaean Hierarchy" (Ereshefsky, 2001); and "Linnaeus's Last Stand?" (Pennisi, 2001). And it is a clever way to couch the debate in favor of phylogenetic nomenclature, because most scientists who only casually follow this issue will undoubtedly side with those advocating the cutting-edge term "phylogenetic" over "Linnaeus," who has been dead for 225 years. However, it takes us away from what the primary debate should focus on; namely, whether taxonomists should abandon our current, simple, rank-based, type system with one that assigns explicit phylogenetic definitions to taxon names.

III. Phylogenetic Nomenclature

In phylogenetic nomenclature, ranks would be abandoned and names would be provided with explicit phylogenetic definitions (de Queiroz & Gauthier, 1990, 1992, 1994; Cantino & de Queiroz, 2000). (1) Under this approach taxonomists would no longer have the option of modifying taxon circumscriptions through lumping and splitting, and the name of a taxon would be effectively attached to a given clade (i.e., the one identified using the explicit phylogenetic definition in a given phylogenetic context). The name would remain attached to this clade regardless of how future shifts in phylogenetic theories might alter the content of the clade.

The types of definitions permitted in phylogenetic nomenclature basically fall into three categories: node-based definitions, stem-based definitions, and apomorphy definitions. Node-based and stem-based definitions effectively triangulate to a node through the use of two or more specifiers, whereas an apomorphy definition effectively "hangs" the name directly on a node through the citation of an apomorphic character. The PhyloCode (Cantino & de Queiroz, 2000) permits substantial leeway in how one crafts these definitions (see also Bryant & Cantino, 2002).

In a node-based definition, a name is defined so that it refers to a clade stemming from the most recent common ancestor of two or more specified organisms, species, or clades (i.e., specifiers). An example of a node-based definition would be Alpha: the clade stemming from the most recent common ancestor of species A and species B. A stem-based definition defines the name of a taxon so that it indicates a clade sharing a more recent common ancestor with one or more specifiers than with another (e.g., Beta: the clade that includes all species sharing a more recent common ancestor with species C than with species D). An apomorphy-based definition defines the name of a clade stemming from the first ancestor to evolve a specified character (e.g., Gamma: the clade stemming from the first ancestor to evolve character X). These definitions can also be worded so that they do not refer to hypothetical ancestors (Cantino et al., 1997; Lee, 1998). For example, the node-based definition could be reworded to "the least in clusive clade that includes species A and species B."

Advocates of rankless classification have argued that taxonomists need to free themselves from the Linnaean hierarchy (Donoghue, in Pennisi, 1996). They have concluded that the elimination of fonnal ranks in taxonomy will promote stability, because a taxon's name will not have to change when new information results in a change in its hierarchical position (e.g., de Queiroz & Gauthier, 1990, 1992, 1994; Cantino et al., 1997; Kron, 1997). They also maintain that, under a rankless approach to nomenclature, taxonomists will no longer have to make arbitrary decisions regarding the rank assignment of taxa. For example, under the phylogenetic nomenclature approach the discovery that birds (Ayes) are nested within reptiles (Reptilia) would not force one to lump Ayes into Reptilia. Rather, both names could be used--Ayes for the smaller clade that includes birds and Reptilia for the larger clade that includes traditional reptiles as well as birds.

Another advantage cited by advocates of rankless nomenclature is that taxonomists do not have the problem of having to create excessive number of ranks when constructing a complete phylogenetic classification for a group. For example, Kron (quoted in Chui, 1999: 1), noted that "you don't have to spend time memorizing whether an infracohort is higher than a subcohort." However, taxonomists' running out of ranks is not a new problem. Bentham and Hooker (1862--1 883) struggled with recognizing additional taxa around the existing recognized ranks. They accomplished this by intercalating an informal rank (termed "series") throughout the Linnaean hierarchy where needed (see Moore, 2001). Thus running out of ranks is not a problem of phylogenetic taxonomy per se, but rather a problem whenever someone wants to construct a highly granular classification system. The larger problem with such classifications ts not too many rank-denoting terms but too many taxon names, and this problem applies to both rank-based and rank less systems.

Many advocates of phylogenetic nomenclature have made comparisons between it and the traditional system of nomenclature (e.g., de Queiroz & Gauthier, 1990, 1992, 1994; Bryant, 1994, 1996, 1997; Schwenk, 1994; Sundberg & Pleijel, 1994; Schander & Thollesson, 1995; Cantino et al., 1997; Kron, 1997; Wyss & Meng, 1997; Hibbett & Donoghue, 1998; Pleijel, 1999). These comparisons basically use recent phylogenetic information to construct classifications under the traditional and phylogenetic nomenclatural systems, and they conclude that the phylogenetic nomenclature approach results in greater nomenclatural stability than does the current system.

Although it is true that phylogenetic nomenclature eliminates one of the sources of nomenclatural instability--rank assignment--these comparisons overemphasize the instability of the current system and deemphasize the potential instability of the phylogenetic system. In the revised classification prepared under the traditional approach, the taxonomist has to modify the existing classification (prepared using traditional nomenclature) and redo it in light of the new phylogenetic information. Obviously, this requires nomenclatural change. However, when the taxonomist constructs a classification using phylogenetic nomenclature, there is no previous classification (constructed using phylogenetic nomenclature) that must be modified. Therefore, it can be constructed without any nomenclatural instability. An appropriate analogy here is that someone wanting to build a house will be able to do so with greater ease on an undeveloped lot (the lot that phylogenetic nomenclators are currently working on) than a developed lot (the lot that traditional nomenclators must work on). Such comparisons do not address the critical question of how much instability there will be when phylogenetic nomenclators--in the face of a revised phylogeny (with perhaps unanticipated changes)--have to revise a taxonomy originally constructed using phylogenetic nomenclature. In other words, how easy will it be for phylogenetic nomenclators to construct a classification on an already developed lot? Although some of the comparisons cited do consider some potential shifts in phylogenetic hypotheses through buffered definitions, none shows what happens when there are unexpected changes in phylogenetic hypotheses.

Therefore, such comparisons should not be used to declare that the phylogenetic system is superior to the traditional system with regard to nomenclatural stability. Rather, both systems need to be studied over time and in the face of changing phylogenies. And it is in these comparisons, as will be shown later, that I believe phylogenetic nomenclature will not fare as well (see also Liden & Oxelman, 1996; Rasnitsyn, 1996; Dominguez & Wheeler, 1997; Liden et al., 1997; Moore, 1998; Stevens, 1998; Benton, 2000; Nixon & Carpenter, 2000).

IV. Differences between the Two Systems


Recently there has been debate about whether taxon names are defined in the current system of nomenclature: Stuessy (2000, 2001) has argued that names of taxa are not defined, whereas de Queiroz (2000) and de Queiroz and Cantino (2001) have argued that they are defined. Assuming that taxon names are defined under the current system, there have also been different characterizations as to just how (de Queiroz & Gauthier, 1990, 1992; Ghiselin, 1997; Ereshefsky, 2001). I am hesitant to wade into this debate, for it ultimately leads one into the philosophical whirlpool of "What is the definition of definition?"

However, I am inclined to agree with Stuessy (2000, 2001) because, under our current system, the name and its "defining" attributes (i.e., its type and rank designation) do not force the application of the name to any single taxon in the context of a given taxonomy or phylogeny. For example, let us accept that the name Asteraceae is to be defined as "the taxon at the rank of family inclusive of the genus Aster:" Let us also assume that the taxonomist, using the name Asteraceae, constructs a cladistic classification from a well-resolved phylogeny for the Asteridae. Under this scenario, the definition of Asteraceae does not indicate to the worker to which dade the name Asteraceae should be applied. Rather, the taxonomist is free to choose among the clades that include the genus Aster. Therefore, the so-called definition does not really define the name Asteraceae.

Rather, the type of the name basically functions as an agreed-upon starting point taxonomists use in developing a circumscription for a given name. The characters of the type specimen in no way restrict how one can circumscribe the group. Names in the current system have been viewed as having ostensive definitions (Ghiselin, 1997; Ereshefsky, 2001). However, the type (the referent in an ostensive definition for a taxon name; see Ghiselin, 1997; Ereshefsky, 2001) and the name's rank do not serve to define the limits of a taxon in the context of a given taxonomy. Therefore, I am disinclined to regard taxon names as having definitions under the current system.

Yet many have maintained that names are defined under the current system through character-based definitions (de Queiroz & Gauthier, 1990, 1992; de Queiroz, 1994; Sundberg & Pleijel, 1994; Lee 1996, 1998). De Queiroz and Gauthier (1990, 1992), in their original arguments advocating the replacement of our current system with a "phylogenetic" approach, stated that a change was needed to "replace character-based definitions" and grant "the concept of evolution a central role in taxonomy." Such a conclusion paints a picture of our current nomenclatural system as having an essentialistic perspective (for an example, see de Queiroz, 1994). However, the current system does not attach characters, only types, to names of taxa. Characters associated with types are not "defining."

Through long-term usage in a particular manner, names may have connotations that are character based. For example, it would be difficult for a botanist to contemplate a circumscription of Angiospermae that included plants that lacked flowers or vascular tissue. However, such a circumscription is technically possible because characters (e.g., vascular tissue, flowers)--even for untypified suprafamilial descriptive names (e.g., Angiospermae)--are not attached to the name,

However, in phylogenetic nomenclature, taxon names clearly have definitions. These definitions are explicit, and, when used in the context of a resolved phylogeny, they precisely dictate what the circumscription of a taxon should be. Most critical is that once a phylogenetic definition has been given to a taxon name, it must be followed under any and all subsequent accepted phylogenetic hypotheses. It alone determines how the name is to be applied. Previous historical usage with regard to circumscription and character associations cannot be weighed when determining how to apply the name in future taxonomic revisions (this point will be more fully developed in the following section).

When crafting a phylogenetic definition for a taxon name, a phylogenetic nomenclator can take into consideration historical usage of the name. For example, when crafting a definition for the name Pinus L., a phylogenetic nomenclator would certainly attempt to craft the definition so that the circumscription of the taxon would include all taxa currently recognized in the genus Pinus L. while excluding all taxa not currently placed in Pinus L. However, once the name is defined the taxonomist is forced to apply the definition regardless of how future revisions in phylogenetic hypotheses may lead to conflicts with historical usage. Thus, under a phylogenetic nomenclature the taxonomist has only one chance (i.e., the formulation of the original definition) to consider the conventional or lexical aspects of a taxon name (for discussions of definition categories, see Robinson, 1954; Yagisawa, 1995).

Because phylogenetic definitions must be followed irrespective of historical usage of the name, they are best characterized as "stipulative" (or "legislative") definitions (see Robinson, 1954; Yagisawa, 1995). Robinson (1954: 68) characterized as one of the "greatest goods to be obtained from stipulative definitions" "the improvement of concepts or the creation of new concepts, which is the key to one of the two or three locks on the door of successful science." Steam (1995: 16, note 1) noted that Linnaeus was engaging in stipulative definitions when he took a word such as corolla, meaning in classical Latin 'a little crown or garland,' and applied it exclusively to the showy inner envelope of the flower surrounding the sexual organs for which there existed no convenient unambiguous collective term." The current system of nomenclature also has an element of stipulation in it in that a taxon's circumscription must include the type once its name has been typified.

Because phylogenetic definitions are stipulative they possess all of the advantages and disadvantages of stipulative definitions. The general advantages are reviewed by Robinson (1954), and the specific advantages of this approach in phylogenetic nomenclature are well described by its advocates (de Queiroz & Gauthier, 1990, 1992, 1994; Bryant, 1994, 1996, 1997; Schwenk, 1994; Sundberg & Pleijel, 1994; Schander & Thollesson, 1995; Cantino et al., 1997; Kron, 1997; Wyss & Meng, 1997; Hibbett & Donoghue, 1998). Most notably, stipulative definitions can lead to the removal of ambiguity from the application of a word (Robinson, 1954). In the case of phylogenetic taxonomy, ambiguity occurs when the same taxon name is applied to different clades or when different names are applied to the same clade by different workers.

However, there are clear disadvantages to stipulative definitions. These are also reviewed by Robinson (1954) and will be further discussed below. Most significant is the fact that stipulative definitions can have unintended consequences. According to Robinson (1954: 75), "stipulation, whatever its purposes, has unintended consequences, some of which are bad." Thus a significant difference between the two systems is that in traditional nomenclature names are not explicitly defined (if they are defined at all), whereas in phylogenetic nomenclature names are explicitly defined and the definition must always be followed (barring intervention by the International Committee on Phylogenetic Nomenclature) in all phylogenetic contexts.


In phylogenetic nomenclature a name is effectively "married" to a clade. The name remains "married" to that clade regardless of how future changes in phylogenetic hypotheses may change the size (content) of the clade. Let us say that Delta is defined as the least inclusive clade containing species E and species F. Let us also say that, under the original phylogenetic hypothesis, Delta was believed to be a taxon comprising three species (B, F, and G). However, let us now say that the original hypothesis regarding the phylogenetic relationship was drastically incorrect because species F is actually much less closely related to species E and G than originally believed and that "the least inclusive dade containing species B and F" is actually a dade that contains 500,000 species. Under phylogenetic nomenclature, the taxonomist would now be required to apply the name Delta to the dade that contains 500,000 species (the name Delta might become synonymized if there were an earlier name for this dade).

Under the traditional system this would not happen. Let us say that the name Delta was typified by species E and was originally circumscribed to include species B, F, and G. Once species F was found to be far more distantly related to species E and G than originally thought, it would simply be removed from Delta, which would now consist of species E and G. Under the traditional approach less is attached to the name, and this provides the taxonomist with much greater flexibility when applying the name under revised phylogenetic hypotheses.

Advocates of phylogenetic nomenclature regard this flexibility as a weakness, because it can result in different taxonomists applying the name to different clades (or applying different names to the same dade). However, this "weakness" is a strength when phylogenetic hypotheses change, because it allows the taxonomist to accommodate new information into the classification while minimizing the disruption to existing usage as much as possible. Under phylogenetic nomenclature there is no limit as to how much change there may be regarding content under revised phylogenetic hypotheses. Chase et al. (2000: 687): "we are not in favour of rank-free classifications, which, in our opinion, is an argument for names to mean nothing."

Furthermore, in phylogenetic nomenclature slight differences in phylogenetic interpretations by different workers can result in different names being applied to taxa with the same content. Let us say worker 1 recognizes a dade (I(JH)), Epsilon (definition: least inclusive dade containing species H and I), and worker 2 recognizes a clade (J(HI)), Zeta (definition: least inclusive dade containing species H and J). Because the workers disagree about the internal relationships with the dade that comprises species H, I, and J, these two workers will apply different names to the dade that comprises species H, I, and J.

Also in phylogenetic nomenclature, the taxonomist has less freedom in accommodating extensional (i.e., circumscriptional) and intensional (character-based) connotations of a name in the face of new discoveries. Based on the current understanding of the phylogeny of the Cyperaceeae (Bruhl, 1995; Plunkett et al., 1995; Muasya et al., 1998, 2000), a phylogenetic definition might be the least inclusive dade containing Cyperus esculentus L. and Hypolytrum latifolium Poir. However, let us say that cyperologists discover a new group of species and that these species form a dade that is sister to the main sedge dade. Based on the previous phylogenetic definition, these new taxa could not be included in the circumscription of Cyperaceae, even if the newly discovered taxa have all the character states previously believed to be synapomorphic for Cyperaceae (e.g., achene fruit).

However, in traditional nomenclature the application of the name Cyperaceae could be shifted to the larger dade that represents the traditional Cyperaceae plus the newly discovered taxa. By making this shift in the application, the taxonomist is able to preserve the intensional (character-based) connotations of the Cyperaceae with minimal changes in the extensional (circumscriptional) connotations, thus balancing the input of new information (in this case the discovery of new species) with historical usage (i.e., the fact that the name Cyperaceae has traditionally been diagnosed using a suite of characters).

The criticisms addressed above have been made repeatedly elsewhere (Liden & Oxelman, 1996; Rasnitsyn, 1996; Dominguez & Wheeler, 1997; Liden et al., 1997; Moore, 1998; Stevens, 1998; Benton, 2000; Nixon & Carpenter, 2000). Although advocates of phylogenetic nomenclature recognize the potential for significant shifts in how a name is applied under this system, they maintain that these problems can be mitigated through the careful use of all of the options available in writing definitions, including buffering. In the Delta example, the phylogenetic nomenclator could have prevented the shift by originally crafting the definition to use species E and species G as specifiers. Alternatively, a definition might be crafted that would include a buffering phrase (see Schander & Thollesson, 1995; Bryant, 1996, 1997; Lee, 1996; Cantino et al., 1997; Wyss & Meng, 1997) that would prevent the name being used in a manner wildly different from what was originally intended. In the Epsilon/Zeta example, the dilemma of two taxo nomists using different name for clades of the same content could be avoided by having the original definition include species H, I and J. In the Cyperaceae example, the intensional connotations could be preserved by simply using an apomorphy definition citing the apomorphic characters that are commonly associated with the name. However, all of these solutions have one problem: They require the taxonomist to anticipate and address the problem at the time the definition is crafted. A few years ago I wrote that buffered definitions solve the content problem only in the "context of a given phylogeny" (Moore, 1998). Lee (1999: 364) claimed that this "misses the point," because buffered definitions "are specifically constructed to remain stable (i.e., refer to clades of similar content) regardless of which of the multiple possible phylogenies is eventually accepted." However, the point I was trying to make was that buffered definitions can be crafted only in the context of a given phylogeny with given ambiguities (a source of instability). Such definitions cannot buffer against unanticipated changes and may actually cause greater instability when unanticipated changes occur, because buffered definitions usually attach more specifiers (each a potential source of instability) to the taxon name (Moore, 1998).

Taxonomists must always recognize the possibility that they may be mistaken, even when they are confident that they are correct. For example, Goldman et al. (2000) have raised concerns involving maximum likelihood tests of topology (e.g., Kishino-Hasegawa test), and Buckley (2001: 125) has stated that this article "will prompt the reassessment of many studies where overconfidence might have been given to the results of a test because of inappropriate statistical assumptions." The phylogenetic "musical chairs" that has occurred regarding the identity of the sister group of the angiosperms (Crane, 1985, 1988; Friis et al., 1987; Hart, 1987; Beck, 1988; Donoghue & Doyle, 1989; Chase et al., 1993; Donoghue, 1994; Doyle et al., 1994; Hughes, 1994; Nixon et al., 1994; Goremykin et al., 1996; Price, 1996; Crepet, 1998; Hansen et al., 1999; Winter et al. 1999; Bowe et al., 2000; Chaw et al., 2000) and the basal-most group of angiosperms (Donoghue & Doyle, 1989; Zimmer et al., 1989; Loconte & Stevenson, 1991; Hamby & Zimmer, 1992; Chase et al., 1993; Doyle et al., 1994; Crane et al., 1995; Soltis et al., 1997, 1999; Mathews & Donoghue, 1999; Qiu et al., 1999; Parkinson et al., 1999; Barkman et al., 2000; Crepet, 2000) are excellent examples of how changes--even unanticipated ones--in our concepts are real possibilities.

Thus, my reply to Bryant and Cantino's (2002: 39) query, "Is taxonomic freedom the fundamental issue?" is an emphatic "Yes." Such freedom allows the taxonomist to deal with unanticipated changes; buffered definitions only allow the phylogenetic nomenclator to deal with anticipated changes.

This real possibility of change is what sets classification of organisms apart from many other classification systems, such as those in chemistry. Cantino (quoted in Milius, 1999: 270) has asked: "Would chemists be satisfied with a system of nomenclature in which naming a newly discovered compound required renaming other compounds?" This question can be refuted by asking an opposing one: "Would chemists be satisfied with a system in which a term such as 'gold' might be forced to include many things not previously recognized as gold?" Classification in chemistry is largely an essentialistic approach (elements being defined by their unique and common atomic structure), and taxonomists would do well not to look there for answers to problems with historical approaches to organismal classification.

The concerns raised here and elsewhere (e.g., Liden & Oxelman, 1996; Rasnitsyn, 1996; Dominguez & Wheeler, 1997; Liden et al., 1997; Moore, 1998; Stevens, 1998; Benton, 2000; Nixon & Carpenter, 2000) arise from the stipulative nature of phylogenetic definitions. Such definitions are unable to handle unanticipated changes, and, as a result, they can have unintended consequences (e.g., gigantic shifts in content). As I discussed elsewhere (Moore, 1998), what if Engler (1887-1889) had stipulated a definition for "Araceae" as the least inclusive taxon containing Anon L. and Acorns L. (based on his taxonomic sequence, such a definition would have captured his circumscription for the family)? Recent evidence (Duvall et al., 1993a, 1993b; Davis, 1995) has shown Acorns to be sister to the rest of the monocots, and application of the definition above would force the circumscription of Araceae to include all monocots.

Robinson (1954: 59) noted this disadvantage of stipulative definitions and identified Humpty Dumpty (Carroll, 1872) as a practitioner of them: "Humpty Dumpty insisted that words were to mean what he chose that they should mean. He did not concern himself with any lexical inquiries, that is, with finding out what some set of people actually had meant by some word." There certainly is an element to Humpty Dumpty's approach in phylogenetic nomenclature, given that, after a taxon name is defined, phylogenetic nomenclature requires the name to mean what the original definer intended it to mean and does not permit any lexical inquiries regarding how the name had historically been used.

To summarize, in traditional nomenclature names are not "wedded" to any particular dade (or, rather, they are "wedded" but can easily be "divorced"). This allows the taxonomist the freedom and flexibility to incorporate new information into a classification while disrupting historical usage as little as possible. In phylogenetic nomenclature a name is "married" to a particular dade. Barring intervention by the International Committee for Phylogenetic Nomenclature, the name stays "married" to that dade, regardless of how new information changes its content. By not attaching the name to a specific dade, the traditional system allows greater consideration for the lexical (conventional) aspects of a name, whereas the phylogenetic nomenclature approach gives greater weight to the stipulation.


I. Uninomials

Under traditional nomenclature ranks are embedded into the system. Detailed rules are provided on the formation of taxon names that permit the taxonomist to determine which rank a given name is assigned. Under traditional nomenclature, none of the ranks is defined, although the sequence is fixed. Despite this, some have noted that biologists have used ranks for comparative purposes as though genera from different families were somehow equivalent (Stevens, 1997). "[E]cologists and macroevolutionists often count numbers of taxa at a particular rank as an erroneous measure of 'biodiversity' " (Mishler, 1999: 311). Even if some biologists misuse ranks, I do not think that the elimination of ranks is warranted. Just because some doctors misprescribe a particular drug, should other doctors be banned from prescribing it? Certainly not.

This highly ordered system allows one working within it to come to conclusions regarding set exclusivity and inclusivity with regard to different taxon names just by looking at the names themselves (see also Moore, 1998; Nixon & Carpenter, 2000). For example, the plant taxonomist can determine that the names Pinophyta, Ephedra L., Rhynchospora subg. Haplostylis Pax, Sapindaceae, Liliopsida, Acorales, Pyxidanthera harbulata Michx., and Viola pedata var. lineariloba D.C. represent taxa at the ranks of division, genus, subgenus, family, class, order, species, and variety, respectively. Furthermore, from the aforementioned list of taxon names, it can be concluded that Ephedra L. is not inclusive of Pinophyta and that the circumscriptions of Pyxidanthera barbulata Michx. and Viola pedata var. lineariloba D.C. are mutually exclusive.

No such conclusions can be made under the phylogenetic system of nomenclature, because the name conveys nothing regarding rank assignment and therefore indicates nothing about set exclusivity. Ranks cannot be used in a formal sense in phylogenetic nomenclature because they are attached to a single clade. The name remains attached to this clade regardless of how the clade's membership (hierarchical position) may change within the tree of life. Some advocates of phylogenetic nomenclature have indicated that ranks are not incompatible with phylogenetic nomenclature, but simply optional (de Queiroz & Gauthier, 1990, 1992; Bryant & Cantino, 2002). However, under such a system the rank itself could not be determined from the name. Therefore, such a ranked system would not convey set exclusivity information the way the current system does.

My conclusions are in conflict with Mishler's (quoted in Pennisi, 2001: 2305, 2307): "Critics have said you'd lose all the hierarchical information, but you wouldn't." Mishler (1999:311) also noted that "it is important to emphasize that despite misrepresentations to the contrary, theorists who advocate getting rid of Linnaean ranks do not at all advocate getting rid of the hierarchy in biological classification." However, Mishler is confusing taxonomy with nomenclature, for critics who have raised this issue (e.g., Moore, 1998; Nixon & Carpenter, 2000) clearly were discussing information loss from the nomenclature (i.e., the names themselves).

This is easily seen in Mishler's (1999: 311) "grocer" example: "[A] grocer might classify table salt as a spice, and group spices together under the category food items. This simple hierarchy is clear, but requires no named ranks to be understood." However, under such a system what can we say about the three "taxa" classified (e.g., table salt, spice, food items) from the names themselves? The answer is "Nothing." There is nothing built into the term "table salt" that allows us to conclude that it is nested within "spice"; nor can we conclude from the word "spice" that it is a "food item." Compare this with the three taxon names Fagus L., Quercus L., and Fagaceae. Someone working with these three names can easily conclude- from simply the names themselves-that Fagus and Quercus are mutually exclusive (one can tell from the name itself that each term refers to a genus) and that Fagus is included within Fagaceae. The information is not complete (e.g., one cannot determine from the names themselves whether Querc us is nested within Fagaceae), but it still is highly useful in information retrieval. For example, one doing research on these three names knows that the information s/he finds for Fagus is not applicable to Quercus, because the two are mutually exclusive circumscriptionally. Phylogenetic nomenclators cannot have it both ways: They cannot claim that they can do away with all the ranks (and the problems they present) while retaining all the information that the ranks provide in our current system.

2. Binomials

Because phylogenetic nomenclature would abandon ranks, the system would also force the abandonment of functional binary nomenclature. The binomial might persist from a visual perspective (e.g., Lamium purpureum L. under the current system might continue to be Lamium purpureum), but it would not function nomenclaturally as a binomial. In other words, combinations would no longer occur. Again there is a loss of information with regard to set exclusivity, because the rank component of the binomial is lost. Taxonomists' ability to change a species forename (i.e., genus name) is useful when the original describer of the taxon was inaccurate in his or her taxonomic placement of the group. For example, a species of sedge that belongs to the genus Rhynchospora Vahl was originally described under the basionym Xyris triquetra Kuntze. Under a rankless system of nomenclature, in which a binomial effectively functions as a uninominal, the taxonomist could not correct this matter. Thus, some taxa could have the forename Xy ris L. even though they do not belong to the taxa Xyridaceae or Xyris.

Clearly, such a system will have less utility with regard to information retrieval. In a rankless system, someone doing an information search on the taxon Xyris could not assume that all information received for species with the forename Xyris applied to the taxon Xyris. Likewise, under such a system one could not assume that all species in the taxon Xyris had the forename Xyris.

Among rankless nomenclature advocates there is disagreement as to whether species should be recognized at all and if so, how they should be handled. Cantino et al. (1999) addressed the use of species names in phylogenetic nomenclature and presented thirteen options for dealing with species names. Meanwhile, Ereshefsky (1999, 2001), Mishler (1999), and Pleijel (1999) have argued that species should simply be abandoned. These disagreements present a serious obstacle to there ever being a single procedure for assigning names in phylogenetic nomenclature for taxa that are currently recognized as species.

Ereshefsky (1999: 296) noted that "species taxa, and only species taxa are assigned binomials." In botanical nomenclature (Greuter et al., 2000) this is incorrect, because all infrageneric names are binary, with the rank-denoting term serving as a connective (see Article 21). Thus in botany there is a generic name Dracunculus Mill. (Araceae) and Artemesia subg. Dracunculus Bessey (Asteraceae). Under the current system of botanical nomenclature these name are not homonyms, and both can be used in a given classification. However, under the PhyloCode (Cantino & de Queiroz, 2000) these two names could not be used simultaneously, because Article 9.2 clearly states that clades are to be designated using uninomials. Infrageneric names could be converted to uninomials through hyphenation (Artemesia-Drancunculus). However, as discussed earlier, this would not guarantee that revision in phylogenetic hypotheses might not change its position so that it was not in the taxon Artemesia. Furthermore, such a name might be con fused as representing a former species name (e.g., Artemesia dracunculus L.) that had been converted into phylogenetic nomenclature under one of the options for treating species by advocates of phylogenetic nomenclature (Cantino et al., 1999).

This is not a minor problem: The name Paniculatae has been used as an infrageneric (i.e., subgenus, section, series) epithet in at least 22 genera. The problem also extends to infrageneric autonyms (e.g., Rhynchospora VahI subg. Rhynchospora). Assuming that the name Rhynchospora would be reserved for the taxon currently recognized as a genus, what name would the autonymic subgenus (i.e., Rhynchospora subg. Rhynchospora) take?

V. Conclusions

Because names are basically a tool for communication, taxonomists need to address two questions: 1) Is the current system of biological nomenclature resulting in an unacceptable amount of miscommunication; and 2) Will the alternative phylogenetic nomenclature system do a better job of communicating information to all users of taxon names? I answer "No" to both questions. However, that is not to say that I have found the proposals put forth by the advocates of phylogenetic nomenclature to be without merit. I find phylogenetic definitions to be quite useful in communication when used in the context of a given phylogeny. However, for the numerous reasons expressed herein. I do not believe that this warrants the replacement of our existing system with this approach.

Taxonomists must not forget that most users of taxon names are not taxonomists. I believe the lack of information content from the name itself in a rankless approach to nomenclature and the serious risk of content change associated with the explicit phylogenetic definitions make this system inappropriate as a replacement for the current system of biological nomenclature. I believe phylogenetic nomenclature would be less useful to most users and, as Bowker and Star (1999: 7) noted, "[a]ny information systems design that neglects use and user semantics is bound for trouble down the line--it will either become oppressive or irrelevant,"

Under the phylogenetic nomenclature approach, I envision the classification process being placed on automatic pilot. Taxonomists would provide the explicit phylogenetic definitions and phylogenies, and the nomenclatural system would take care of the rest. This appears to be fine to some, such as Donoghue, who recently complained (quoted in Milius, 1999: 269) that "Renaming goes on on a daily basis. We're busy. We have better things to do. It doesn't make sense for scientists to be doing things like this." However, as opposed to having an explicit system (where the definitions do all the work), having an inexplicit system of nomenclature with the taxonomist playing a key role in the classification process (i.e., our current system) recognizes the "balancing act" (see Bowker & Star, 1999) that must go on in classification. As Bowker & Star (1999: 324--325) put it: "Classification schemes always represent multiple constituencies. They can do so most effectively through the incorporation of ambiguity--leaving cer tain terms open for multiple definitions across different social worlds: they are in this sense boundary objects. Designers must recognize these zones of ambiguity, protecting them where necessary to leave free play for the schemes to do their organizational work." I regard the current system as providing a higher level of "free play." This is best summarized by Wheeler (2001:15), who stated that traditional nomenclature "is stable enough to say what we know, flexible enough to accommodate what we learn; independent of specific theories, yet reflective of known empirical data; compatible with phylogenetic theory, but not a slave to it; particular enough for precise communication, general enough to reflect refuted hypotheses." Therefore, I answer "No" to the question I raised in the title of this article.

Lastly, in this time of severe threats to biodiversity, as well as efforts to conserve biodiversity, taxonomists must recognize the critical role they play in the description and identification of biodiversity. Discussion about nomenclature should take place, but taxonomists should not become bogged down in a debate about naming, or "book-keeping," as Stevens (2000) put it. As Wilson (quoted in DeFilipps, 2001: 11) noted, considering radical changes to our current codes of nomenclature would be like "rewriting the operating manual for the Titanic."

VI. Acknowledgment

The author acknowledges support from the Brooklyn Botanic Garden.

VII. Note

(1.) Other rankless approaches to nomenclature have been advocated (e.g., Harlin, 1998, 1999; Harlin & Sundberg, 1998; Ereshefsky, 1999, 2001; Mishler, 1999) that in one way or another differ from the approach outlined by de Queiroz and Gauthier (1990, 1992, 1994) and spelled out in detail in the PhyloCode (Cantino & De Queiroz, 2000). The discussion of "phylogenetic nomenclature" in this article refers to the de Queiroz and Gauthier approach presented in the PhyloCode. However, many of the issues raised herein could also he applied to these alternative approaches.

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Author:Moore, Gerry
Publication:The Botanical Review
Geographic Code:1USA
Date:Jan 1, 2003
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