A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Second Meeting of the International Society for Phylogenetic Nomenclature: a Report

The Second Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Yale University in New Haven from June 28 to July 2, 2006. In addition to contributed talks, the conference included symposia on phylogenetic nomenclature of species, phyloinformatics, and implementing phylogenetic nomenclature. Other discussion focused on recent controversial additions to the draft PhyloCode concerning the choice of names for total clades, and the Committee on Phylogenetic Nomenclature (CPN) was encouraged to revisit this issue. A proposal to permit emendation of phylogenetic definitions without CPN approval under certain circumstances was well received, and there was wide support for a proposed mechanism to use Linnaean binomina in the context of phylogenetic nomenclature without extending the PhyloCode to govern species names. The ISPN Council voted to expand the CPN from 9 to 12 members.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

A Perspective on Protistan Nomenclature

ABSTRACT. The nomenclature of protists is more complicated than that of plants or animals because more than one code of nomenclature applies (i.e. the taxa may be ambiregnal), because of the frequent absence of type material, and because of changing perspectives of the phylogenetic relationships of various groups of protists. These factors often lead to uncertainty over the meaning of names of taxa. If nomenclatural instability is to be avoided, some changes in current practices are required. The nature of the problems and some possible changes are discussed.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

Stems,nodes, crown clades,and rank‐free lists: is Linnaeus dead?

Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications, and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings, Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have gained strong support among some vocal theoreticians, and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In pratice, phylogenetic nomenclature will bc disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phlylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.     

The Linnaean system and its 250-year persistence

The Linnaean system of nomenclature has been used and adapted by biologists over a period of almost 250 years. Under the current system of codes, it is now applied to more than 2 million species of organisms. Inherent in the Linnaean system is the indication of hierarchical relationships. The Linnaean system has been justified primarily on the basis of stability. Stability can be assessed on at least two grounds: the absolute stability of names, irrespective of taxonomic concept; and the stability of names under changing concepts. Recent arguments have invoked conformity to phylogenetic methods as the primary basis for choice of nomenclatural systems, but even here stability of names as they relate to monophyletic groups is stated as the ultimate objective. The idea of absolute stability as the primary justification for nomenclatural methods was wrong from the start. The reasons are several. First, taxa are concepts, no matter the frequency of assertions to the contrary; as such, they are subject to change at all levels and always will be, with the consequence that to some degree the names we use to refer to them will also be subject to change. Second, even if the true nature of all taxa could be agreed upon, the goal would require that we discover them all and correctly recognize them for what they are. Much of biology is far from that goal at the species level and even further for supraspecific taxa. Nomenclature serves as a tool for biology. Absolute stability of taxonomic concepts—and nomenclature—would hinder scientific progress rather than promote it. It can been demonstrated that the scientific goals of systematists are far from achieved. Thus, the goal of absolute nomenclatural stability is illusory and misguided. The primary strength of the Linnaean system is its ability to portray hierarchical relationships; stability is secondary. No single system of nomenclature can ever possess all desirable attributes: i.e., convey information on hierarchical relationships, provide absolute stability in the names portraying those relationships, and provide simplicity and continuity in communicating the identities of the taxa and their relationships. Aside from myriad practical problems involved in its implementation, it must be concluded that “phylogenetic nomenclature” would not provide a more stable and effective system for communicating information on biological classifications than does the Linnaean system.     

The importance of designating type material for uncultured taxa

Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single amplified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.     

Classification of apocynaceae s.l. according to a new approach combining Linnaean and phylogenetic taxonomy

A new approach to a nomenclatural system, including elements from both Linnaean and phylogenetic nomenclature, is proposed. It is compatible with the existing Linnaean system, including "standard names" corresponding to principal and secondary ranks, and uses a variant of the definitions from the Phylocode system. A new infrafamilial classification, using this nomenclatural approach, of the Apocynaceae s.l. (i.e., including the Asclepiadaceae) based mainly on analyses of rbcL and ndhF data is discussed. Twenty-one tribes and four rankless taxa are defined.     

How objective are genera in euascomycetes?

Intra- and intergeneric distances derived from maximum-likelihood phylogenetic trees inferred from 254 nuclear ITS rDNA sequences were examined for seven families of euascomycetes, representing five classes. The intra- and intergeneric distances were well separated in most cases, but the distances varied between families. The analysis of the distance distributions provides a powerful tool for identifying certain taxa with highly deviating distances and thus cases of excessive lumping or splitting. Some cases of lumping and splitting found in different families are briefly discussed. The results of the analysis show that the generic concepts differ between the families. The consequences for nomenclature are discussed and a method abandoning binomial nomenclature while keeping the style of species names is recommended to ensure nomenclatural stability.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Advantages of naming species under the PhyloCode: An example of how a new species of Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) may be named

A new species of Discodorididae is described from the Pacific coasts of Mexico and Panama. It is named using a modified version of the epithet-based nomenclature proposed by Url Lanham 40 years ago. The species described here can be placed confidently in the clade Discodorididae, but not in any of its subclades (traditionally taxa of genus rank). The unique, epithet-based name of the species is “aliciae Dayrat, 2005”. The combination Discodorididae aliciae may also be used, once the unique, epithet-based name has been cited. Discodorididae aliciae is an example of how a new species of Discodorididae could be named in the context of phylogenetic nomenclature. I argue that epithet-based species names and their combinations with clade addresses should be very appealing to people who think phylogenetically. I also discuss two advantages of such combinations: first, they should be more stable than Linnaean binomials, which often change for arbitrary (e.g. non-phylogenetic) reasons; second, they should help taxonomists avoid creating multiple names for the same species.     

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.     

Suppression subtractive hybridization analysis reveals expression of conserved and novel genes in male accessory glands of the ant Leptothorax gredleri

An issue arising from recent progress in establishing the placental mammal Tree of Life concerns the nomenclature of high-level clades. Fortunately, there are now several well-supported clades among extant mammals that require unambiguous, stable names. Although the International Code of Zoological Nomenclature does not apply above the Linnean rank of family, and while consensus on the adoption of competing systems of nomenclature does not yet exist, there is a clear, historical basis upon which to arbitrate among competing names for high-level mammalian clades. Here, we recommend application of the principles of priority and stability, as laid down by G.G. Simpson in 1945, to discriminate among proposed names for high-level taxa. We apply these principles to specific cases among placental mammals with broad relevance for taxonomy, and close with particular emphasis on the Afrotherian family Tenrecidae. We conclude that no matter how reconstructions of the Tree of Life change in years to come, systematists should apply new names reluctantly, deferring to those already published and maximizing consistency with existing nomenclature.     

Name typification of Umbelliferae taxa described by Joseph Franz Freyn

Thirty-three new species and 12 new infraspecific taxa of the Umbelliferae have been described by Bohemian botanist Joseph Franz Freyn (1845–1903). The names of these taxa are typified, in most cases by material preserved at the Herbarium of the Moravian Museum (BRNM) in Brno. The names of nine species proposed by Freyn are accepted in the present-day nomenclature of the family; five others are the basionyms of presently accepted names. Type material from BRNM has enabled rehabilitation of the specific status of Angelica brachyradia Freyn from Bosnia and Pastinaca dentata Freyn & Sint. from Turkey. A new nomenclatural combination is proposed (Taeniopetalum urbani (Freyn & Sint. ex H. Wolff) Pimenov). Notes on the distribution of the taxa concerned are added.     

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree‐thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.