Naming taxa from cladograms: A cautionary tale

Most biologists nowadays agree that biological classification should provide information on the phylogenetic relationships between organisms. Although the real tree of life will probably remain unknown, at least in its details, hypotheses can be proposed regarding the structure of this tree, and these hypotheses (cladograms) can be taken as a basis for building classifications (taxonomies). Once recognized by biologists, taxonomic units or taxa (singular taxon) are usually denominated by “scientific names” or nomina (singular nomen; Dubois, 2000). Although often confounded, the two processes are distinct: taxa can be recognized but not named (e.g., in systems called “numeric latures”; e.g., Johnson, 1970) and nomina can be created without designating taxa (e.g., the nomina nuda of zoological and botanical nomenclatures). In order for nomina to allow efficient, unambiguous and universal communication among biologists, their allocation to taxa requires following precise and stringent rules. Several nomenclatural systems have been and still are used by biologists.

In zoology, the traditional nomenclatural system is described in the International Code of Zoological Nomenclature (Anonymous, 1999, Polaszek and Wilson, 2005), sometimes abbreviated ICZN, and designated below as “the Code”. Among others, a new system of nomenclature for living organisms, initially called “phylogenetic nomenclature” (De Queiroz and Gauthier, 1990, De Queiroz and Gauthier, 1994), was recently formalised in the project of a new code called “the Phylocode” (Laurin and Cantino, 2004; <http://www.ohiou.edu/phylocode>; see also Dubois, 2005a: note 6). This new system has elicited a number of comments, both favorable (recent references: Pleijel and Rouse, 2003, Donoghue and Gauthier, 2004, Laurin and Cantino, 2004, Laurin et al., 2005, Laurin et al., 2006, De Queiroz, 2006) and unfavorable (recent references: Kraus, 2004, Sluys et al., 2004, Dubois, 2005a, Pickett, 2005a, Pickett, 2005b, Rieppel, 2006). The purpose of the present paper is not to discuss again the respective merits of the Code and of the Phylocode, but to address a specific question: can the same nomina be available and valid under both systems, and if so under which conditions?

This question is not only theoretical, as will be shown here with the detailed analysis of the nomenclatural problems posed by a recent paper (Hillis and Wilcox, 2005). The Code and the Phylocode are widely distinct nomenclatural systems, as they rely on different theories of nomenclature. The use of a nomenclature following the Code, either alone or in parallel with a nomenclature following the Phylocode for the same taxonomy, requires a good understanding and knowledge of the Code. To be valid under the Code, a nomen must have strictly followed the rules in force at several distinct steps of the nomenclatural process. As any juridical text, the Code is not a simple, “self-speaking” text that could be mastered by simple intuition or an impressionist approach, but its proper use requires spending some time and effort reading and understanding it (Dubois, 2005a). Some of the problems raised in the example analysed here are not unique to this publication and, if no care is taken from the part of editors and referees of scientific publications, they may tend to become more and more frequent, thus contributing to undermining the universality and reliability of zoological nomenclature. Starting from this paper, the following problems are discussed below: (1) the publication of nomina nuda for taxa recognized on the basis of a cladogram, often obtained from molecular data, but for which no diagnostic characters are provided; (2) the invalid use of junior homonyms; (3) the invalid use of junior synonyms; (4) the use of ranks not allowed in the current Code; (5) problems in the etymological formation of nomina.

Full understanding of the text below requires a few preliminary clarifications:

• (1)

  A distinction is made between taxa and clades. Although the aim of taxonomy is to provide a classificatory scheme that accounts for the patterns of evolution and phylogeny of organisms, a distinction is made here between these patterns or clades, and taxa. Taxa are concepts or models used in biological classification, that account for some particularities of the organisms. Under a cladistic approach of taxonomy, a taxon can be recognized only for a group of organisms that is considered holophyletic, a concept for which the synonymous terms phylon (Dubois, 1991), cladon (Mayr, 1995) and phylo-taxon (Joyce et al., 2004) have been coined. The decision to recognize such taxa for some organisms rests on hypotheses about the real clades of the real world, but these taxa are concepts, not the clades themselves. Thus, if clades may be viewed ontologically as individuals, it is not the case of taxa, which are classes of organisms, recognized on the basis of criteria such as hypothesized relationships.

• (2)

  Further distinctions are made between taxa and nomina, and between nomina and ranks. Taxa are taxonomic classes of organisms, whereas nomina are “just” labels given to these taxa to designate them unambiguously and universally, but without any explanatory, descriptive or other rôle or value by themselves (Dubois, 2005a, Dubois, 2005b, Dubois, 2006a). This distinction is clear in the Code, but not so in the Phylocode. The Code only provides rules for the allocation of nomina to taxa, not for the definition of taxa, so that there exists no such things as “ICZN-taxa” (Joyce et al., 2004), whereas in the Phylocode the definition of the taxon and of the nomen are simultaneous. It is fully conceivable to define taxa under the philosophy of the Phylocode (e.g., by node-based, stem-based or apomorphy-based definitions), but to name them under the Code philosophy (using onomatophores and nominal-series). Ranks as used in the Code are distinct from nomina. The same nomen can be used to designate distinct (i.e., more or less inclusive) taxa at different ranks in the nomenclatural hierarchy. This is because of the existence in the Code of a Rule of Coordination, discussed in more detail below. No Rule of Coordination exists in the Phylocode.

• (3)

  In a paper like this, adjectives or other devices are needed to qualify the rules or principles that follow the two basic philosophies of nomenclature discussed here. This need appears in all recent publications devoted to a discussion or comparison of these two systems, but no satisfactory solution has been found so far. Phrases such as “names governed by the Phylocode” or “names governed by the preexisting rank-based codes”, as found e.g., in Article 6.1 of the draft Phylocode, are too cumbersome to be used repeatedly in a publication. Adjectives directly based on the terms Code and Phylocode, such as “codian” or “phylocodian”, would be barbarisms, as are compound names based on abbreviations, such as “ICZN-taxon names” (Joyce et al., 2004). The use of an adjective like “phylogenetic” to designate nomenclature under the Phylocode is not appropriate as it would seem to mean that nomenclature under the Code is not compatible with a taxonomy based on cladistic hypotheses, which is simply wrong. Lidén et al. (1997) found an elegant and unpolemical way to designate the two systems, calling the Code “Charlie” and the Phylocode “Phyllis”, but these names do not allow the formation of clear, short and euphonious adjectives. Another solution to this problem may be to call both systems after the patronyms of their original proponents. The adjective “Linnaean” has been widely used to designate the nomenclature following the Code, but this is largely misleading (Moore, 2003, Dubois, 2005a) as the rules of the latter are widely different from the original nomenclatural rules of Linnaeus (1758). It would be more justified to call these rules “Linnaean and Stricklandian” or “Linnaean-Stricklandian”, to do justice to the major contribution of the so-called “Strickland’s code” (Strickland et al., 1843) to the building of the current Code. A counterpart to this denomination for the Phylocode would be “Queirozian and Gauthierian”, or “Queirozian-Gauthierian”, although in this case also the system initially proposed by De Queiroz and Gauthier, 1990, De Queiroz and Gauthier, 1994 has gone through important changes since then. I proposed elsewhere (Dubois, 2005a, Dubois, 2006a) the shorter term “Queirauthian”, a combination–contraction of the latter denomination, which in my mind was in no way “insulting”, but it was apparently understood as such by some readers, so I suggest abandoning it; furthermore, use of this denomination might be embarrassing for the authors of this system. Another possibility is to use terms based on some of the particularities of the nomenclatural systems at stake, but the choice of terms must be done carefully as some designations may be misleading. Thus, the current Code is certainly “rank-based”, but the nomenclatural philosophy of the Code would not be drastically changed if the Code abandoned ranks, as exemplified by the rules proposed by Dubois (2006a) for the nomenclature of higher taxa. The genuine basic difference between the two systems is the way nomina are allocated to taxa, by pointing to onomatophores in the Codeand by phylogenetic definitions in the Phylocode (Dubois, 2005a). The first system can thus be called “onomatophore-based”, and the second one “definition-based”. These designations are neuter, unpolemical, and they designate accurately the main difference between the two systems, so they will be used below. Alternatively, the expressions “ostension-based” and “intension-based”, which have the same meaning (see below), can also be used, but they may appear less familiar to many readers.

• (4)

  In the discussion below, generic and specific nomina following the Code are written as they have been in most publications for more than one century, i.e., in small characters Italics: Lithobates or Lithobates Fitzinger, 1843. In contrast, nomina following the Phylocode are written under the format proposed by Dubois (2005a): 〈Lithobates〉, 〈Lithobates Hillis and Wilcox, 2005〉 or 〈Lithobates [Fitzinger, 1843] Hillis and Wilcox, 2005〉. The philosophy behind this proposal is discussed at more length in the Conclusion of the present paper.