What's in a Name?

A special issue of Zootaxa has come out in the last week, under the title Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants. As the title indicates, it's a collection of papers discussing various aspects of the role(s) of nomenclature in taxonomy. Some of them are open-access via the link above, if you want to take a look, such as one by Alessandro Minelli discussing reaction to the Strickland Code of 1842, generally regarded as the first formal attempt to propose a set of regulations for taxonomic nomenclature. The Strickland Code was proposed to cover zoology, and Minelli presents a suggestion by Charles Bonaparte, vertebrate zoologist and nephew to the Emperor, that the Strickland Code or some variant thereof be extended to cover all biology, both zoology and botany. That suggestion, sadly, failed (long story short - the botanists felt that their nomenclature was in a pretty good state anyway, and while slack zoologists might need a code, the botanists were perfectly happy following the examples of Linnaeus and de Candolle), and the opportunity was lost to avoid a lot of subsequent irritation.

This post, however, will be devoted to another, more theoretically based paper by Alain Dubois - Dubois, A. 2008. Phylogenetic hypotheses, taxa and nomina in zoology. Zootaxa 1950: 51-86. (All quotes given below are taken from this paper.) Alain Dubois has published a whole series of papers on nomenclatorial theory in recent years, and while I'm guessing that he has probably given a lot more thought to the issues than I have, there were still a couple of things that didn't add up for me.

I should warn you, too, that Dubois (2008) is not an easy read. Dubois suffers from one of the most terrible afflictions to affect a theoretician - neologorrhoea, the overwhelming compulsion to coin new terminology*. The introduction of neologisms is not necessarily a bad thing - the cladistic revolution, for instance, carried a whole swag of new terminology. Some of these terms (e. g. synapomorphy, plesiomorphy) have become part of biology's everyday stock in trade. Others (e.g. adelphotaxon) - not so much. Time will tell how many of Dubois' neologisms gain currency.

*Spot the irony.

At the heart of Dubois' thesis is the superiority of the current hierarchical, onomatophore-based system (onomatophore, "name-bearer", is Dubois' replacement for the arguably more vague term type) over suggested phylogeny-based systems (most prominently the PhyloCode, though there are other such propositions).

Taxonomic paradigms have changed several times during the history of taxonomy, yet a single nomenclatural system, so-called Linnaean, has remained in force all along. It is theory-free regarding taxonomy as it relies on ostensional allocation of nomina to taxa, rather than on intensional definitions of nomina (e.g., “phylogenetic definitions”).

The supposed theory-free nature of the taxonomic codes as they currently stand is often cited as their main advantage. A creationist could follow the ICZN just as happily as anyone else. Phylogeny-based systems, for instance (or maybe, just to be really contrary, a quinarian system), may be closely tied to a particular paradigm of how organisms originate, or a specific model of the best way to interpret diversity. This is one of my personal reasons for doubt about such systems - the PhyloCode, for instance, works best as it currently stands with a branching model of evolution and speciation, and I think that it is worth asking to what extent that is really the best model to be using. However, the current hierarchical systems are not entirely theory-free. For instance, the binomial system that demands organisms be assigned to at least two taxa (genus and species) effectively demands the recognition of at least a certain proportion of paraphyletic taxa, because the common ancestor of two genera must itself be assigned to a genus. Totally ignoring the question of the virtues or otherwise of recognising paraphyletic taxa, I do feel the question needs to be asked whether it is even possible to develop a nomenclatorial system that is completely theory-free. And if not, then the question becomes what implicit theories we can best live with.

Whereas taxa can be cladistically defined by apognoses [apomorphy-based definitions] or cladognoses [tree-based definitions], nomina should remain attached to taxa through onomatophores, combined in some cases with a Principle of Coordination. Under such a system, the allocation of nomina to taxa is automatic, unambiguous and universal, and nomenclature does not infringe upon taxonomic freedom.

And this, I think, is where Dubois is just plain wrong. The allocation of names to taxa under the current system is far from "automatic, unambiguous and universal", as covered here in an earlier post. While designating Homo sapiens as the type of the family Hominidae automatically means that the one is always included in the other, this completely ignores the point that there is no governance on how far that "family" spreads. Hominidae might include H. sapiens only, it may include the bipedal clade only, it might include all apes, it might include all primates if you were feeling perverse enough. One might argue that this is what is meant by "taxonomic freedom" (though I don't think that this is necessarily what Dubois means), but if so, then is "taxonomic freedom" really worth it? This issue is, in my opinion, the major problem with the current systems. I don't actually have too great an issue with different names applying to the same taxon. What does cause no end of hassle is the same name applying to different taxa. Back to this point later.

In conclusion, for the time being, there exists no method for a general standardization of the “meaning” of ranks over the whole of zoology and palaeontology. The “meaning” of the rank family or genus is by no way equivalent in flatworms, beetles and birds. Therefore, any comparison between faunas or taxonomies using the ranks of taxa as a criterion (e.g., quantitative comparisons based on numbers of taxa at some ranks) is unwarranted and misleading (Minelli 2000). This statement was one of the main reasons why several recent authors rejected the use of ranks in taxonomy. But is this reason valid? It would be so only if nomenclatural ranks were viewed as identical with taxonomic categories, an opinion that is shared by many but that is questionable. Dubois (2005c, 2007a) proposed to recognize a basic distinction between these two concepts, stating that one refers to taxonomy and the other one to nomenclature.

The criteria of equivalence between taxa briefly reviewed above are of two kinds: biological and chronological. Biological criteria are all of limited use for equivalence, as they can be used only at low taxonomic levels (species and genus), and are not relevant in various situations. Chronological criteria are potentially general but face three problems (missing data, applicability only for synchronic taxa and taxonomic tradition) that preclude their implementation over the whole of zoology for the time being. This is true, but, as discussed below, the use of such criteria in some situations can however be informative as it allows to obtain useful information regarding the patterns of evolution. Sets of taxa defined by such criteria can be designated as taxonomic categories. Taxonomic categories are categories of taxa that share some common features and are equivalent by some taxonomic criterion. They do not provide information on cladogenetic relationships, but this information can be provided by nomenclatural ranks. On the other hand, nomenclatural ranks are nomenclatural tools which only provide information on the detailed hierarchical structure of a taxonomic hierarchy, but no information on the evolutionary peculiarities of the taxa in this hierarchy.

The first point here is a basic one that I have no quarrel with - ranks are not comparable between non-hierarchically related taxa. A "family" of birds is not comparable to a "family" of plants. This has lead to the suggestion that we should abandon the concept of ranks because too many people have an almost unconscious urge to make exactly that mistake, as shown, for instance, by widely-repeated statements such as "Rodentia is the largest order of mammals". However, Dubois maintains that, despite this, ranks remain useful because of what they can tell us about the relationships between hierarchically related taxa. If I know that Homo sapiens is a member of order Primates, family Hominidae and subfamily Homininae, I automatically know that Homininae is a subset of Hominidae, which is in turn a subset of Primates. The problem is that in order to be able to make that judgement, I have to know that those taxa are hierarchically related in the first place - in which case, I probably already know that Hominidae is a subset of Primates. The only case where this might be useful is if I found one reference that gave one higher taxon (family Hominidae, for instance) and another reference that gave another (subfamily Homininae). I would then be informed that Homininae is a subset of Hominidae, right? Wrong. Because then I come against the issue cited above, that these concepts lack definition. Homininae is always a subset of Hominidae, but how can I assume that the Hominidae of one author is the same as the Hominidae of another author? And if one author uses a broader concept for Hominidae, he might also use a broader concept for Homininae. One author's Hominidae might even be a subset of another author's Homininae. Overall, I think the hierarchical information potentially available from ranks is insignificant compared to the comparative disinformation encouraged by them.

This taxonomic hierarchical representation of phylogeny can be expressed nomenclaturally, and this is the role of ranks. Although ranks were not used for this purpose in the early days of taxonomy, it turned out that they can play this role very well. However, to use the nomenclatural hierarchy as a reflection of the structure of a cladogram or a phylogenetic tree requires a few assumptions. It seems that misunderstanding these assumptions played a role in the recent rejection of ranks by some taxonomists.

The first important assumption is that sister taxa must always be referred to the same nomenclatural rank (Raikow 1985; Sibley & Ahlquist 1990): they are therefore parordinate (Dubois 2006b: 827). Second, any taxon is subordinate to a single upper taxon, which must be referred to the just upper rank. It may be superordinate to two or more taxa of just lower rank. In such a system, the relations between all taxa that are connected by superordination, parordination or subordination are relations of coordination. In the absence of such relations between them, two taxa may be described as being in a relation of alienordination (from the Latin alienus, “foreign”, and ordo, “order”). Thus, in the recent AMPHIBIA, according to the cladistic relationships currently agreed upon by most authors (e.g., Frost et al. 2006), and according to the higher nomenclature of Dubois (2004a, 2005d), the taxon BATRACHIA is the sister-taxon of the GYMNOPHIONA: they are parordinate taxa that must be given the same rank, in this case that of superorder. Both are subordinate to the subclass NEOBATRACHI, and the superorder BATRACHIA is superordinate to the orders ANURA and URODELA. The latter are alienordinate to any other taxon that is not directly related to them by coordination, e.g., the GYMNOPHIONA. [Note that Dubois indicates suprafamilial taxa by printing them in capitals]

To his credit, Dubois is attempting to suggest a system that potentially answers my repeated grievance above - the question of what is a family. The hierarchy, according to Dubois, automatically indicates what taxon goes at what rank. If a family is united with another family in a higher taxon, and the next rank up from family is a superfamily, then that higher taxon has to be a superfamily. You can't skip a few ranks and call it a suborder.

The first complaint that might be made is the supposed shortage of named ranks compared to the total number of levels required. Dubois replies that by searching through the literature, he has collated a hierarchy of some 209 ranks. Aren't you glad we got that one sorted.

Also, the sister taxon of a family has to be another family. Towards the end of the paper, Dubois weighs in at length against what he calls "pseudoranked" classifications. Such classifications are those in which sister taxa are not placed at the same rank. According to Dubois, such "rankings" are meaningless because they are hierarchically uninformative. Hmm, he might have a point there. As an example of a pseudoranked classification, he takes part of the Amphibian Tree of Life of Frost et al. (2006 - poor Frost et al. has become a bit of a whipping-boy in these sorts of situations):

Taxon HYLOIDES 2006
      Taxon NOTOGEANURA 2006
            Taxon AUSTRALOBATRACHIA 2006
                  Familia BATRACHOPHRYNIDAE 1875
                        3 genera
                  Superfamilia MYOBATRACHOIDEA 1850
                        Familia LIMNODYNASTIDAE 1971
                              8 genera
                        Familia MYOBATRACHIDAE 1850
                              13 genera
            Taxon NOBLEOBATRACHIA 2006
                  Familia HEMIPHRACTIDAE 1862
                        1 genus
                  Taxon MERIDIANURA 2006
                        Familia BRACHYCEPHALIDAE 1858
                              15 genera
                        Taxon CLADOPHRYNIA 2006
                              Familia CRYPTOBRANCHIDAE 2006
                                    2 genera
                              Taxon TINCTANURA 2006
                                    Familia AMPHIGNATHODONTIDAE 1882
                                          2 genera
                                    Taxon ATHESPHATANURA 2006
                                          Familia HYLIDAE 1815
                                                Subfamilia HYLINAE 1815
                                                      38 genera
                                                Subfamilia PELODRYADINAE 1858
                                                      1 genus
                                                Subfamilia PHYLLOMEDUSINAE 1858
                                                      7 genera
                                          Taxon LEPTODACTYLIFORMES 2006
                                                Taxon CHTHONOBATRACHIA 2006
                                                      Familia CERATOPHRYIDAE 1838
                                                            Subfamilia CERATOPHRYINAE 1838
                                                                  6 genera
                                                            Subfamilia TELMATOBIINAE 1843
                                                                  1 genus
                                                      Taxon HESTICOBATRACHIA 2006
                                                            Taxon AGASTOROPHRYNIA 2006
                                                                  Familia BUFONIDAE 1825
                                                                        48 genera
                                                                  Superfamilia DENDROBATOIDEA 1850
                                                                        Familia DENDROBATIDAE 1850
                                                                              11 genera
                                                                        Familia THOROPIDAE 2006
                                                                              1 genus
                                                            Familia CYCLORAMPHIDAE 1850
                                                                  Subfamilia CYCLORAMPHINAE 1850
                                                                        11 genera
                                                                  Subfamilia HYLODINAE 1858
                                                                        3 genera
                                                Taxon DIPHYABATRACHIA 2006
                                                      Familia CENTROLENIDAE 1951
                                                            Subfamilia ALLOPHRYNINAE 1978
                                                                  1 genus
                                                            Subfamilia CENTROLENINAE 1951
                                                                  3 genera
                                                      Familia LEPTODACTYLIDAE 1838
                                                            11 genera
      Familia SOOGLOSSIDAE 1931
            2 genera

Dubois then converts this into a "properly" ranked classification using his system:

Anofamilia HYLAIDAI 1815
      Hyperfamilia HYLAIDIA 1815
            Epifamilia MYOBATRACHOIDIA 1850
                  Superfamilia BATRACHOPHRYNOIDEA 1875
                        Familia BATRACHOPHRYNIDAE 1875
                              3 genera
                  Superfamilia MYOBATRACHOIDEA 1850
                        Familia LIMNODYNASTIDAE 1971
                              8 genera
                        Familia MYOBATRACHIDAE 1850
                              13 genera
      Epifamilia HYLOIDIA 1815
                  Superfamilia HEMIPHRACTOIDEA 1862
                        Familia HEMIPHRACTIDAE 1862
                              1 genus
                  Superfamilia HYLOIDIA 1815
                        Familia BRACHYCEPHALIDAE 1858
                              15 genera
                        Familia HYLIDAE 1815
                              Subfamilia CRYPTOBRANCHINAE 2006
                                    2 genera
                              Subfamilia HYLINAE 1815
                                    Infrafamilia AMPHIGNATHODONTINEI 1882
                                          2 genera
                                    Infrafamilia HYLINEI 1815
                                          Tribus HYLINI 1815
                                                Subtribus HYLINA 1815
                                                      38 genera
                                                Subtribus PELODRYADINA 1858
                                                      1 genus
                                                Subtribus PHYLLOMEDUSINA 1858
                                                      7 genera
                                          Tribus BUFONINI 1825
                                                Subtribus BUFONINA 1825
                                                      Infratribus CERATOPHRYITA 1838
                                                            Clanus CERATOPHRYITOI 1838
                                                                  6 genera
                                                            Clanus TELMATOBIITOI 1843
                                                                  1 genus
                                                      Infratribus BUFONITA 1825
                                                            Clanus BUFONITOI 1825
                                                                  Subclanus BUFONILOI 1825
                                                                        48 genera
                                                                  Subclanus DENDROBATILOI 1850
                                                                        Infraclanus DENDROBATISOI 1850
                                                                              11 genera
                                                                        Infraclanus THOROPISOI 2006
                                                                              1 genus
                                                            Clanus CYCLORAMPHITOI 1850
                                                                  Subclanus CYCLORAMPHILOI 1850
                                                                        11 genera
                                                                  Subclanus HYLODILOI 1858
                                                                        3 genera
                                                Subtribus LEPTODACTYLINA 1838
                                                      Infratribus CENTROLENITA 1951
                                                            Clanus ALLOPHRYNITOI 1978
                                                                  1 genus
                                                            Clanus CENTROLENITOI 1951
                                                                  3 genera
                                                      Infratribus LEPTODACTYLITA 1838
                                                            11 genera
      Hyperfamilia SOOGLOSSAIDIA 1931
            Familia SOOGLOSSIDAE 1931
                  2 genera

Not only would this revised classification result in taxa very different from those used in the past - different names for many, and massively changed coverage for a number of names - it would also be highly unstable. For a start, imagine if a new taxon is discovered that is the sister taxon to Hylini exclusive of Bufonini in the classification above. That taxon would have to get its own tribe, and those two tribes together would have to become the infrafamily Hylinei, effectively moving Bufonini out of Hylinei. What was Hylinae would have to become Hylidae, and so on and so forth. What is more, for every taxon that has to move up a step, its sister taxon has to move up a step, so Bufonini becomes Bufoninei, Amphignathodontinei becomes Amphignathodontinae, and so on. And it should also be obvious that even if no new taxa are discovered, such a system is dependent on a stable phylogeny or other concept of relationship.

The Principle of Coordination is a major rule of the Code [i.e. the ICZN], which states that, within a nominal-series, among all the parordinate taxa that are subordinate to the same superordinate taxon, one, called in the Code the “nominotypical taxon”, must bear the same nomen (with the same nomenclatural author and date) as this superordinate taxon...

The existence of the Principle of Coordination in the Code results in this nomenclatural system being partly polysemic. In grammar and linguistics, monosemy applies to a situation where one word has only one meaning, whereas in polysemy one word has several meanings...

A few final words of caution must be added here regarding the meaning of the term eponymy. The situation it describes can be, and has been, confused with two other situations regarding biological nomenclature. Eponymy is the situation where the same nomen (same author, date and onomatophore) is used in the same ergotaxonomy [i. e. classification] as the valid nomen for several distinct, coordinate taxa. In contrast, homonymy is the situation where different nomina (generally with different authors, dates and onomatophores, with a few exceptions, when the same author used the same nomen for naming two different nominal taxa) are nomenclaturally available — which results in one of them, usually the junior one, being rejected as invalid. Finally, a third situation results from the fact that zoological nomina under the Code are not defined by closed intension or extension, but attached to taxa by ostension (Stuessy 2000, 2001; Keller et al. 2003). This results in the same nomen being liable to designate quite different taxa in different ergotaxonomies, the only requirement being that these taxa must include the onomatophore of this nomen. The reasons why this is highly preferable to a system of closed intension or extension were explained in detail elsewhere (Dubois 2005a, 2006c, 2007a): if a nomen corresponded to a strict, unchangeable definition and/or content of the taxon, a new nomen would have to be coined every time a subordinate taxon or even a specimen is added to the taxon or removed from it, so that there would be no continuity in the use of nomina and no simple way to understand the taxonomic history of a group, as is now possible through “synonymies” or more exactly logonymies (see Dubois 2000b). The situation here described, where the same nomen applies to different taxa, but in different ergotaxonomies, is neither homonymy nor eponymy, and its clear distinction from the latter two requires a special designation. For this situation, I propose the term astatonymy (from the Greek astatos, “unstable”, and onoma, “name”). This situation is extremely common in zoology, by far more than the situation where the nomen has always designated exactly the same taxon since its creation, which may be called menonymy (from the Greek meno, “I stay, I am stable”, and onoma, “name”).

Dubois doesn't regard the potential changes in his taxonomic system above as "real" changes, because there is no change in the type taxon. The different names at different ranks are, technically speaking, the same name with different terminations. I'm sorry, but while such a system may work well for establishing priority, it doesn't work as a practical guide. To the non-taxonomist, Homininae and Hominidae are different names, and when they are asked to think of them as identical, confusion is usually the result (trust me, I know). It's bad enough when Hominidae is always equivalent to Homininae - when it's only sometimes equivalent, things stop being just confusing and move on to hopeless. And while one might argue that taxonomists are the best-placed to judge the accuracy of taxonomies, one should never forget that, as often as not, it will be non-taxonomists who are the end-users.

The last part of this is Dubois' reply to my complaint about a "family" being a different thing to different authors, which is basically to say, "define different". If a taxon is effectively defined as the list of organisms (whether real or theoretical) assigned to that taxon, then even the discovery of a new organism could render it a "different taxon". You can smell the straw in this one. Nobody is going to claim that Vertebrata is a "different taxon" because of the description of a new species of rodent. What matters, essentially, are changes in the definition of the taxon - how we decide whether a given organism belongs to a given taxon or not. The current codes supply no working rules on definition.

Definitions of taxa are a matter of taxonomy, not of nomenclature. Different taxonomic “schools” use different kinds of definitions of taxa. Nowadays, no taxonomic school claims to be “Linnaean”, i.e., to use “Linnaean” definitions of taxa. There exist no such things as “ICZN-taxa” (Joyce et al. 2004) because the Code does not provide any guideline for defining taxa, being theory-free regarding taxonomy. In current taxonomy, only two kinds of definitions of taxa are widely used: phenetic definitions or diagnoses; and cladistic or “phylogenetic” definitions, or cladognoses (Dubois 2007a: 43).

Ultimately, I think this sums up the problem I'm having with Dubois' thesis. Dubois claims that the current system is preferable by virtue of being theory-free; my reaction is to ask whether a theory-free system is so great in the first place. Anarchy sounds like a wonderful system - we would all like to be able to live our lives exactly how we choose without anyone else's say-so. But it only works if one person's ideal doesn't clash with another person's ideal. And in an anarchy, no-one wants to be the one to unblock the toilet.

Dubois himself states near the beginning of the paper that "nomenclature is not a science but a technique, a tool at the service of taxonomy". And as I've said so many times before, the use of that tool is communication. In attempting to expunge theory from nomenclature, Dubois ultimately ends up eliminating the usefulness of that nomenclature in communication. It's like being presented with a specially-designed asparagus cooker, and then told that you can't have any asparagus. All you're left with is a complicated device that no-one can agree on how to use it.