Stability and Universality in the Application of Taxon Names in Phylogenetic Nomenclature

A major task for biological nomenclature and taxonomy is to provide names and tools for communication about biodiversity. This is even more important in times of bioinformatics where scientists often search GenBank and other databases for phylogenetic information. Comparative studies on a large number of unrelated taxa by scientists that are not taxonomic specialists are likely to become even more common in the future. Hence, a nomenclatural system that helps scientists to unequivocally find information about a particular taxon has high priority. One step towards achieving such a system is the phylogenetic system of nomenclature (PSN) initially developed by de Queiroz and Gauthier (1990, 1992). The PSN differs from traditional rank-based nomenclature (RSN) in that it avoids the connection of a name to a particular taxonomic rank and type. And perhaps more importantly, PSN utilizes more than one reference point (i.e., specifiers) for each name. A major advantage with two specifiers (instead of one type) is that given the specifiers and a phylogenetic tree (including the specifiers), it is rather straightforward to find out the extension of the taxon in question. This is much more difficult within an RSN because the extension of a taxon name is not spelled out in a formal definition. Thus, the PSN seems ideal to provide taxonomic information to users in an explicit and unequivocal way. This is indeed an important task for nomenclature and taxonomy in the future. Nevertheless, the merits of PSN, as compared to RSN, are still controversial and much debated in systematics. Much of this debate concerns what is meant by a name and the importance of taxonomic stability. While proponents of RSN often highlight the importance of taxonomic content, proponents of PSN instead highlight the importance of common ancestry (Bryant and Cantino, 2002). Taxonomic stability, also referred to as stability in content (Lee, 1996) and circumscriptional stability (Moore, 1998), corresponds to the stability in the extension of names and is measured in terms of all taxa included in a group referred to by a name; taxa missing in each application of a name compromises this stability (Nixon and Carpenter, 2000). Related to the issue of stability is the importance for a taxonomic name to be applicable in a wide range of biological contexts; i.e., to have high universality. In phylogenetic nomenclature high universality for a phylogenetic name (hereafter referred to as phylonames) should mean that it could be used in a wide range of phylogenetic analyses and trees. And, as a corollary, high universality of a name also implies that all biologists should use the same name for the same taxon (de Queiroz, 1997; see also Harlin, 2003, 2005). Although initially agnostic on the issue on taxon content, proponents of PSN have lately come up with methods to stabilize taxonomic content when the choice of phylogenetic hypotheses shift. One such method is to increase the number of specifiers used in a taxon name definition. In the present paper we argue that there is a trade-off between stability and universality in terms of number of specifiers. That is, the current trend in PSN to emphasize stability in content by increasing the number of specifiers in phylogenetic definitions is actually limiting the communication efficiency of phylonames. Thus, even if this practice may increase taxon content stability, it tends to compromise the universality in the application of these names. And the effect may be that we lose the advantage gained by introducing PSN as a replacement for RSN in the first place.