2008/02/01 by Philip D. Cantino, Richard G. Olmstead · 1 citation
Earth and Planetary Sciences · Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · Mathematics · #Evolution and Paleontology Studies #Genomics and Phylogenetic Studies #Plant Diversity and Evolution #Specifier #Biology #Tree (set theory) #Evolutionary biology #Mathematics #Combinatorics #Computer science #Artificial intelligence
paper · doi:10.1080/10635150701883873
openalex publication_date 2008/02/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/15
In a recent paper in this journal, Bertrand and Harlin (2006; henceforth BH e.g., de Queiroz and Gauthier, 1992, and references cited therein.) Specifically, B&H maintained that increasing the number of specifiers in a phylogenetic definition beyond the minimal two, which is often done to maximize compositional stability, reduces the universality of the names, and they therefore advocated using only two specifiers. We argue here that the problem created by using more than two specifiers was overstated by B&H and, secondarily, that universality (hereafter used in the sense of B&H) is not always desirable. The primary role for multiple specifiers is in the naming of a clade for which monophyly is well supported but within which the basal relationships are uncertain (e.g., for a node-based name) or for which the sister group is uncertain (e.g., for a branch-based name). In either case, using multiple specifiers permits construction of an explicit phylogenetic definition that will apply to the same clade composition under a variety of plausible phylogenies, whereas using only two specifiers increases the risk that further refinement in phylogenetic understanding will result in the name applying to a different clade composition than was intended. We consider it undesirable to sacrifice compositional stability (by reducing the number of specifiers) in order that users can apply the name in the context of a higher proportion of published phylogenies without considering external information. We believe that compositional stability, gained by using more than two specifiers when needed, is a more important goal of biological nomenclature than universality (in the sense of B&H). A second role for multiple specifiers—to restrict a clade name to a particular phylogenetic hypothesis—is also discussed briefly below. Specifiers are the species, specimens, and apomorphies that are cited in a phylogenetic definition as reference points to specify the clade to which the name applies (Cantino and de Queiroz, 2006). Every phylogenetic definition includes at least two specifiers, but it is common practice to use more than two. The reasoning of B&H was essentially as follows: (1) When applying a previously defined name to a new phylogenetic tree, every specifier in the definition must be present on the new tree in order to apply the name in the context of that tree (i.e., to identify the clade, if any, to which the name applies). (2) The probability that all of the specifiers in a phylogenetic definition will be found in any given tree decreases as the number of specifiers increases. (3) Therefore, increasing the number of specifiers beyond the minimum of two reduces the probability that the definition can be applied in the context of a wide range of trees— i.e., the universality of the name. They went on to argue that definitions should be restricted to two specifiers because maximizing universality of taxon names is more important than stabilizing taxon content. We disagree with their first premise and therefore their conclusions. To demonstrate their point, B&H took a number of names that have been phylogenetically defined in two groups (Lamiales [an angiosperm clade] and Foraminifera) and then inspected a series of published trees to see if they could identify the clades to which the names applied by finding the specifiers on those trees. In most cases, one or more of the specifier species were not present on the tree, and B&H concluded that the name could not be applied on that tree. Similarly, they concluded that any definition that used an apomorphy specifier could not be applied on a tree on which that apomorphy has not been optimized. B&H’s central premise—that every specifier must be present on a tree in order to apply a phylogenetically defined name in the context of that tree—assumes that