2011 POINTS OF VIEW 887 Downloaded from sysbio.oxfordjournals.org Syst. Biol. 60(6):887–892, 2011 Published by Oxford University Press on behalf of Society of Systematic Biologists 2011. DOI:10.1093/sysbio/syr070 Advance Access publication on August 24, 2011 Phylogenetic Nomenclature, Three-Taxon Statements, and Unnecessary Name Changes by guest on October 18, 2011 1, 2 KEVIN DE QUEIROZ ∗ AND MICHAEL J. DONOGHUE 1Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA; and 2Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8106, USA; ∗Correspondence to be sent to: Division of Amphibians and Reptiles, National Museum of Natural History, Smithsonian Institution, PO Box 37012, NHB, W-200, MRC 162, Washington, DC 20013-7012, USA; E-mail: [email protected]. Received 4 April 2011; reviews returned 13 June 2011; accepted 16 June 2011 Associate Editor: Frank E. Anderson Criticisms of phylogenetic nomenclature (see de Platnick’s argument involves a numerical comparison Queiroz and Gauthier 1994) and of the PhyloCode of the information content, as measured by implied (Cantino and de Queiroz 2010) have been addressed three-taxon statements (propositions about cladistic re- in the literature (e.g., de Queiroz 1997, 2006; Cantino lationships), of what he called “Linnaean classification” 2000; de Queiroz and Cantino 2001; Lee 2001; Bryant versus a “node-based system” (we place these terms in and Cantino 2002; Laurin et al. 2005; see http://www. quotation marks to indicate that they are misleading, as phylonames.org/ [literature/replies to critiques] for ad- will be explained below). Here, we show that Platnick’s ditional references). Many of the supposed problems re- negative conclusions about phylogenetic nomenclature sult from misunderstandings, whereas others can and are incorrect and result from inappropriate compar- have been dealt with by making appropriate adjust- isons. Moreover, they are based on a criterion that is ir- ments (including changes in the PhyloCode). One re- relevant for comparing different approaches to nomen- cent argument against phylogenetic nomenclature has clature. When a nomenclaturally relevant criterion is not yet been addressed, at least not in print. That argu- used, phylogenetic nomenclature outperforms its rank- ment was presented by Platnick in a debate that took based counterpart in all of the examples considered by place at the Linnean Society of London on 5 December Platnick. 2005 and was later published in his “Letter to Linnaeus” (Platnick 2009). Although we responded to Platnick’s ar- gument verbally during the debate, we take the oppor- THREE-TAXON STATEMENTS tunity to do so here because some readers of his letter Platnick’s comparisons are based on an example may believe that his conclusions are damaging to phy- originally used by de Queiroz and Gauthier (1994) logenetic nomenclature. to illustrate the consequences of phylogenetically 888 SYSTEMATIC BIOLOGY VOL. 60 defined names in the context of a new hypothesis of [unranked] Agamidae (ABCDEFGHI) phylogenetic relationships. In that example, Agamidae [unranked] Chamaeleonidae (GHI) and Chamaelonidae (two lizard taxa traditionally ranked allows one to deduce only 18 three-taxon statements: as families) are composed of species that are origi- (GH)A, (GH)B, and so forth, representing a reduction nally thought to be mutually exclusive in terms of in the information content of the classification by about their cladistic relationships (Fig. 1a), but a new phy- 71%. logenetic hypothesis suggests that some of the species We do not dispute the number of three-taxon state- referred to Agamidae are more closely related to the ments that can be deduced from the two taxonomies; species in Chamaeleonidae than to other species in Agami- however, the comparison itself is inappropriate in that dae (Fig. 1b). This example is simplified from a real it matches a “Linnaean classification” under the original case described by Frost and Etheridge (1989), and phylogenetic hypotheses against a “node-based classi- Platnick’s presentation of it implicitly but incorrectly fication” under the new phylogenetic hypothesis. Ap- placed Agama in Clade ABC, which he treated as more propriate comparisons would use either the original distantly related to Chamaeleonidae than is clade DEF phylogenetic hypothesis or the new hypothesis, not a (under the new phylogenetic hypothesis). We have cor- mixture of the two. If we use the original hypothesis, rected his examples by applying names based on the the “node-based classification” name Agama to Clade DEF, the one that is more closely [unranked] Agamidae (ABCDEF) related to Chamaeleonidae, and we have applied a real [unranked] Chamaeleonidae (GHI) name (based on the name Leiolepis) to the more distantly related clade ABC. We have also added the more inclu- allows one to deduce the same 63 three-taxon state- sive taxon Acrodonta (which was not ranked but could ments as does the equivalent “Linnaean classification”; Downloaded from have been ranked as an infraorder) as it is relevant to no information is lost. Note that considering the taxa some of the examples. These changes were made for the to be unranked is irrelevant as phylogenetic nomencla- sake of accuracy, thus better connecting the examples ture does not prohibit the use of ranks. The only rele- vant consideration is that application of the names is de- to previous literature; none of them affect Platnick’s or sysbio.oxfordjournals.org our own conclusions about the number of implied three- termined by phylogenetic definitions. Conversely, if we taxon statements. use the new phylogenetic hypothesis, then a “Linnaean Under standard node-based phylogenetic definitions classification” based on uniting (lumping) the two fam- based on the original hypotheses of composition (Fig. 1), ilies (as in the actual proposal of Frost and Etheridge 1989) for the same two nested clades considered in the the names “Agamidae” and “Chamaeleonidae” end up by guest on October 18, 2011 referring to nested rather than mutually exclusive taxa “node-based classification” under the new phylogenetic hypothesis (Fig. 1b). Accor- Family Chamaelonidae (ABCDEFGHI) ding to Platnick, the original “Linnaean classification” Subfamily Chamaeleoninae (GHI) allows one to deduce the same 18 three-taxon statements Family Agamidae (ABCDEF) as under the corresponding “node-based classification.” Family Chamaeleonidae (GHI) Thus, regardless of whether the application of taxon names is governed by rank-based or phylogenetic defi- allows one to deduce 63 three-taxon statements: (AB)G, nitions, the taxonomies contain exactly the same amount (AB)H, AB(I), (AC)G, and so forth, whereas the “node- of information in the form of implied three-taxon based classification” statements. FIGURE 1. Example used by de Queiroz and Gauthier (1994) to illustrate the application of names under phylogenetic nomenclature in the context of different hypotheses of phylogenetic relationships. a) Original phylogenetic hypothesis, b) new phylogenetic hypothesis. Open and filled circles in the original example have been replaced with the letters A–F and G–I (respectively), aswasdoneby Platnick (2009), and the more inclusive taxon Acrodonta has been added. For the examples involving phylogenetically defined names in the sections Three-Taxon Statements and Unnecessary Name Changes, the following standard node-based definitions are used: Acrodonta = the smallest clade containing both A and G; Agamidae = the smallest clade containing both A and D; Chamaeleonidae = the smallest clade containing G, H, and I; Leiolepidinae = the smallest clade containing A, B, and C; Agaminae = the smallest clade containing D, E, and F. 2011 POINTS OF VIEW 889 The “Linnaean classification” based on lumping the [New name required] (DEFGHI) two families, as used in de Queiroz and Gauthier’s Agaminae (DEF) original example, is not the only possible way to make Chamaeleonidae (GHI) all names refer to monophyletic taxa under the new phylogenetic hypothesis and rank-based nomenclature. This taxonomy implies exactly the same number of Thus, Platnick considered two alternative “Linnaean three-taxon statements (81) as does the fully subor- classifications” under the new phylogenetic hypothesis: dinated “Linnaean classification.” In this case, both first, a taxonomy based on dividing (splitting) the family Acrodonta and Agamidae are considered candidate names Agamidae, rather than lumping it with Chamaeleonidae, for the largest clade because the PhyloCode is not yet but leaving the more inclusive clades (ABCDEFGHI and in operation and therefore precedence between those DEFGHI) unnamed: names has not been established. Thus, when appropriate comparisons are made Leiolepididae (ABC) between taxonomies (i.e., those based on the same phy- Agamidae (DEF) logenetic hypothesis and involving the same named Chamaeleonidae (GHI) clades), those taxonomies contain exactly the same And second, a fully subordinated taxonomy based on amount of information in terms of implied three-taxon both splitting and lumping in which all five hypothe- statements regardless of whether the taxon names are sized clades are named: governed by rank-based or phylogenetic nomenclature. This conclusion should be neither controversial nor sur- Chamaeleonoidea (ABCDEFGHI) prising because the information is contained in the tax- Leiolepididae (ABC) onomies, not in the names.