Syst. Biol. 54(4):595–619, 2005 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/106351591007453 The Logical Basis of Phylogenetic Taxonomy PAUL C. SERENO Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th Street, Chicago, Illinois 60637, USA; E-mail: [email protected] Abstract.—Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The following points are made: (1) cladograms, rather than trees or hybrid clado- Downloaded from https://academic.oup.com/sysbio/article/54/4/595/2842925 by guest on 26 September 2021 gram-trees, provide the framework for the simplest graphical depiction of phylogenetic definitions; (2) a complete notational scheme for phylogenetic definitions is presented that distinguishes symbolic notation from shorthand and longhand versions; (3) phylogenetic definitions are composed of three components (paradigm, specifier, qualifier) arranged in two fundamental patterns—node and stem; (4) apomorphies do not constitute a fundamental definitional pattern but rather serve to qualify a stem-based definition (as do time and geographic range); (5) formulation of phylogenetic definitions involves three heuristic criteria (stability, simplicity, prior use); (6) reasoned definitional revision is encouraged and better defined (textual substi- tution, first- and second-order revision); and (7) a database, TaxonSearch, allows rapid recall of taxonomic and definitional information. [Content; definition; node; notation; PhyloCode; stem; taxonomy; TaxonSearch.] Phylogenetic taxonomy, as originally conceived does not entail endorsement of either phylogenetic tax- (Gauthier et al., 1988; de Queiroz and Gauthier, 1990, onomy or phylogenetic nomenclature. 1992) and as currently formalized in a draft code of nomenclature (draft PhyloCode, hereafter “dPC”; THEORETICAL FOUNDATION Cantino and de Queiroz, 2004), has not fully disen- gaged from two longstanding traditions of modern Phylogenetic taxonomy was founded on (1) the dis- Linnean taxonomy: (1) recourse to a phylogenetic tree tinction between taxonomic diagnosis and definition and ancestor-descendant lineages in graphical depic- (Ghiselin, 1966, 1984) and (2) a protocol for formulating tions and terminological definitions and (2) the contin- taxonomic definitions based on the branching topology ued use of morphology in addition to phylogeny in clade of phylogeny that identifies specific clades (de Queiroz recognition. and Gauthier, 1990, 1992). A brief history outlining how As shown below, these shortcomings have generated each of these founding propositions has fared is given be- unnecessary interpretive complexity, a flawed abbre- low. Both arose in direct response to the use of Linnean viational scheme, and the false equation of apomor- categorical ranks and the construction of trait-based tax- phies and taxonomic entities in phylogenetic definitions. onomic diagnoses, as practiced in traditional (precladis- Rather than addressing these fundamental issues re- tic) Linnean taxonomy and phylogenetic systematics. garding the logical foundations of phylogenetic defini- Other aspects of phylogenetic taxonomy are not novel, tions, advocates of the PhyloCode have focused their although sometimes misinterpreted as such. Restricting attention elsewhere: retrofitting “widely used” names to taxa to monophyletic groups (clades) that are presumed crown clades, devising associated naming conventions to have arisen from a common ancestor, for example, (e.g., “pan” prefix, “gens” suffix), revising/discarding is certainly not a proposition new to phylogenetic tax- the Linnean binomen, elaborating procedures for def- onomy but rather central to phylogenetic systematics initional priority, and establishing an official registry (Wiley, 1981; Scotland, 1992; Nixon and Carpenter, 2000, of phylogenetic definitions for new and converted taxa 2003). Discarding Linnean categorical ranks or redun- (Cantino et al., 1999; Gauthier and de Queiroz, 2001; dant (monotypic) taxa, likewise, is hardly unique to phy- Laurin and Anderson, 2004; Laurin and Cantino, 2004). logenetic taxonomy. Hennig (1966) and others (Nelson, In this article, “phylogenetic taxonomy” refers to the 1972; Farris, 1976; Løvtrup, 1977; Wiley, 1981; Avise and logic and procedures underpinning the construction of Johns, 1999) have offered a range of proposals to elimi- taxonomic definitions on the basis of phylogeny (de nate redundant taxa and either eliminate rank altogether Queiroz and Gauthier, 1992). Phylogenetic taxonomy or calibrate it with less arbitrary temporal or topological per se does not entail endorsement of a formalized information (for a recent review, see Ereshefsky, 2001). code governing taxonomic definitions (i.e., the dPC), for which the term “phylogenetic nomenclature” is reserved Diagnosis Versus Definition (de Queiroz and Gauthier, 1994). Neither of these terms Recently, Keller et al. (2003) provided an excellent his- should be confused or conflated with “phylogenetic sys- torical review of the debate regarding diagnosis and defi- tematics,” which has been widely used to refer to the gen- nition in taxonomy, so only a few key references are cited eral practice of Hennigian cladistics in the determination here. The argument is rooted in the philosophical posi- of phylogenetic relationships. Phylogenetic systematics tion that taxa (including species) represent individuals 595 596 SYSTEMATIC BIOLOGY VOL. 54 rather than classes (Ghiselin, 1966, 1974; Hull, 1976). Tax- sary and sufficient properties,” although this amounts to onomy, it followed, might better be viewed as an ex- a subtle distinction in so-called apomorphy-based defini- ercise in “systematization” rather than “classification” tions. To discern group membership one needs a branch- (Griffiths, 1974). ing diagram—an independent description of phylogeny In classification, diagnoses are used to delineate taxon based on observed characters. Most phylogenetic defini- membership on the basis of traits. Shared traits, hence, tions provide little or no information about identifying function at first glance like Aristotelian essences, as nec- traits within a clade. essary and sufficient properties for membership (Hull, Taxonomic diagnoses and phylogenetic definitions, 1965; de Queiroz and Gauthier, 1990; de Queiroz, 1992, thus, are readily distinguished operationally and, as a 1994). Indeed, this was clearly Linneaus’ original inten- result, are the subject of vigorous polemic over which tion (Ereshefsky, 2001). In reality, however, shared traits will provide a better foundation for delineation of taxa. Downloaded from https://academic.oup.com/sysbio/article/54/4/595/2842925 by guest on 26 September 2021 are rarely unique and nearly always subject to trans- Their philosophical underpinning, in contrast, seems not formation, loss, or dissociation. Linnean taxonomic di- to have affected proponents of either view and may well agnoses under an evolutionary paradigm, thus, operate remain an ineffective means to prefer one to the other. more like disjunctive definitions, in which some, but not all, traits are sufficient for group membership. If, on the other hand, taxa constitute unique histori- Protocol for Phylogenetic Definitions cal individuals produced by a natural system (biological Initial definitions.—The first phylogenetic definitions evolution), and if taxonomy is an attempt to capture the were coined prior to the appearance of a protocol for their singular tree of life, then taxa could be defined by some formulation. They appeared (ironically) within lengthy other means than shared traits—say, by the topology of taxonomic diagnoses in an analysis of saurischian di- the tree of life itself. Although the branching pattern nosaurs (Gauthier, 1986). Aves (in this case, crown-group of phylogeny remains a hypothesis subject to revision birds) was given a node-based definition, although def- and competing arrangements, a phylogenetic definition initional types had not yet been named. Six other def- could aspire to point to one, and only one, clade for initions were given, all stem-based and all delimiting any given phylogeny. In this way, taxa could be defined taxa whose basal members were extinct (Saurischia, ostensively simply by “pointing at them” (Ghiselin, 1974, Theropoda, Tetanurae, Coelurosauria, Maniraptora, 1995; de Queiroz, 1988a; de Queiroz and Gauthier, 1990). Ornithurae). Linnean categorical ranks were eliminated. Later, the relationship between a phylogenetic definition Gauthier et al. (1988) and Estes et al. (1988) pub- and its designated taxon was interpreted as nominalist, lished 35 phylogenetic definitions for Lepidosauromor- such that a taxon was merely an abbreviation for its def- pha and its major subgroups, clearly distinguishing inition, which amounts to a description based on mono- definition from diagnosis (see also de Queiroz, 1988a). phyly (de Queiroz, 1992, 1994). Others have countered Definitions now regarded as node-based were used that constructing such taxonomic definitions is as essen- exclusively for crown groups; stem-based definitions tialist as trait-based diagnoses (Frost and Kluge, 1994), were used sparingly for a few higher taxa with ex- because “they appear to be