BwlagicalJoumal ofthc Linnean .So&& (1997),62: 495-503. With 2 figures Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names HAROLD N. BRYANT Provincial Museum of Alberta, 12845-102 Avenue, Edmonton, Alberta T5N OM6, Canada Received 1 5 November 1996; acceptedfor publication 3 31441997 A phylogenetic definition of a taxon name associates that name with a clade through its reference to a particular ancestor and all of its descendants. Depending on one’s perspective, phylogenetic definitions name either clades on the one true, but unknown, phylogeny, or components on cladograms (clades on hypotheses regarding the true phylogeny). Phylogenetic definitions do not contain enough information to iden* Components without a reference cladogram. As a result, (1) if clades are equated with components on cladograms, a phylogenetic definition may associate a taxon name with different clades on different cladograms, and (2) the inclusiveness, diagnostic synapomorphies, and distribution in time and space of the clade with a particular name can differ markedly depending on the phylogenetic hypothesis one chooses to adopt. This potentially unacceptable lability in the clade to which a name refers can be avoided by using a taxon name in conjunction with only phylogenetic hypotheses on which specific taxa are related in a particular fashion. This de@nated phyfogmtic context can be described in an n-taxon statement that would be appended to the phylogenetic definition. Use of the taxon name would be considered inappropriate in conjunction with cladograms on which the relationships contradict those in the n-taxon statement. Whereas phylogeneticdefinitions stabilize the meaning of taxon names, designated phylogenetic contexts would stabilize the usage of those names. 0 1997 The Linnean Society of London ADDITIONAL, KEY WORDS:-clade - component - crown clade - n-taxon statement phylogenetic taxonomy. CONTENTS Introduction . . . . . . . . . . . . . . Perspectives on phylogenetic definitions and clades Cladistic information in phylogenetic definitions . Designated phylogenetic context . . . . . . Acknowledgements . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496 496 497 500 502 502 Correspondence to: Harold N. Bryant, present address: Royal Saskatchewan Museum, 2340 Albert Street, Regina, Saskatchewan S4P 3V7, Canada. 0024-4066/97/I20495+09 $25.00/0/bj970170 495 Q 1997 The Linnean Society of London H. N. BRYANT 496 INTRODUCTION A taxonomy is a scheme of names that can represent either internested classes (a classification)or the product of a system, such as common descent (Griffiths, 1974; de Queiroz, 1988). Although the principle of common descent is the central tenet of modern biology, current biological taxonomy is based on the pre-Darwinian Linnean hierarchy. De Queiroz & Gauthier (1990, 1992, 1994) have outlined the basic framework of an alternative, truly phylogenetic taxonomy, with principles and rules that are formulated based on the principle of common descent. Thus, phylogenetic taxonomy is that part of phylogenetic systematics that represents phylogenetic relationships through a system of names (de Queiroz & Gauthier, 1992). Given that taxa are historical entities (species, clades), “taxon names are names of clades” (de Queiroz & Gauthier, 1992:452) or species. The names of clades are defined through reference to a particular common ancestor and all of its descendants (Ghiselin, 1984). For example, the name of the clade (A, B) on the left cladogram in Figure 1 could have the node-based definition ‘the most recent common ancestor of A and B and all of its descendants’. Taxon names can also be defined using stem- or apomorphy-based definitions (de Queiroz & Gauthier, 1990; see below). The characteristics (inclusiveness, diagnostic synapomorphies, distribution in time and space) of the clade named through a phylogenetic definition depend upon the phylogenetic hypothesis (cladogram) one chooses to adopt as a reference point (de Queiroz & Gauthier, 1990; Schander & Thollesson, 1995; Bryant, 1996); as a result, the characteristics of the clade with a particular name can differ considerably on different cladograms. For example (Fig. l), although the phylogenetic definition above refers to the clade consisting of only taxa A and B on the left cladogram, on the right cladogram this definition refers to the clade consisting of all five taxa. This lability in the inclusiveness, or other characteristics, of clades with particular names is associated with the limited information regarding phylogenetic relationships in phylogenetic definitions. This limited cladistic information might be perceived as allowing unacceptably high instability in the clade with a particular taxon name as that name is used on cladograms with differing topologies. I propose a mechanism to deal with this problem whereby taxon names in phylogenetic taxonomy would be used in conjunction with only particular phylogenetic relationships among specific taxa. A B C D E B C D A E Figure 1. Two hypotheses of relationships among five taxa, illustrating that a change in the phylogenetic position of a single taxon (A) can result in no equivalent components on the two cladograms despite the fact that the relationships among the other taxa are the same. PERSPECTIVES ON PHYLOGENETIC DEFINITIONS AND GLADES The perceived necessity of restricting the use of taxon names to only certain phylogenetic hypotheses may be influenced by one’s perspective regarding the clade DESIGNATED PHYLOGENETIC CONTEXTS FOR TAXON NAMES 497 to which a phylogenetic definition refers. Alternative perspectives are implicit in differing claims made by de Queiroz & Gauthier (1994) and Bryant (1996). De Queiroz & Gauthier (1994:30) argued that “under a phylogenetic system of nomenclature, names retain their associations with particular clades or ancestors despite changes in ideas about relationships”. This statement contrasts with the claim that the association between taxon names and clades depends not only on the phylogenetic definition of the name, but also on the particular cladogram one uses as a reference (Bryant, 1996). Using two contrasting phylogenetic taxonomies of the Carnivora that were based on different phylogenetic hypotheses (Wolsan, 1993; Wyss & Flynn, 1993),Bryant (1996)argued that some phylogenetic definitions referred taxon names to different clades on the two reference cladograms. The view that a phylogenetic definition associates a name with the same clade regardless of the phylogenetic hypothesis one uses as a reference (e.g. de Queiroz & Gauthier, 1994) appears to be based on the fact that, given the assumption that one true phylogeny exists, a phylogenetic definition will associate a taxon name with only one particular clade on that phylogeny. From this perspective, which focuses on the true phylogeny and sees that phylogeny as providing the stable reference point for the identification of clades, our phylogenetic hypotheses do not i d e n e clades but instead make claims as to the content and other characteristics of those clades. Because the phylogenetic definition is considered as the mechanism for permanently linking a taxon name to one clade on the true phylogeny, limiting the usage of names to only particular phylogenetic contexts might seem to be unnecessary (but see below). The perspective implicit to Bryant (1996) focuses, not on the true phylogeny, but instead on our hypotheses regarding that phylogeny. From this perspective clades are identified through phylogenetic analyses and are equated with components on cladograms. Given that there may be several hypotheses regarding the phylogeny of a particular group of taxa, identification of the same individual clade on two or more cladograms becomes an issue, as does the question of whether a phylogenetic definition refers a taxon name to the same clade on different cladograms. Recognition of this perspective is important to understanding the arguments in Bryant (1996), especially the claim that the identity of the individual clade referred to by a phylogenetic definition of a taxon name depends on which cladogram one chooses as the reference point. Because, from this perspective, the association between taxon names and clades is not fixed by phylogenetic definitions, the need for limiting the use of names to only certain phylogenetic hypotheses (cladograms) may be more apparent. CLADISTIC INFORMATION IN PHYLOGENETIC DEFINITIONS Phylogenetic definitions of taxon names lack sufficient information to identlfir a particular component in the absence of a reference cladogram. Wilkinson (1994: 344) defined components as “statements of relationships that apply, through inclusion or exclusion, to all taxa under consideration”. A component is a type of cladistically informative n-taxon statement. An n-taxon statement divides a complete set of taxa into two subsets; taxa in the inside set are more closely related to each other than any of these taxa is related to any taxon in the oukide set (Wilkinson, 1994). An ntaxon statement contains cladistic information if “logically possible relationships are 498 H.N. BRYANT Figure 2. Two hypotheses regarding the relationships among three extant taxa (A, B and E) and two fossil taxa (C and D; indicated by t),illustrating that phylogenetic definitions can refer a taxon name to different components on different phylogenies (see text). Both of these cladograms include the component (A,B,C,D).The component to which the crown clade definition ‘the most recent common ancestor of A and B and all of its descendants’ refers depends on the relationship among the extant clades and the two fossil taxa; C and D are excluded from this crown clade on the left cladogram but are included on the right cladogram. Thus, if clades are components, a crown clade represents a particular phylogenetic context, rather than an individual clade. prohibited or conversely when some restricted subset of relationships is asserted” (Wilkinson, 1994:344). A three-taxon statement (e.g. (A,B)C) is the least inclusive cladistically informative n-taxon statement (Gafiey, 1979; Nelson & Platnick, 1981; Wilkinson, 1994). Components are identified in a phylogenetic analysis through the division of the terminal taxa under consideration (complete set) between the inside set, those that are included in the component, and the outside set, those that are excluded from the component. Thus, in a phylogenetic analysis of taxa A through E (Fig. l), on the left cladogram A, B and C constitute a component because they form a cluster to the exclusion of taxa D and E. In other words, components are identified by determining not only the taxa that are included, but also those that are explicitly excluded. This component can be represented by the five-taxon statement (A,B, C)D,E; this n-taxon statement describes a component because n equals five, the number of taxa included in the phylogenetic analysis (Wilkinson, 1994). The relationships among the taxa within the component (A, B and C) have no influence on its individuality or identity; thus, ((B,C)A)is the same component as ((A,C)B)or ((AYBF). A node-based phylogenetic definition such as ‘the most recent common ancestor of A and B and all of its descendants’ contains no cladistic information. Two members (A and B) of the inside set in the equivalent n-taxon statement are identified, but there is no reference to the outside set. Although node-based definitions refer to common ancestry, “logically possible relationships” (Wilkinson, 1994:344) are not prohibited and therefore the definition is compatible with any hypothesis of relationships. A reference cladogram that includes A and B is required to determine the node that represents the most recent common ancestor of these two taxa, thus identiftrlng the component to which the taxon name applies. The association of the name with a component occurs only within the context of a reference cladogram. Consider the two cladograms in Figure 2. The phylogenetic definition ‘the most recent common ancestor of B and D and all of its descendants’ refers to the same component (A,B,C,D) on both cladograms. In contrast the definition ‘the most recent common ancestor of A and B and all of its descendants’ refers to a smaller component (A,B) on the left cladogram but refers to the larger component (A,B,C, D) on the right cladogram. Given that this definition refers to a smaller component DESIGNATED PHYLOGENETIC CONTEXTS FOR TAXON NAMES 499 on the left cladogram, even though the larger component is also present, this definition refers to differentcomponents on the two cladograms. If clades are equated with components, the clade specified by the definition depends on the particular cladogram one uses as a reference and phylogenetic definitions can refer names to different clades on different cladograms (Bryant, 1996). Stem-based definitions differ from standard node-based definitions in that they refer to both the inside and outside sets in an n-taxon statement. The stem-based definition ‘A and all members of X more closely related to A than to D’ explicitly includes A (inside set) and excludes D (outside set) from the clade being named. However, these definitions also lack sufficient cladistic information to identrfy a component in the absence of a reference cladogram. The n-taxon statement may not be cladistically informative (smu Wilkinson, 1994),and even ifit is, the definition itself does not indicate whether the n-taxon statement refers to all taxa in a phylogenetic analysis and therefore identifies an individual component. Because there may be no ‘members of X more closely related to A than to D’, the definition above refers explicitly to only two taxa and is therefore equivalent to (A)D, which is not a cladistically informative n-taxon statement (if the name A has also been defined phylogenetically, for example as the most recent common ancestor of Y and Z, one could argue that the above definition is indirectly equivalent to the cladistically informative n-taxon statement (Y,Z)D). In contrast, the definition ‘A and B and all members of X more closely related to these taxa than to D’ is directly equivalent to the n-taxon statement (A,B)D. This definition is incompatible with cladograms that contradict this n-taxon statement. However, this cladistically informative definition does not identifjr a component because it is uncertain whether n is equal to all taxa in a phylogenetic analysis. The exclusivity required to identify an individual component can only be determined through the interpretation of that definition within the context of a particular cladogram. The cladistic information in a stem-modified node-based definition (Meng & Wyss, 1994; Wyss & Meng, 1996) such as ‘the clade stemming from the most recent common ancestor of A and all Recent members of X more closely related to A than to D’ is similar to that of a standard stem-based definition. Apomorphy-based definitions make direct reference to no members of either the inside or outside set in an n-taxon statement. The definition ‘the first species to possess structure X and all of its descendants’ identifies an ancestor based on the origin of structure X, but the component to which it refers can only be identified when the character-state transformations associated with structure X have been optimized on a reference cladogram. Given that phylogenetic definitions lack the cladistic information needed to identifjr particular components in the absence. of a reference cladogram, and if clades are equated with components (perspective of Wilkinson, 1994; Bryant, 1996), a phylogenetic definition may associate a name with different clades on different cladograms. From this perspective, if the maintenance of the association between taxon names and particular clades is a goal of phylogenetic taxonomy, phylogenetic definitions may have to be emended when phylogenetic relationships are revised (Bryant, 1996). Repeated emending of phylogenetic definitions with on going revisions to phylogenetic hypotheses to preserve the association between taxon names and individual components would unduly undermine the stability of the nomenclatural system. Small differences in the position or number of taxa on cladograms can change the 500 H. N. BRYANT association between taxon names and components. The number of equivalent components can be reduced, often markedly, by differences in the phylogenetic position of even a single taxon (Fig. l), and differences in the terminal taxa on cladograms. In the interests of nomenclatural stability the meaning (wording) of definitions should be unaffected by differences among phylogenetic hypotheses. Emending definitions to preserve the association between names and individual components on cladograms is neither appropriate nor practical. Bryant (1996) concluded differently that phylogenetic definitions would need to be emended with revisions to cladograms because he inadvertently attempted to apply a goal consistent with the perspective of de Queiroz & Gauthier (taxon names should remain associated with the same clade) to an alternative perspective that views clades as components, to which this goal is not appropriate. DESIGNATED PHYLOGENETIC CONTEXT Because phylogenetic definitions have limited cladistic information, the clade denoted by a particular name can differ markedly on different cladograms (see examples in Schander & Thollesson, 1995; Bryant, 1996). This difference may be viewed in terms of the content of clades (de Queiroz & Gauthier’s perspective) or the identity of clades (if clades are equated with components). In both instances, the diagnostic synapomorphies, inclusiveness, and distribution in time and space of the clade with a particular name can differ depending on the phylogenetic hypothesis one chooses to adopt. Changes to clades with particular taxon names due to revisions to phylogenetic hypotheses can potentially undermine the stability in the usage of those names. Marked lability in the characteristics of the clade to which a name refers is usually caused by incorporating names that refer to taxa of uncertain phylogenetic position in the phylogenetic definitions of taxon names (Schander & Thollesson, 1995; taxon A in Fig. 1). Many of the phylogeny-dependent differences in the clades to which the phylogenetic definitions of Wyss & Flynn (1993) and Wolsan (1993)refer (Bryant, 1996: fig. 1) reflect the difference in the position of Amphicyonidae on their phylogenetic hypotheses. Schander & Thollesson (1995) concluded that this problem could be avoided by using only names of clades whose relationships are highly corroborated, and therefore unlikely to change with revisions to phylogenies, in phylogenetic definitions. However, the likelihood of changes in the phylogenetic position of taxa cannot always be predicted in advance, and relationships associated with clades that we wish to name will not always be stable. Some other more broadly applicable mechanism is needed to deal with differences to the clade to which a particular name refers that are associated with differences among reference cladograms. The source of the stability afforded to the usage of many taxon names defined using the crown clade convention suggests a solution to this problem. In the crown clade convention ‘widely known taxon names’ are defined by reference to the most recent common ancestry of clades with extant members (Gauthier et al., 1989; Gauthier, Estes & de Queiroz, 1988; Rowe, 1988; de Queiroz & Gauthier, 1992). For example, Rowe (1987:209) defined Mammalia as “the most recent common ancestor of its two principal divisions, Monotremata and Theria, and all of its DESIGNATED PHYLOGENETIC CONTEXTS FOR TAXON NAMES 50 1 descendants.” Although this definition refers explicitly to only Monotremata and Theria, there is an implicit phylogenetic context associated with the definition in that the ancestry of these two extant clades is presumed to exclude other extant clades (e.g.Aves, Crocodylia and Lepidosauria).The common ancestry of Monotremata and Theria to the exclusion of these other vertebrate clades is highly corroborated and therefore Rowe’s definition consistently associates the name Mammalia with a clade that is congruent with this implicit phylogenetic context. Thus, the stability in the clade named Mammalia by this definition is due in part to stability in the phylogenetic relationships among particular extant clades. If our hypotheses regarding the phylogeny of vertebrates changed so that other extant clades were considered more closely related to Theria than Monotremata is, the name Mammalia would become associated with a clade with very Werent diagnostic synapomorphies, inclusiveness, and distribution in time and space, for which the name Mammalia might be deemed inappropriate. Thus, the phylogenetic relationships for which the use of Mammalia is appropriate are equivalent to the n-taxon statement ((Monotremata, Theria) other clades of vertebrates with extant members). This n-taxon statement contains phylogenetic information that is absent from Rowe’s definition of Mammalia and denotes the appropriate phylogenetic context for the use of that name. Formal recognition of the appropriate phylogenetic context for the use of taxon names would stabilize phylogenetic taxonomy. I define the desz&atedphylogenetic context (similar in concept to ‘recommended usage’ of Bryant, 1996) for a taxon name as the ntaxon statement that describes the phylogenetic relationships that are considered appropriate for the use of that name. Because a standard node-based phylogenetic definition lacks cladistic information, the appendance to this type of definition of an n-taxon statement that denotes the designated phylogenetic context for the name would stabilize the usage of that name. An explicit designated phylogenetic context for Mammalia seems unnecessary only because views regarding the relationships among the extant clades relevant to the usage of the name are extremely stable. As a result, use of Mammalia is appropriate on essentially all cladograms that include monotremes and therians. Phylogenetic hypotheses relevant to the usage of most taxon names are not as highly corroborated or stable. Stem-based and stem-modified nodebased definitions with sufficient and appropriate inherent cladistic information would not require an appended designated phylogenetic context. Formal recognition of designated phylogenetic contexts is consistent with the fact that names of supraspecific taxa are usually associated with specific explicit or implicit phylogenetic relationships. As a result, it seems appropriate to limit the use of those names to only trees that have those specific relationships. Gardiner (1982) proposed that Aves and Mammalia are extant sister taxa and named the crown clade consisting of these two taxa ‘Haemothermia (emended to Haematothermia without explanation in Gardiner, 1993). Gardiner’s conceptualization of Haemothermia is based on these specific phylogenetic relationships, which provide the phylogenetic context for the use of the name. Haemothermia might be defined as ‘the most recent common ancestor of Aves and Mammalia and all of its descendants’, and its designated phylogenetic context would be the n-taxon statement ((Aves, Mammalia) other clades of vertebrates with extant members). Because this n-taxon statement is not congruent with the orthodox view regarding the phylogenetic relationships among vertebrates, use of Haemothermia is not appropriate within the 502 H.N. BRYANT context of those cladograms. Nonetheless, use of Haemothermia remains appropriate within the context of Gardiner’s (1982, 1993) cladograms. The use of designated phylogenetic contexts will facilitate nomenclatural stability. Phylogenetic definitions, together with appropriate rules of priority, can establish and stabilize the meaning of taxon’names, but do not pertain directly to the usage of those names. Limiting the usage of taxon names to designated phylogenetic contexts will largely eliminate the need to emend phylogenetic definitions. Instances may still occur in which the definitions of well known names will need to be emended to preserve their historical usage (see Carnivora example in Bryant, 1996). Many of these instances will involve the lack of care in the initial wording of the definition to allow for possible changes to the clade with revisions to phylogenetic relationships. Regardless of one’s perspective regarding the clade named by a phylogenetic definition, stability in the use of taxon names would be facilitated by the recognition of the appropriate phylogenetic contexts for those names. Because phylogenetic definitions have limited cladistic information, the phylogenetic context of taxon names can differ considerably on different cladograms. Phylogenetic definitions of taxon names without sufficient cladistic information should be accompanied by an n-taxon statement that denotes the designated phylogenetic context for the use of the name. 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