International Code of Phylogenetic Nomenclature (PhyloCode)

Division II. Rules

Chapter IV. Establishment of Names

Article 11. Specifiers and Qualifying Clauses

11.1

Specifiers are species, specimens, or apomorphies cited in a phylogenetic definition of a name as reference points that serve to specify the clade to which the name applies. All specifiers used in minimum-clade and maximum-clade definitions, and one of the specifiers used in apomorphy-based definitions, are species or specimens. The other specifier used in an apomorphy-based definition is an apomorphy.

Note 11.1.1

Although subordinate clades cannot be specifiers, they may be cited in a phylogenetic definition of the name of a more inclusive clade to clarify the phylogenetic position of a specifier.

Example 1

Aves could be defined as “the crown clade originating in the most recent common ancestor of Struthio camelus Linnaeus 1758 (Palaeognathae) and Vultur gryphus Linnaeus 1758 (Neognathae).” Alternatively, the definition could be worded “the crown clade originating in the most recent common ancestor of Palaeognathae (Struthio camelus Linnaeus 1758) and Neognathae (Vultur gryphus Linnaeus 1758).” In both definitions, Palaeognathae and Neognathae are not specifiers; they simply provide additional information about the phylogenetic position of the true specifiers.

11.2

An internal specifier is a species, specimen, or apomorphy that is explicitly included in the clade whose name is being defined; an external specifier is a species or specimen that is explicitly excluded from it. All specifiers in minimum-clade (including minimum-crown-clade), apomorphy-based, and apomorphy-modified crown-clade definitions are normally internal (though external specifiers may be used to prevent use of a name under certain hypotheses of relationships, clade composition, or both; see Art. 11.13, Ex. 1), but maximum-clade (including maximum-crown-clade and maximum-total-clade) definitions always have at least one specifier of each type.

11.3

When a species is used as a specifier, the author and publication year of the species name must be cited.

Note 11.3.1

Names of species used as specifiers are governed by the rank-based codes (e.g., ICNAFP, ICZN); see Article 21.

Note 11.3.2

The ICNAFP and ICZN differ in their conventions for citing authorship and publication year when the author of the currently accepted binominal combination differs from the author of the epithet (i.e., the author of the original combination). Because the purpose of citing authorship and year is to identify the specifiers unambiguously, the conventions used by the appropriate rank-based code should be used for species names governed by that code.

11.4

Because species names are governed by the rank-based codes, they are generally associated with type specimens, which serve as reference points for the names; this situation bears on the use of species as specifiers under this code. In effect, whichever currently accepted species includes the type specimen of the species name cited in the definition is the specifier. If the species name originally cited in a definition is no longer accepted, then the species name with which it has been synonymized becomes the name of the specifier species. However, should the species name originally cited in the definition become the accepted name of a species at a later time, that name would again become the name of the specifier species. The status of a species as a specifier is unaffected by the designation of a new or different type under the appropriate rank-based code. A species may be used as a specifier even if its name lacks a type. See also Recommendation 11H, regarding the naming of low-level clades.

11.5

When a type specimen is used as a specifier, the species name that it typifies and the author and publication year of that species name must be cited.

Recommendation 11.5A

When type specimens are used as specifiers in the definitions of the names of low-level clades (see Rec. 11H), holotypes or lectotypes should be used. If there is no holotype or lectotype that, if designated as a specifier, would result in the name being applied to the intended clade, and a syntype is selected instead, it is recommended that the same syntype be simultaneously designated as the lectotype under the appropriate rank-based code.

11.6

When a type specimen is used as a specifier, it retains its status as a specifier even if a different type for the species name that it typified is subsequently designated under the relevant rank-based code, or if the species name that it typifies is no longer accepted because the species has been re-circumscribed and the name relegated to synonymy.

11.7

Specimens that are not types may not be used as specifiers unless: (1) the specimen that one would like to use as a specifier cannot be referred to a named species, so that there is no type specimen that could be used instead; or (2) the clade to be named is nested entirely within a species; or (3) the clade to be named includes part of a non-monophyletic species and its descendants but the type of the non-monophyletic species is either excluded from that clade or it is not possible to determine whether it is included.

Note 11.7.1

There may be differences in taxonomic opinion as to whether a specimen can be referred to a named species (see Art. 11.7: situation 1). Article 11.7 is not intended to provide a basis for challenging the establishment of a clade name by adopting a different species definition from that of the definitional author and thereby challenging the claim that a particular specifier cannot be referred to a named species. However, wholesale rejection of the species category cannot be used as a basis for claiming that a particular specimen cannot be referred to any species, and the use of non-types as specifiers based on such an argument constitutes grounds for challenging the establishment of the name.

Recommendation 11.7A

If a specimen that is not a type is used as a specifier in the first situation described in Article 11.7, and a species that includes this specimen is subsequently named under the appropriate rank-based code, this specimen should be chosen as the type of the species name.

11.8

When a specimen that is not a type is used as a specifier in a phylogenetic definition, the institution or collection in which the specifier is conserved must be identified, as well as the collection number or other information needed to identity the specimen unambiguously.

11.9

When a specimen that is not a type is used as a specifier in a phylogenetic definition, either a brief description or an image or reference to a published image of the specimen must be provided, sufficient to convey a mental image to a non-specialist and distinguish the specimen from organisms with which it might be confused. If a copyrighted image is submitted, the registration database (see Art. 8.1) must be provided with written authorization to share it with database users. If a reference to a published image is submitted, it must include all the information necessary to locate it.

11.10

In the interest of avoiding confusion, a clade name should not be based on the name of another taxon that is not part of the named clade. Therefore, when a clade name is converted from a preexisting name that is typified under a rank-based code or is a new or converted name derived from the stem of a typified name, the definition of the clade name must use the type species of that preexisting typified name or of the genus name from which it is derived (or the type specimen of that species) as an internal specifier.

Example 1

If the preexisting name Magnoliales, which is based on the genus name Magnolia, is converted to a clade name, its definition must use the type species of Magnolia or its type specimen as an internal specifier.

Example 2

If Ajugina, which is not a preexisting name but is based on the preexisting genus name Ajuga, is adopted as the name of a clade, the definition of Ajugina must use the type species of Ajuga or its type specimen as an internal specifier.

Example 3

If the preexisting subgenus name Calosphace is converted to a clade name, the definition of Calosphace must use the type species of subgenus Calosphace or its type specimen as an internal specifier.

Example 4

If the preexisting name Caprifoliaceae, which is based on the genus name Caprifolium, is converted to a clade name, its definition must use the type species of Caprifolium or its type specimen as an internal specifier. This is true even though the name Caprifolium is a later synonym of Lonicera under the ICNAFP and therefore is not an accepted genus name.

Recommendation 11.10A

If it is questionable whether a type species of a preexisting name is part of the clade to be named, then the type species should not be used as a specifier (see Rec. 11B), and neither that preexisting name nor a name derived from the stem of that name should be defined as referring to that clade.

Example 1

If it is questionable whether the type species of Magnolia belongs to a clade that is to be named, this species should not be used as a specifier, and the clade should not be named Magnolia, Magnoliales, or any other name based on the stem of the name Magnolia.

Note 11.10A.1

Failure to include the type species of a preexisting name in an analysis is not, in itself, reason to invoke Recommendation 11.10A. There may be evidence suggesting that another species that was included in the analysis shares a recent common ancestor with the type.

Recommendation 11.10B

If it is questionable whether the type specimen of a preexisting name belongs to the clade to be named (e.g., because of the fragmentary nature of the specimen), then neither that specimen nor the species name that it typifies should be used as a specifier (see Rec. 11C), and the corresponding name should not be converted to a clade name.

Example 1

Under the ICNAFP, the names Cordaites, Cordaixylon, and Mesoxylon refer to genera of extinct seed plants. The types of the latter two names are fossil stems, but it has been possible to reconstruct whole plants that belonged to each genus. The oldest of the three names, Cordaites, is typified by fossil leaf material that could have been produced by a member of either Cordaixylon or Mesoxylon. If a clade is named that includes plants with Cordaixylon-type stems but not Mesoxylon-type stems, neither the type specimen of Cordaites nor the species name that it typifies should be cited as a specifier because they may not belong to this clade, and the clade should not be named Cordaites.

11.11

In order for the reference phylogeny to be useful, either the specifiers used in the phylogenetic definition must be included in the reference phylogeny (see Art. 9.13) or the protologue must include a statement indicating how the specifiers are related to the taxa that are included in the reference phylogeny.

Note 11.11.1

An acceptable mechanism for indicating how the specifiers are related to the taxa in the reference phylogeny is to cite a taxon name that is labeled on the reference phylogeny parenthetically after the name of the specifier in the definition.

Note 11.11.2

If a clade name is converted from a typified name under a rank-based code, or is derived from the stem of such a name, and the type of that name is not included in the reference phylogeny, the type must still be used as an internal specifier (see Art. 11.10), and its relationship to taxa included in the reference phylogeny must be stated in the protologue.

11.12

In order to prevent use of a name under certain hypotheses of relationships, clade composition, or both, phylogenetic definitions may include qualifying clauses specifying conditions under which the name cannot be applied to any clade (see Exs. 1 and 2).

Note 11.12.1

The following conventions are adopted for abbreviated qualifying clauses such as those in Examples 1 and 2: | = on the condition that; ~ = it does not; () = contain; ∨ = or; anc = the ancestor in which the clade originated. See Note 9.4.1 for the other abbreviations used in these examples.

Example 1

The name Pinnipedia is traditionally applied to a group composed of sea lions (Otariidae), walruses (Odobenidae), and seals (Phocidae). However, under some phylogenetic hypotheses, the sister group of one or more of these taxa is a group of terrestrial carnivorans (e.g., Ursidae, Procyonidae, Mustelidae). If the name Pinnipedia were to be defined as “the clade originating in the most recent common ancestor of Otaria byronia de Blainville 1820, Odobenus rosmarus Linnaeus 1758, and Phoca vitulina Linnaeus 1758, provided that it does not include Ursus arctos Linnaeus 1758 or Procyon lotor (Linnaeus 1758) or Mustela erminea Linnaeus 1758”, then the name would not be applicable to any clade in the context of phylogenetic hypotheses in which the most recent common ancestor of Otaria byronia, Odobenus rosmarus, and Phoca vitulina was also inferred to be an ancestor of Ursus arctos or Procyon lotor or Mustela erminea. The phrase “provided that it does not include Ursus arctos Linnaeus 1758 or Procyon lotor (Linnaeus 1758) or Mustela erminea Linnaeus 1758” is a qualifying clause. This definition may be abbreviated min (Otaria byronia de Blainville 1820 & Odobenus rosmarus Linnaeus 1758 & Phoca vitulina Linnaeus 1758) | ~ (Ursus arctos Linnaeus 1758 ∨ Procyon lotor (Linnaeus 1758) ∨ Mustela erminea Linnaeus 1758) (see Note 11.12.1).

Example 2

The name Pinnipedia is traditionally applied to a group composed of sea lions (Otariidae), walruses (Odobenidae), and seals (Phocidae). However, under some phylogenetic hypotheses, the sister group of one or more of these taxa is a group of terrestrial carnivorans. If the name Pinnipedia were to be defined as “the clade originating in the most recent common ancestor of Otaria byronia de Blainville 1820, Odobenus rosmarus Linnaeus 1758, and Phoca vitulina Linnaeus 1758, provided that the ancestor in which the clade originated possessed flippers synapomorphic with those in the aforementioned species,” then the name would not be applicable to any clade in the context of phylogenetic hypotheses in which the most recent common ancestor of these species was inferred not to have had flippers. The phrase “provided that it possessed flippers synapomorphic with those in the aforementioned species” is a qualifying clause. (However, the apomorphy “flippers” should be illustrated or described because it is a complex apomorphy (see Recs. 9.7A, 9.7B).) This definition may be abbreviated min (Otaria byronia de Blainville 1820 & Odobenus rosmarus Linnaeus 1758 & Phoca vitulina Linnaeus 1758) | anc possessed flippers synapomorphic with those in the aforementioned species (see Note 11.12.1).

11.13

The use of a name under certain hypotheses of relationships, clade composition, or both can also be prevented by using a minimum-clade definition with external specifiers (Ex. 1) or a maximum-clade definition with more than one internal specifier (Ex. 2) or an apomorphy-based definition with more than one internal specifier (Ex. 3). These definitions have the same effect as qualifying clauses (Art. 11.12) in that under some phylogenetic hypotheses, the name cannot be applied to any clade.

Example 1

If a name is defined through a minimum-clade definition (or a minimum-crown-clade definition) with an external specifier, and one internal specifier is later found to share a more recent common ancestor with the external specifier than with the other internal specifier, the definition does not apply to any clade. For example, suppose the name Halecostomi had been defined as referring to the smallest clade containing Amia calva Linnaeus 1766 and Perca fluviatilis Linnaeus 1758 but not Lepisosteus osseus Linnaeus 1758. And suppose that subsequent analyses indicated that Lepisosteus osseus and Perca fluviatilis share a more recent common ancestor with one another than either does with Amia calva. If so, then there would be no clade that fits the definition of Halecostomi (because there would be no clade that includes both Amia calva and Perca fluviatilis but not Lepisosteus osseus), and that name could not be used in the context of that hypothesis.

Example 2

If a name is defined through a maximum-clade definition (or a maximum-crown-clade definition or a maximum-total-clade definition) with more than one internal specifier, and one internal specifier is later found to share a more recent common ancestor with the external specifier than with the other internal specifier, the definition does not apply to any clade. For example, suppose the name Halecostomi had been defined as referring to the largest clade containing Amia calva Linnaeus 1766 and Perca fluviatilis Linnaeus 1758 but not Lepisosteus osseus Linnaeus 1758. And suppose that subsequent analyses indicated that Lepisosteus osseus and Perca fluviatilis share a more recent common ancestor with each other than either does with Amia calva. If so, then there would be no clade that fits the definition of Halecostomi (because there would be no clade that includes both Amia calva and Perca fluviatilis but not Lepisosteus osseus), and that name could not be used in the context of that hypothesis.

Example 3

If a name is defined through an apomorphy-based definition with multiple internal specifiers, and it is later found that the apomorphy is not homologous in all of the internal specifiers, the definition does not apply to any clade. For example, Cantino, Doyle, and Donoghue defined Apo-Spermatophyta in Phylonyms as the clade characterized by seeds as inherited by Magnolia tripetala (Linnaeus) Linnaeus 1759, Podocarpus macrophyllus (Thunberg) Sweet 1818, Ginkgo biloba Linnaeus 1771, Cycas revoluta Thunberg 1782, and Gnetum gnemon Linnaeus 1767. Suppose that subsequent analyses indicated that the seeds of cycads arose separately from those of the other specifiers (though this hypothesis is not supported by any modern analysis). If so, then there would be no clade that fits the definition, and the name Apo-Spermatophyta could not be used in the context of that hypothesis.

11.14

The application of a name with respect to clade composition under alternative hypotheses of relationship can be restricted by defining it relative to the name of another clade (Ex. 1). However, unlike the mechanisms described in Articles 11.12 and 11.13, the name does not become inapplicable under the alternative phylogenetic hypothesis.

Example 1

Gauthier et al. (1988) proposed the name Lepidosauriformes (max (Lacerta agilis Linnaeus 1758 ~ Youngina capensis Broom 1914) for a subclade of Lepidosauromorpha (max (Lacerta agilis Linnaeus 1758 ~ Crocodylus niloticus Laurenti 1768)), which was itself proposed for a subclade of Sauria (min (Lacerta agilis & Crocodylus niloticus)). If Youngina capensis turned out to be outside of the clade originating in the most recent common ancestor of Lacerta agilis and Crocodylus niloticus (i.e., Sauria), then the name Lepidosauriformes would refer to a larger clade than Lepidosauromorpha, reversing the former hierarchical relationships of the clades designated by those names. To prevent that reversal, the name Lepidosauriformes could have been defined as “the largest clade within Sauria containing Lacerta agilis but not Youngina capensis,” in which case Lepidosauriformes would become a synonym of Lepidosauromorpha (rather than the name of a larger clade) in the context of the new phylogenetic hypothesis. In contrast to the original definition, the addition of “within Sauria” in the alternative definition restricts application of the name to a subclade of Sauria. (Note that a similar restriction could be achieved by using Crocodylus niloticus as an additional external specifier.)

11.15

Provided that a clade name is acceptable, it remains eligible for use even if there is no clade that fits its definition under a subsequently proposed phylogenetic hypothesis. The name would not be used in the context of that hypothesis, but it would remain eligible for future use under any hypotheses in which there is a clade that fits its definition.

Example 1

Although the name Pinnipedia is inapplicable under certain phylogenetic hypotheses if the qualifying clause in Article 11.12, Example 1 is used, the name remains eligible for use under other hypotheses.

Recommendation 11A

Definitions of converted clade names should be stated in a way that attempts to capture the spirit of traditional use to the degree that it is consistent with the contemporary concept of monophyly. Consequently, such a definition should not necessitate (though it may allow) the inclusion of subtaxa that have traditionally been excluded from the taxon designated by the preexisting name, as well as the exclusion of subtaxa that have traditionally been included in the taxon. To accomplish this goal, internal specifiers of converted clade names should be chosen from among the taxa that have been considered to form part of a taxon under traditional ideas about the composition of that taxon, and they should not include members of subtaxa that have traditionally been considered not to be part of the taxon.

Example 1

The name Dinosauria was coined by Owen for the taxa Megalosaurus, Iguanodon, and Hylaeosaurus, and traditionally the taxon designated by that name has included these and certain other non-volant reptiles. It has not traditionally included birds. Although birds are now considered part of the dinosaur clade, the name Dinosauria should not be defined using any bird species as internal specifiers. Such a definition would force birds to be dinosaurs, thus trivializing the question of whether birds are dinosaurs. Instead, internal specifiers should be chosen from among taxa that have traditionally been considered dinosaurs, e.g., Megalosaurus bucklandii Mantell 1827, Iguanodon bernissartensis Boulenger in Beneden 1881, and Hylaeosaurus armatus Mantell 1833.

Note 11A.1

Traditional use may refer to early or recent traditions. Because it is not always possible to be faithful to all traditions simultaneously, which tradition is most important to maintain is left to the discretion of the author of the converted name.

Recommendation 11B

If there is reason to question that a species is a member of a particular clade, that species should not be used as a specifier in the definition of the name of that clade.

Recommendation 11C

Because they are commonly based on taxonomically ambiguous types, ichnotaxa (taxa based on the fossilized work of organisms, including fossilized trails, tracks, and burrows; ICZN (1999) glossary, Art. 1.2.1) and ootaxa (taxa based on fossilized eggs) should not be used as specifiers. When this recommendation is combined with Article 11.10, it follows that clade names should not be based on the names of ichnotaxa or ootaxa.

Recommendation 11D

In a minimum-clade definition, it is best to use a set of internal specifiers that includes representatives of all subclades that credible evidence suggests may be sister to the rest of the clade being named, unless doing so would be contrary to Recommendation 11A and/or 11B. Constructing a minimum-clade definition in this way will reduce the chance that, under a new phylogenetic hypothesis, the name will refer to a less inclusive clade than originally intended.

Recommendation 11E

In a maximum-clade definition, it is best to use a set of external specifiers that includes representatives of all clades that credible evidence suggests may be the sister group of the clade being named. Constructing a maximum-clade definition in this way will reduce the chance that, under a new phylogenetic hypothesis, the name will refer to a more inclusive clade than originally intended.

Recommendation 11F

If it is important to establish two names as applying to sister clades regardless of the phylogeny, reciprocal maximum-clade definitions should be used in which the single internal specifier of one is the single external specifier of the other, and vice versa. To establish a name as applying to the larger clade composed of those two sister-clades, the name of the former should be given a minimum-clade definition using the same two internal specifiers (Ex. 1). A similar approach may be used to establish two names as referring to crown clades that are each other’s closest extant relatives by using reciprocal maximum-crown-clade definitions (Ex. 2).

Example 1

If one wishes to define the names Saurischia and Ornithischia such that they will always refer to sister clades, Saurischia might be defined as the largest clade containing Megalosaurus bucklandii Mantell 1827 but not Iguanodon bernissartensis Boulenger in Beneden 1881, and Ornithischia would be defined as the largest clade containing Iguanodon bernissartensis but not Megalosaurus bucklandii. To stabilize the name Dinosauria as referring to the clade comprising Saurischia and Ornithischia, Dinosauria should be defined as the smallest clade containing Megalosaurus bucklandii and Iguanodon bernissartensis.

Example 2

If one wishes to define the names Lamioideae and Scutellarioideae such that they will always refer to crown clades that are each other’s closest extant relatives, Lamioideae might be defined as the largest crown clade containing Lamium album L. 1753 but not Scutellaria galericulata L. 1753, and Scutellarioideae would be defined as the largest crown clade containing Scutellaria galericulata but not Lamium album.

Recommendation 11G

Clade names (new or converted) that combine certain prefixes or suffixes with another clade name (the base name) should be defined in a manner consistent with the hierarchical relationships implied by the prefix or suffix and the phylogenetic definition of the base name (if established), unless doing so would be inconsistent with the predominant current use of a preexisting name (see also Note 11G.2).

Example 1

If preexisting names Parahebe and Hebe are converted, the internal specifiers of each name should not include any member of the other clade, but this alone will not ensure the mutual exclusivity implied by the name Parahebe. Mutual exclusivity can be ensured by using the type of each name as an external specifier for the other name, or by including a qualifying clause making the name Parahebe inapplicable in the context of any phylogeny in which the two clades are not mutually exclusive. However, neither of these approaches should be taken if the accepted usage (at the time when the definition is prepared) treats Hebe and Parahebe as nested.

Note 11G.1

The following prefixes and suffixes imply greater inclusiveness than the base name: Holo-, Pan-, -formes, -morpha. The following prefixes imply lesser inclusiveness than the base name: Eo-, Eu-, Neo-, Proto-. The following prefixes imply mutual exclusivity with the base name: Pseudo-, Para-. These are not intended to be exhaustive lists.

Note 11G.2

The creation of new clade names that add such a prefix to a preexisting or converted name with a rank-specific ending may lead to confusion for users of the rank-based system because the new name may be incorrectly taken to imply the existence of a genus name with the same prefix.

Example 1

The creation of a new clade name Protobrassicaceae from the base name Brassicaceae might be incorrectly taken to imply the existence of a genus Protobrassica.

Recommendation 11H

When defining the names of low-level clades that coincide with or overlap the boundaries of species, differences in species criteria and hypothesized species boundaries may result in a phylogenetically defined name being applied to different clades even in the context of the same phylogeny. Recommendations 11H and I are intended to reduce the likelihood of this undesirable outcome and address it when it occurs. If the definitional author is aware that using a particular species as a specifier may result in the application of the name to a different clade than if the type specimen of that species’ name were instead used, one or the other should be unambiguously selected as the specifier (see Arts. 11.4 and 11.6 for the ramifications of that choice), and the situation should be clearly explained in the protologue.

Recommendation 11I

If, after establishment of a clade name, it is discovered that a species or type specimen used as a specifier results in the name being applied to a different clade (in the context of the same phylogeny) than if the other entity, i.e., the type specimen or species, had been used instead, and if the ambiguity would be eliminated by selecting the other entity as the specifier, then an unrestricted emendation (Arts. 15.1115.13) designating that entity as the specifier may be published (see also Rec. 11J). It is preferable, though not required, that the emendation be published by the original definitional author(s) (Art. 15.14). If such an emendation is published by anyone other than the original definitional author(s), the intent of the original author(s) should be considered carefully and addressed in the protologue of the emendation (see Note 15.11.4 and Arts. 15.12 and 15.13). If the protologue of the original definition included a discussion of the choice of species versus type specimens as specifiers (see Rec. 11H), this should be viewed as part of the author(s)’ intent. Specifically, if the author(s) stated that their preference for using type specimens (or conversely, species) as specifiers regardless of the effect on clade composition, that preference should be honored; in such a case, an unrestricted emendation by anyone other than the author(s) would be inappropriate.

Recommendation 11J

If an emendation is published in the situation described in Recommendation 11I, and if a species originally used as a specifier has more than one type (i.e., syntypes), whichever syntype is chosen as the new specifier should be simultaneously designated as the lectotype of that species under the appropriate rank-based code.