International Code of Phylogenetic Nomenclature (PhyloCode)

Note 9.3.1

The application of a phylogenetic definition, and thus also of a phylogenetically defined clade name, requires a hypothesized phylogeny. To accommodate phenomena such as speciation via hybridization, species fusion, and symbiogenesis (see Note 2.1.3), the hypothesized phylogeny that serves as the context for the application of a phylogenetically defined name need not be strictly diverging.

Note 9.4.1

The following conventions are adopted for abbreviated definitions: max = the largest; min = the smallest; ∇ = clade; () = containing (but see Note 10.5.1); [] = as exhibited by; apo = characterized by apomorphy [followed by the name or description of the apomorphy]; & = and; ∨ = or; ~ = but not; A, B, C, etc. = species or specimens used as internal specifiers (see Art. 11.2); Z, Y, X, etc. = species or specimens used as external specifiers (see Art. 11.2); M = an apomorphy used as an internal specifier.

Recommendation 9.4A

Because poorly chosen wordings of phylogenetic definitions can lead to undesirable consequences (i.e., the application of the name in a way that contradicts the author’s intent), the wordings provided in Articles 9.5–9.7 and 9.9–9.10 should generally be used for the corresponding kinds of definitions. If an alternative wording is used, it should be accompanied by the standard abbreviation (as provided in Arts. 9.5–9.7, Arts. 9.9–9.10 and Note 9.4.1) to clarify the intent of the author in case the alternative wording is ambiguous or confusing. If the definition in words and its abbreviated form appear to be in conflict, the latter should be weighted most heavily in interpreting the author’s intent. This recommendation does not preclude the use of other kinds of definitions that are not addressed in Articles 9.5–9.7 and 9.9–9.10.

Note 9.5.1

A directly-specified-ancestor definition is a special case of the minimum-clade definition in which the ancestor in which the clade originated is specified directly rather than indirectly through its descendants. A directly-specified-ancestor definition may take the form “the clade originating in A” or “the smallest clade containing A”, where A is an internal specifier (Art. 11.2). A directly-specified-ancestor definition may be abbreviated “min ∇ (A)”. For defining the names of crown clades using directly-specified-ancestor definitions, see Note 9.9.2.

Note 9.5.2

Provided that the internal specifiers have a common ancestor, a minimum-clade definition as described in Article 9.5 necessarily identifies a clade; there can be disagreements about the composition of the clade when the definition is applied in the context of different phylogenetic hypotheses, but not about its existence. It is possible to formulate a minimum-clade definition according to which the defined name does not apply to any clade under particular phylogenetic hypotheses through the use of a qualifying clause (see Art. 11.12) or external specifiers (see Art. 11.13, Ex. 1).

Note 9.6.1

Provided that the internal and external specifiers have a common ancestor, a maximum-clade definition as described in Art. 9.6 necessarily identifies a clade; there can be disagreements about the composition of the clade when the definition is applied in the context of different phylogenetic hypotheses, but not about its existence. It is possible to formulate a maximum-clade definition according to which the defined name does not apply to any clade under particular phylogenetic hypotheses through the use of a qualifying clause (see Art. 11.12) or multiple internal specifiers (see Art. 11.13, Ex. 2).

Note 9.6.2

It is important to use the appropriate operator, “and” (“&”) versus “or” (“⌵”), in definitions employing multiple external specifiers (only the “and” operator would normally be used in definitions employing multiple internal specifiers). The “and” operator is to be used when the intent is to exclude jointly all of the external specifiers from the named clade. For example, it would be appropriate to use “and” when using a maximum-clade definition with multiple external specifiers to deal with uncertainty regarding the sister group of the named clade—that is, to exclude jointly every taxon that is a potential sister group. By contrast, the “or” operator is to be used when the intent is to exclude, whether individually or jointly, any one (or more) of the external specifiers from the named clade. For example, it would be appropriate to use “or” when using a minimum-clade definition with multiple external specifiers, including those used in qualifying clauses, to render the defined name inapplicable in the context of phylogenetic hypotheses in which any one (or more) of the external specifiers is more closely related to some of the internal specifiers than those internal specifiers are to other internal specifiers (see Art. 11.12, Ex. 1).

Note 9.7.1

An apomorphy-based definition as described in Article 9.7 necessarily identifies a clade provided that there is only one internal specifier; there can be disagreements about the composition of the clade when the definition is applied in the context of different phylogenetic hypotheses, but not about its existence. It is possible to formulate an apomorphy-based definition according to which the defined name does not apply to any clade under particular phylogenetic hypotheses through the use of a qualifying clause (see Art. 11.12) or multiple internal specifiers (see Art. 11.13, Ex. 3).

Recommendation 9.7A

If an apomorphy-based definition is used, or if an apomorphy is cited in a qualifying clause (see Art. 11.12, Ex. 2), the apomorphy should be described or illustrated in sufficient detail that users of the definition will understand the author’s intent.

Recommendation 9.7B

If an apomorphy-based definition is used, and if the apomorphy is a complex character that could have evolved in a stepwise fashion, then the author should identify in the protologue which aspect(s) of that apomorphy must be present in order for an organism to be considered to belong to the clade whose name is defined by that apomorphy.

Note 9.9.1

Minimum-crown-clade definitions can be either implicit (if all of the internal specifiers are extant but application to the name of a crown clade is not expressly stated) or explicit (if application to the name of a crown clade is expressly stated).

Note 9.9.2

If a directly-specified-ancestor definition (see Note 9.5.1) is used and the single internal specifier is an extant species, then the named clade is a crown clade (see Art. 2.2) consisting of that species and any descendants it might have. Such a definition may take the form “the crown clade originating in A” or “the smallest crown clade containing A”, where A is an extant internal specifier (Art. 11.2). It may be abbreviated “min crown ∇ (A)”. This kind of definition may be useful in defining the names of crown clades comprising single extant species.

• A maximum-clade definition (Art. 9.6) is a crown-clade definition if (1) at least one of the (explicitly mentioned) internal specifiers (Art. 11.2) is extant and (2a) the word “extant” is included before “organisms” under the first wording (Art. 9.6) or (2b) the word “crown” is included before “clade” under the third wording (Art. 9.6). A maximum-crown-clade definition (formerly known as a branch-modified or a stem-modified node-based definition4) may thus take the form “the crown clade originating in the most recent common ancestor of A and all extant organisms or species that share a more recent common ancestor with A than with Z” or “the largest crown clade containing A but not Z”, where A is an extant internal specifier and Z is an external specifier (Art. 11.2). A maximum-crown-clade definition may be abbreviated “max crown ∇ (A ~ Z)”. Additional internal specifiers (e.g., C & D & E, etc.) and external specifiers (e.g., Y & X &W, etc.) may be used as needed (e.g., if the extant outgroup relationships of the named clade are poorly supported in the case of external specifiers, or if the author intends for the name not to apply to any clade in the context of particular phylogenetic hypotheses in the case of internal specifiers, as described in Article 11.13, Ex. 2; but see Note 9.6.2). If this kind of definition is used and “extant” is intended to mean anything other than extant on the publication date of the definition (thus affecting the concept of a crown clade; see Art. 2.2), the author should specify the intended meaning (within the restrictions described in Art. 9.11)—e.g., the internal specifiers were extant (and thus the clade was a crown clade) at a particular time in human history.
• An apomorphy-based definition is not to be used to define the name of a crown clade, as that practice requires certainty that the defining apomorphy and the crown clade originated in the same ancestor. Nonetheless, a minimum-clade definition can be modified by the use of an apomorphy to define the name of a crown clade. An apomorphy-modified crown-clade definition (formerly known as an apomorphy-modified node-based definition3) may thus take the form “the crown clade originating in the most recent common ancestor of A and all extant organisms or species that inherited M synapomorphic with that in A” or “the crown clade for which M, as inherited by A, is an apomorphy relative to other crown clades,” or “the crown clade characterized by apomorphy M (relative to other crown clades) as inherited by A”, where (in all three wordings) A is an extant specifier species or specimen and M is a specifier apomorphy (Arts. 11.1–11.2). An apomorphy-modified-crown-clade definition may be abbreviated “crown ∇ apo M[A]”. If this kind of definition is used and “extant” is intended to mean anything other than extant on the publication date of the definition (thus affecting the concept of a crown clade; see Art. 2.2), the author must indicate explicitly or implicitly the intended meaning (within the restrictions described in Art. 9.11)—e.g., that the internal specifiers were extant (and thus the clade was a crown clade) at a particular time in human history.

Note 9.9.3

If some or all of the internal specifiers are extinct in a minimum clade definition or if all of the internal specifiers are extinct in a maximum-clade definition or an apomorphy-based definition, and if the name is not explicitly stated as applying to the name of a crown clade, then the defined name may nevertheless apply to a crown clade in the context of a particular phylogenetic hypothesis. However, it is not considered to be a crown-clade definition because the defined name does not necessarily apply to a crown clade in the context of all relevant phylogenetic hypotheses.

Recommendation 9.9A

When a minimum-clade definition is intended to define the name of a crown clade, application to a crown clade should be stated explicitly.

Note 9.10.1

Maximum-total-clade definitions can be either implicit (if at least one of the internal specifiers and all of the external specifiers are extant but application to the name of a total clade is not expressly stated) or explicit (if application to the name of a total clade is expressly stated).

Note 9.10.2

Crown-based total-clade definitions with formulation 1 (including those of panclade names; see Art. 10.5) differ from all other definitions described in Articles 9.5–9.7 and 9.9–9.10 in not using any explicit specifiers, which instead are implicit. The internal specifiers in such definitions are those of the crown-clade name used in the definition of the total-clade name. The external specifiers are all extant species or organisms that are not members of that crown clade.

Recommendation 9.10A

When a maximum-clade definition is intended to define the name of a total clade, application to a total clade should be stated explicitly.

Example 1

If a name were defined as applying to the smallest crown clade containing Alca torda and Pinguinus impennis†, use of Pinguinus impennis† (which became extinct during the nineteenth century) as an internal specifier in the definition would implicitly indicate that the author’s concept of that crown clade is based on species that were extant during the nineteenth century, even if currently extinct. By contrast, if the name were defined as applying to the largest crown clade containing Alca torda but not Alle alle (which are both extant), but the author(s) intended the name to apply to a crown clade that includes Pinguinus impennis†, they would have to state explicitly that their concept of the named crown clade is based on species that were extant during the nineteenth century.

Note 9.13.1

A reference phylogeny is not part of the definition and does not prevent the name from being applied in the context of alternative phylogenies.

Note 9.13.2

The reference phylogeny may be published in the same work in which the name is being established, or a previously published phylogeny may be cited.

Recommendation 9.13A

A reference phylogeny should be derived via an explicit, reproducible analysis.

Recommendation 9.13B

If more than one reference phylogeny is cited in the protologue, one of them, and ideally a single figure or tree, should be designated as the primary reference phylogeny.

Note 9.15.1

Errors in the bibliographic citation for a preexisting name should be corrected by subsequent authors, but they do not invalidate the establishment of the corresponding converted name.

Note 9.15.2

Demonstrating “prior application of the name to a taxon approximating the clade for which it is being established” does not necessarily require a modern phylogenetic analysis, and it does not require that the author of the prior application conceptualized the taxon as a clade. Application of a name in an earlier publication to a taxon approximating the clade for which it is being converted can be demonstrated based on information in that work—e.g., a list of subordinate taxa that are broadly consistent with, though not necessarily identical to, the composition of that clade, a description including diagnostic characters that we now understand to be apomorphies of that clade, or statements and diagrams about phylogenetic relationships. When composition is used to assess the prior application of a name, the historical inclusion of taxa that are no longer considered to belong to the clade in question, or the historical exclusion of taxa that are now considered to belong to this clade, does not necessarily disqualify it as a preexisting name for the clade, provided that its application to that clade approximates traditional use to the degree that it is consistent with the contemporary concept of monophyly.

Recommendation 9.15A

If possible, the bibliographic citation demonstrating authorship of the preexisting name should refer to the original publication of the name (but see Note 19.1.1), spelled the same way as when converted and regardless of the rank and composition originally associated with the name (provided it is not a homonym; see Note 9.15A.2). If the original publication of the name cannot be determined, the earliest publication that can be found in which the name is validly published (ICNAFP, ICNP) or available (ICZN) may be cited. If the publication cited is likely not to be the one in which the name was originally published, it should be explicitly stated that the author cited is likely not to be the nominal author (see Art. 19.1) of the name. Under certain conditions (see Notes 9.15A.3 and 9.15A.4), a differently spelled name may be cited. If a citation is for a different spelling than the one adopted in the converted name, the difference in the spelling of the name should be explicitly stated.

Note 9.16.1

If the protologue or subsequent use of the name to which a bibliographic citation refers is part of a long publication, it may be beneficial to cite (in the text) the page on which the protologue or subsequent use appears, in addition to citing the range of pages of the entire publication (in the bibliography).

Note 9.16.2

If an author or editor does not use a surname, as is true in some cultures, the person’s full name as used in the publication should be cited.

Note 9C.1

A diagnosis or description is required for simultaneous valid publication (ICNAFP, ICNP) or availability (ICZN) of the name under the appropriate rank-based code.