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The PhyloCode
Glossary
A B C D E G H I L M N O P Q R S T U
acceptable name. An established name that is not a (non-conserved) later homonym and thus may potentially be an accepted name.
accepted name. The name that must be adopted for a taxon under this code.
ancestor. An entity from which another entity is descended.
apomorphy. A derived character state; a new feature that arose during the course of evolution.
apomorphy-based clade. A clade originating from the ancestor in which a particular derived character state (apomorphy) originated; a clade whose name is defined using an apomorphy-based definition.
apomorphy-based definition. A definition that associates a name with a clade originating with the first ancestor of specified organisms and/or species (internal specifier taxa) to evolve a particular apomorphy (internal specifier apomorphy). See Note 9.3.1.
apomorphy-modified node-based definition. A node-based definition that incorporates wording from apomorphy-based definitions to include all extant organisms as internal specifiers without explicitly naming them. See Note 9.3.1. Apomorphy-modified node-based definitions can be used to associate names with crown clades when basal relationships within the crown are poorly understood or when the author intends to include in the named taxon subsequently discovered extant organisms that possess a particular apomorphy.
binomen (binomina). A name composed of two words; commonly used to refer to species names composed of a generic name and a specific name (ICZN) or epithet (ICNB, ICBN) under the rank-based codes, or of a prenomen and a species name under this code.
branch. An edge or internode (connection between two nodes) on a tree (graph theory); on a phylogenetic tree, a branch is commonly used to represent a lineage, whether ancestral or terminal. The term is sometimes also used for an internode and all nodes and internodes distal to (descended from) it.
branch-based clade. A clade originating from a particular branch (internode) on a phylogenetic tree; a clade encompassing a particular branch on a phylogenetic tree and all nodes and branches descended from that branch; a clade whose name is defined using a branch-based definition. See Art 2.2.
branch-based definition. A definition that associates a name with a clade originating with a branch (on a phylogenetic tree) representing the ancestral lineage of specified organisms and/or species (internal specifiers) after its divergence from the ancestral lineage of other specified organisms and/or species (external specifiers). See Note 9.3.1.
branch-modified node-based definition. A node-based definition that incorporates wording from branch-based definitions to include all extant organisms as internal specifiers without explicitly naming them. See Note 9.4.1. Branch-modified node-based definitions can be used to associate names with crown clades when basal relationships within the crown are poorly understood or when the author intends to include in the named taxon subsequently discovered extant organisms that share a more recent common ancestor with the currently known members of the named taxon than with other currently known taxa.
categorical rank. A formal category denoting position in a hierarchy of nested taxa. The categorical ranks commonly used in taxonomy comprise seven principal categories (kingdom, phylum, class, order, family, genus, and species), which are often treated as mandatory, as well as additional primary categories (e.g., cohort, tribe) and secondary categories (e.g., superorder, subfamily). Note that the species category is treated as a rank in rank-based nomenclature but as a level of biological organization in phylogenetic nomenclature.
clade. An ancestor (an organism, population, or species) and all of its descendants.
conditionally suppressed name. A name that is suppressed only in phylogenetic contexts in which it is a synonym of a particular conserved name (see suppressed name).
conserved name. An established name that the Committee on Phylogenetic Nomenclature has ruled should have precedence over earlier synonyms or homonyms.
conversion. The act of establishing a preexisting name in accordance with the rules of this code.
converted (clade) name. A preexisting name that has been established in accordance with the rules of this code (see new (clade) name).
crown clade. A clade originating with the most recent common ancestor of two or more extant species (or organisms). Crown clades are a subset of node-based clades. See Art. 2.2.
crown clade definition. Any definition that necessarily ties a name to a crown clade—e.g., branch- and apomorphy-modified node-based definitions and standard node-based definitions in which all the specifiers represent extant species or organisms.
definition. A statement specifying the meaning of a name (i.e., the taxon to which it refers).
definitional author. The person(s) who published a phylogenetic definition for a name—either the original definition or an emended one (see nominal author).
description. A statement of the features of a taxon (or its component organisms), not limited to those that distinguish it from other taxa with which it might be confused (see diagnosis).
diagnosis (diagnoses). A brief statement of the features of a taxon that collectively distinguish it from other taxa with which it might be confused.
emendation. A formal change in the phylogenetic definition of a name.
epithet. In the ICBN, a word that, when combined with the name of a genus, forms the name of an infrageneric taxon (e.g., species, subgenus, section, series) or, when combined with the name of a species, forms the name of an infraspecific taxon (e.g., subspecies, variety, form). The ICNB also uses the term "epithet" but only at and below the species rank.
established name. A name that is published in accordance with Art. 7 of this code, which may or may not be an acceptable or accepted name.
extant (of a taxon). Having one or more living representatives (organisms) at the present time, or at some specified time since humans began keeping written historical records.
external specifier. A species or specimen that is explicitly excluded from the clade whose name is being defined (see internal specifier). Branch-based and branch-modified node-based definitions have external specifiers, but apomorphy-based, standard node-based, and apomorphy-modified node-based definitions do not.
genus (genera). One of the categorical ranks of rank-based nomenclature; more specifically, it is the primary rank above the rank of species and below that of family. The genus rank is mandatory in rank-based nomenclature not only because it is one of the seven principal ranks (kingdom, phylum, class, order, family, genus, species), which are commonly treated as mandatory, but also because the generic name is part of the species binomen.
heterodefinitional. Based on different phylogenetic definitions (see synonym).
homodefinitional. Based on the same phylogenetic definition (see synonym).
homologous. Shared by virtue of inheritance from a common ancestor. A character or character state shared by two organisms (which may represent different species or clades) is said to be homologous if that character or character state was present in all of their ancestors back to and including their most recent common ancestor.
homonym. A name that is spelled identically to another name that refers to a different taxon. See Art. 13.1.
hybrid formula. An expression consisting of the names of two taxa separated by a multiplication sign, designating a single organism or set of organisms of hybrid origin.
ICBN. International Code of Botanical Nomenclature.
ICNB. International Code of Nomenclature of Bacteria: Bacteriological Code.
ICVCN. International Code of Virus Classification and Nomenclature.
ICZN. International Code of Zoological Nomenclature.
infraspecific name. Under the ICZN, the third word in a subspecific or infrasubspecific trinomen.
internal specifier. A species, specimen or apomorphy that is explicitly included in the clade whose name is being defined (see external specifier). Every phylogenetic definition has at least one internal specifier, and all of the specifiers in standard node-based, apomorphy-modified node-based, and apomorphy-based definitions are internal.
lineage. A series of entities (e.g., organisms, populations) that form a single unbroken and unbranched sequence of ancestors and descendants. That a lineage is unbranched does not deny the existence of side-branches, which are not parts of the lineage in question, or of branching at lower organizational levels (e.g., organelle lineages within a population lineage). There may even be branching at the organizational level in question as long as it is judged to be temporary.
monophyletic. A set consisting of an ancestor and all of its descendants; usually used for groups the members of which share a more recent common ancestor with one another than with any non-members, though monophyletic groups of organisms within sexually reproducing species/populations may not have this property.
name. A word or words used to designate (refer to) an organism or a group of organisms. See acceptable name, accepted name, established name, replacement name, scientific name, taxon name.
new (clade) name. A newly proposed name that has been established in accordance with the rules of this code (see converted (clade) name)
node. A point or vertex on a tree (graph theory); on a phylogenetic tree, a node is commonly used to represent the split of one lineage to form two or more lineages (internal node) or the lineage at the present time (terminal node).
node-based clade. A clade originating from a particular node on a phylogenetic tree; a clade encompassing a particular node on a phylogenetic tree and all branches (internodes) and nodes descended from that node; a clade whose name is defined using a node-based definition. See Art 2.2.
node-based definition. A definition that associates a name with a clade originating at a node (on a phylogenetic tree) representing the most recent common ancestor of specified descendant organisms and/or species (internal specifiers). See Note 9.3.1.
nomen cladi conversum. See converted (clade) name.
nomen cladi novum. See new (clade) name.
nomen substitutum. See replacement name.
nominal author. The person(s) who first published a name, regardless whether it was phylogenetically defined (see definitional author).
orthography. The spelling of a name.
panclade name. A name that is derived from the name of a crown clade by the addition of the prefix Pan- and is used to designate the total clade of that crown clade. See Arts. 10.3–10.6.
paraphyletic. A set including an ancestor but excluding some or all of its descendants.
phylogenetic. Of or pertaining to the history of ancestry and descent.
phylogenetic definition. A statement explicitly linking a taxon name with a particular clade.
phylogenetic hypothesis (hypotheses). A proposition about the relationships among biological entities (e.g., species) in terms of common ancestry.
phylogenetic system (of nomenclature). An integrated set of principles and rules governing the naming of taxa and the application of taxon names that is based on the principle of common descent. This code describes a phylogenetic system of nomenclature.
phylogenetic tree. The diagrammatic representation of phylogeny as a tree in the sense of a minimally connected graph (number of branches = number of nodes minus one).
phylogeny. Evolutionary history; the history of descent with modification, whether in general or a particular part thereof. The term is also sometimes used for a hypothesis of phylogenetic relationships (as in the term reference phylogeny).
precedence. The order of preference among established names, used to select the accepted name from among them. In general, precedence is based on the date of establishment, with earlier-established names having precedence over later ones, but later-established names may be conserved over earlier ones.
preexisting name. A scientific name that, prior to its establishment under this code, was either: (a) "legitimate" (ICBN, ICNB), "potentially valid" (ICZN), or "valid" (ICVCN); or (b) in use but not governed by any code (e.g., zoological names ranked above the family group).
prenomen (prenomina). The first part of a species binomen in phylogenetic nomenclature. The prenomen of a species binomen in phylogenetic nomenclature is spelled the same as a genus name of rank-based nomenclature, but is not necessarily associated with the rank of genus.
protologue. Everything associated with a name when it was first established (under this code), validly published (ICBN, ICNB), or made available (ICZN), for example, description, diagnosis, phylogenetic definition, registration number, designation of type, illustrations, references, synonymy, geographical data, specimen citations, and discussion.
qualifying clause. A part of a phylogenetic definition that specifies conditions under which the defined name cannot be applied.
rank. The position in a hierarchy; in the case of biological nomenclature, the position in a hierarchy of nested taxa.
rank-based codes. The codes that govern the rank-based system of nomenclature—specifically, the International Code of Botanical Nomenclature, the International Code of Zoological Nomenclature, the International Code of Nomenclature of Bacteria and the International Code of Virus Classification and Nomenclature.
rank-based system (of nomenclature). An integrated set of principles and rules governing the naming of taxa and the application of taxon names that is based on taxonomic ranks (e.g., kingdom, phylum, etc.). Also referred to as the "traditional system."
reference phylogeny. A phylogenetic hypothesis that provides a context for applying a clade name by means of its phylogenetic definition.
replacement name. A new name explicitly substituted for a previously established name that is not acceptable because it is a later homonym. A replacement name is equivalent to a nomen substitutum in this code. (The term "replacement name" has been used in a broader sense under the ICZN to include what the ICBN refers to as a superfluous name and the ICZN refers to as an unnecessary substitute name.)
restricted emendation. A formal change in a phylogenetic definition that requires approval by the Committee on Phylogenetic Nomenclature; a restricted emendation is intended to change the application of a name through a change in the conceptualization of the clade to which it refers. See unrestricted emendation.
scientific name. A name that either is formed and governed by one of the codes of biological nomenclature or is of a similar Latinized form (e.g., zoological names ranked above the family group).
sister clade. One member of a pair of clades originating when a single lineage splits into two. Sister clades thus share an exclusive common ancestry and are mutually most closely related to one another in terms of common ancestry.
species. A segment of a population-level lineage that is evolving separately from other such lineage segments as indicated by one or more lines of evidence (e.g., distinguishability, reproductive isolation, monophyly, etc.).
specific name. Under the ICZN, the second word in a species binomen.
specifier. A species, specimen, or apomorphy cited in a phylogenetic definition of a name as a reference point that serves to specify the clade to which the name applies.
stem-based definition. See branch-based definition.
stem-modified node-based definition. See branch-modified node-based definition.
suppressed name. A name that would normally have precedence but does not, due to a decision by the Committee on Phylogenetic Nomenclature to give precedence to a later synonym or homonym.
synapomorphy. A shared, derived character state. In this code, a synapomorphy is a shared, derived character state inherited from a common ancestor that possessed that state; a shared, independently derived character state is not considered to be a synapomorphy in the sense the term is used in this code.
synonym. A name that is spelled differently than another name that refers to the same taxon. In the case of clade names, synonyms may be homodefinitional or heterodefinitional.
taxon (taxa). A taxonomic group of organisms. In this code, taxa may be clades or species.
taxon name. The word (or, in rank-based codes, words) used to designate a taxon.
total clade. A clade composed of a crown clade and all organisms (and species) that share a more recent common ancestor with that crown clade than with any extant organisms or species that are not members of that crown clade. Total clades are a subset of branch-based clades. See Art. 2.2.
type (= nomenclatural type). In the rank-based codes, the specimen, specimens, or subordinate taxon to which a taxon name is permanently attached; the type provides the standard of reference that determines the application of a name.
typified name. A name whose application is determined by a type under a rank-based code.
unconditionally suppressed name. A name that has been suppressed by the Committee on Phylogenetic Nomenclature in all phylogenetic contexts (see suppressed name); there are no conditions under which it would have precedence over any other name.
uninomen (uninomina). A name composed of a single word; in this code, the term is used to refer to the second part of a species binomen that is being treated as the name of a species (though the names of clades are also uninomina).
unrestricted emendation. A formal change in a phylogenetic definition that does not require approval by the Committee on Phylogenetic Nomenclature; an unrestricted emendation is intended to prevent undesirable changes in the application of a particular name (in terms of clade conceptualization) when the original definition is applied in the context of a revised phylogeny. See restricted emendation.