Glossary
This is a compilation of all of the necessary terms to help completely understand phylogenetics, herpetology, and herpetoculture.  Most of the phylogenetic terms were derived from the PhyloCode.  These are very valuable terms and should be read and looked over with care.
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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 conceptualized in terms of an apomorphy (i.e., a clade stemming from the ancestor in which a particular 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 9.4.1.


apomorphy-modified node-based definition
A node-based definition that incorporates wording from apomorphy-based definitions to include certain (usually extant) organisms as internal specifiers without explicitly naming them. See Note 9.4.1. 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.


categorical rank
In the preexisting codes, a formal taxonomic rank such as family or genus.


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.


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 within which both of the basal branches have extant representatives.


crown clade definition
Any definition that ties a name to a crown clade—e.g., stem- 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).


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
A brief statement of the features of a taxon that collectively distinguish it from other taxa with which it might be confused.

established name
A name that is published in accordance with Article 7 of this code, which may or may not be an acceptable or accepted name.


external specifier
A specifier that is explicitly excluded from the clade whose name is being defined. Stem-based definitions have external specifiers, but node- and apomorphy-based definitions do not (see internal specifier).


heterodefinitonal
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 but potentially refers to a different taxon. In this code, homonyms are established and identically spelled clade names based on different phylogenetic definitions.


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.


internal specifier
A specifier that is explicitly included in the clade whose name is being defined. All specifiers in node-based and apomorphy-based definitions are internal, but only some of the specifiers in stem-based definitions are (see external specifier).


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-based clade
A clade conceptualized in terms of a node (i.e., a clade encompassing all branches stemming from a particular node on a phylogenetic tree); a clade whose name is defined using a node-based definition.


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 9.4.1.


nomen cladi conversum
See converted (clade) name.


nomen cladi novum
See new (clade) name.


nomen substitutum
Replacement name.


orthography
The spelling of a name.


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 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.


polyphyletic
A group that has multiple phylogenetic origins and thus excludes the most recent common ancestor of its members.


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 codes
The codes of biological nomenclature that were in operation when the PhyloCode was drafted (1997-2000)—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.


preexisting name
A scientific name that, prior to its establishment under the PhyloCode, was either: (a) "legitimate" (ICBN, BC), "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).


protologue
Everything associated with a name when it was first established (PhyloCode), validly published (ICBN, BC), 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-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."


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 and this code refer to as a superfluous name and the ICZN refers to as an unnecessary substitute name.)


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).


species
A segment of a population-level lineage that is separate from other such lineage segments as indicated by one or more of various possible criteria (e.g., distinguishability, reproductive isolation, monophyly, etc.).


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 clade
A clade conceptualized in terms of a branch or stem (i.e., a clade consisting of one entire branch stemming from a particular node on a phylogenetic tree); a clade whose name is defined using a stem-based definition.


stem-based definition
A definition that associates a name with a clade originating with a stem (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 9.4.1.


stem-modified node-based definition
A node-based definition that incorporates wording from stem-based definitions to include certain (usually extant) organisms as internal specifiers without explicitly naming them. See Note 9.4.1. Stem-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.


superfluous name
A name that was substituted for another name that was acceptable and should therefore have been used.


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
A taxonomic group of organisms. In this code, taxa may be clades or species, though the rules of this code apply only to clade names.


taxon name
The word (or, in preexisting codes, words) used to designate a taxon.


total clade
A clade composed of a crown clade and all species and/or organisms that share a more recent common ancestor with that crown clade than with any other mutually exclusive crown clade.


type (= nomenclatural type)
In the preexisting 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.


unconditionally suppressed name
A name that has been suppressed by the CPN in all phylogenetic contexts (see suppressed name); there are no conditions under which it would have precedence over any other name.