Editing PhyloCode (section)

==Phylogenetic nomenclature==
{{main|Phylogenetic nomenclature}}

Unlike rank-based [[Nomenclature code|nomenclatural codes]] (''ICN'', ''ICZN'', ''ICNB''), the ''PhyloCode'' does not require the use of [[taxonomic rank|ranks]], although it does optionally allow their use.<ref>{{cite web|url=http://phylonames.org/code/articles/3 |title=International Code of Phylogenetic Nomenclature, Version 4b - Article 3. Hierarchy and Rank |publisher=Ohiou.edu |access-date=2010-07-07}}</ref><ref>Although note that the ''PhyloCode'' does not permit a taxon's name to change when its rank changes, while the rank-based codes require this for at least some names.</ref> The rank-based codes define [[taxon|taxa]] using a rank (such as [[genus]], [[family (biology)|family]], etc.) and, in many cases, a [[Biological type|type specimen or type subtaxon]]. The exact content of a taxon, other than the type, is not specified by the rank-based codes.

In contrast, under phylogenetic nomenclature, the content of taxa are delimited using a definition that is based on [[phylogeny]] (i.e., ancestry and descent) and uses specifiers (e.g., species, specimens, apomorphies) to indicate actual [[organisms]]. The formula of the definition indicates an ancestor. The defined taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically defined taxon relies on a phylogenetic hypothesis.

The following are examples of types of phylogenetic definition (capital letters indicate specifiers):<ref>{{cite web|url=http://phylonames.org/code/articles/9 |title=International Code of Phylogenetic Nomenclature, Version 4b - Article 9. General Requirements for Establishment of Clade Names |publisher=Ohiou.edu |access-date=2010-07-07}}</ref>
* '''Node-based''': "the clade originating with the [[most recent common ancestor]] of A and B" or "the least inclusive clade containing A and B"
* '''Branch-based''': "the clade consisting of A and all organisms or species that share a more recent common ancestor with A than with Z" or "the most inclusive clade containing A but not Z."  Another term for definitions of this sort is '''stem-based'''.
* '''Apomorphy-based''': "the clade originating with the first organism or species to possess apomorphy M inherited by A".
Other types of definition are possible as well, taking into account not only organisms' phylogenetic relations and apomorphies but also whether or not related organisms are [[Extant taxon|extant]].

The following table gives examples of phylogenetic definitions of clades that also have ranks in traditional nomenclature. When all the specifiers in a node-based definition are extant specimens or species, as in the following definition of Mammalia, a [[crown group]] is defined. (The traditional definition of Mammalia is less restrictive, including some fossil groups outside of the crown group.)<ref>{{cite journal|last=Anderson|first=Jason S.|title=Use of Well-Known Names in Phylogenetic Nomenclature: A Reply to Laurin|journal=Systematic Biology|year=2002|volume=51|issue=5|pages=822–827|doi=10.1080/10635150290102447|pmid=12396594|doi-access=free}}</ref> 
{| class="wikitable"
|-
! Name
! Rank
! Type
! Possible phylogenetic definition
|-
| [[Tyrannosauridae]]
| Family
| ''[[Tyrannosaurus]]''<br />Osborn 1905
| Least inclusive clade containing ''[[Tyrannosaurus rex]]'' Osborn 1905, ''[[Gorgosaurus libratus]]'' Lambe 1914, and ''[[Albertosaurus sarcophagus]]'' Osborn 1905
|-
| [[Mammalia]]
| Class
| N/A
| Clade originating with the most recent common ancestor of humans, ''[[Human|Homo sapiens]]'' Linnaeus 1758, and platypuses, ''[[Platypus|Ornithorhynchus anatinus]]'' Shaw 1799
|-
| [[Rodent]]ia
| Order
| N/A
| Most inclusive clade containing the house mouse, ''[[House mouse|Mus musculus]]'' Linnaeus 1758, but not the eastern cottontail, ''[[Eastern cottontail|Sylvilagus floridanus]]'' Allen 1890
|-
| [[Neornithes]]<br>(Modern birds){{check|date=March 2025}}<!-- shouldn't that be Theropoda (if Ornithoscelida is accepted) or Saurischia (if Ornithoscelida is rjected)? -->
| Subclass
| N/A
| Clade originating with the most recent common ancestor of the extant members of the most inclusive clade containing the house sparrow [[house sparrow|''Passer domesticus'']] Linnaeus 1758 but not the dinosaur [[Stegosaurus|''Stegosaurus armatus'']] Marsh 1887
|-
| [[Tetrapoda]]
| Superclass
| N/A
| Clade originating with the earliest ancestor from which ''[[Human|Homo sapiens]]'' Linnaeus 1758 inherited limbs with fingers or toes
|}