What Is Phylogenetic Nomenclature?

Sometimes when discussing the PhyloCode, I get the feeling a lot of potentially interested parties don't understand what phylogenetic nomenclature actually is. I have gone into excruciating detail on this topic elsewhere, but who wants to be excruciated? So here's a brief summary of the process of creating a phylogenetic taxonomy.

1. Declare Operational Taxonomic Units

Result: Alpha Taxonomy

The very first step is to decide what your units are. Are you dealing with individual organisms? Populations? Species? Which ones? Whatever you select, there should be an unambiguous way of referring to these taxonomic units (specimen numbers, species names, etc.).

Phylogenetic nomenclature is flexible as to how you determine and name taxonomic units. (Although the names must be relateable to those used in definitions [see Step 3].)

Example: My operational taxonomic units are the whale species Aetiocetus cotylalveus, Balaena mysticetus, Balaenoptera physalus, Delphinus delphis, and Monodon monoceros.

Operational Taxonomic Units
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0

2. Declare Intensional Sets

Result: Unions of Taxonomic Units

To be a be part of an intensional set, a unit must exhibit a certain state. Intensional sets include sets based on a derived character state (an apomorphy) as well as sets like "living organisms" or "extant organisms".

Note: This step is optional, but skipping it may make some definitions (Step 3) inapplicable.

Example: The extant operational units are Balaena mysticetus, Balaenoptera physalus, Delphinus delphis, and Monodon monoceros. The operational units exhibiting baleen are Aetiocetus cotylalveus, Balaena mysticetus, and Balaenoptera physalus.

Intensional Sets
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0

3. Associate Names with Phylogenetic Definitions

Result: System of Phylogenetic Nomenclature

Select a taxonomic name. Now associate it with a phylogenetic definition. The definition must refer to taxonomic units, either directly (by name) or indirectly (by referring to an intensional set). And the definition must require an ancestor-descendant relation for the units, but it must make no assumptions about the pattern of that relation (except that it be a partial order).

At this stage it is also useful to declare the priority of the names, in case any turn out to be synonyms.

Note: This step is the essence of what the PhyloCode will do. (Technically, I could have put it first.)

Example: "Delphinoidea" (Flower 1865) refers to the clade stemming from the final common ancestor of  Delphinus delphis and Monodon monoceros. "Apo-Mysticeti" (new name) refers to the clade stemming from the initial ancestor of Balaena mysticetus to exhibit baleen synapomorphic (homologous) with that of B. mysticetus. "Mysticeti" (Cope 1891) refers to the clade stemming from the final common ancestor of all extant apo-mysticetes. Priority of these names, from most to least preferred, goes: "Delphinoidea", "Mysticeti", "Apo-Mysticeti".

4. Determine Patterns of Descent

Result: Phylogenetic Hypothesis

Organize your units into an ancestor-descendant relation (a partial order). You will likely need to posit some hypothetical taxonomic units as ancestors. It may be necessary to infer hypothetical character states for them, for any apomorphy-based intensional sets.

Cladistic analysis is one way of coming up with a posited ancestor-descendant relation, but it is not the only one. Phylogenetic nomenclature is agnostic as to your methods.

Example: I posit four hypothetical units (A, B, C, and D) in addition to my five operational units. A is ancestral to all other units. B is ancestral to C, Aetiocetus cotylalveus, Balaena mysticetus, and Balaenoptera physalus. C is ancestral to Balaena mysticetus and Balaenoptera physalus. D is ancestral to Delphinus delphis and Monodon monoceros. None of the hypothetical units are extant. Units B and C are inferred to exhibit baleen synapomorphic (homologous) with that in Aetiocetus cotylalveus, Balaena mysticetus, and Balaenoptera physalus.

Hypothetical Taxonomic Units
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0

Phylogenetic Hypothesis
(Ancestry Relation, Reduced to Immediate Ancestry)
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0

Intensional Sets for All Units, Hypothetical and Operational
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0

5. Apply the Definitions

Result: Beta Taxonomy

At this point, the process of applying the definitions in Step 3 to the phylogeny in Step 4 is straightforward and objective.

Example: The final common ancestor of Delphinus delphis and Monodon monoceros is D, so Delphinoidea includes D, Delphinus delphis, and Monodon monoceros. B is the initial ancestor of Balaena mysticetus to exhibit baleen synapomorphic with that of B. mysticetus, so Apo-Mysticeti includes B, C, Aetiocetus cotylalveus, Balaena mysticetus, and Balaenoptera physalus. The extant apo-mysticetes are Balaena mysticetus and Balaenoptera physalus, and their final common ancestor is C, so Mysticeti includes C, Balaena mysticetus, and Balaenoptera physalus. None of these names are synonymous in this context, so priority is not needed to select between synonyms.

Phylogenetic Taxonomy
Silhouettes by Chris huh and T. Michael Keesey, taken from PhyloPic.
Image license: CC-BY-SA 3.0