PhyloCode: Division II. Rules; Chapter I. Taxa

Article 1. Categories of Taxa

1.1

The groups of organisms or species considered potential recipients of scientific names are called taxa (singular: taxon). The only taxa whose names are governed by this code are clades. However, species, whose names are governed by the rank-based codes, are frequently used to define clade names in this code.

Article 2. Clades

2.1

In this code, a clade is an ancestor (an organism, population, or species) and all of its descendants.

Note 2.1.1

Every individual organism (on Earth) belongs to at least one clade (i.e., the clade comprising all extant and extinct organisms, assuming that they share a single origin). Each organism also belongs to a number of nested clades (though the ancestor of the clade comprising all life—again assuming a single origin—does not belong to any other clade).

Note 2.1.2

It is not necessary that all clades be named.

Note 2.1.3

Clades are often either nested or mutually exclusive; however, phenomena such as speciation via hybridization, species fusion, and symbiogenesis can result in clades that are partially overlapping (Fig. 1).

Fig. 1

Speciation via hybridization (a) and species fusion (b) can result in clades that are partially overlapping. In (a), the origin of species X via hybridization (represented by the dashed line) between members of species B and C results in partial overlap between the largest clade containing A but not D (or the smallest clade containing both A and B), which is composed of A, B, and X, and the largest clade containing D but not A (or the smallest clade containing C and D), which is composed of C, D, and X, in that X is part of both clades. In (b), fusion of species G and H to form species Y (with the two parent species disappearing in the process) results in partial overlap between the largest clade containing E but not J (or the smallest clade containing both E and G), which is composed of E, F, G, and Y, and the largest clade containing J but not E (or the smallest clade containing both H and J), which is composed of H, I, J, and Y, in that Y is part of both clades.

2.2

In this code, a clade is called a crown clade if it originates in the most recent common ancestor of two or more extant species or organisms. A clade is called a total clade if it is composed of a crown clade and all species or organisms that share a more recent common ancestor with that crown clade than with any extant species or organisms that are not members of that crown clade. This code governs all formal clade names, many of which designate neither crown nor total clades.

Article 3. Hierarchy and Rank

3.1

The system of nomenclature described in this code is independent of categorical rank (e.g., genus, family, etc.). Although clades are hierarchically related, and therefore intrinsically ranked in the sense that some are more inclusive than others, assignment of categorical ranks is not part of the formal naming process and has no bearing on the spelling or application of clade names.

Example 1

If the name Iguanidae were defined as referring to a clade originally ranked as a family, and if that clade were later ranked as a subfamily and (at the same time) a larger clade ranked as a family, the reference of the name Iguanidae would not change to the larger clade, nor would the spelling of that name change (i.e., to Iguaninae) to reflect the new rank of the clade to which it refers.

Note 3.1.1

This code does not prohibit, discourage, encourage, or require the use of categorical ranks.

3.2

The concepts of synonymy, homonymy, and precedence adopted in this code (see Arts. 12–14) are, in contrast to the rank-based codes, independent of categorical rank.