Clade

A clade is a taxonomic group (such as one of organisms) comprising a single common ancestor and all the descendants of that ancestor. Any such group is considered to be a monophyletic group, and can be represented by both a phylogenetic analysis, as in a tree diagram, and by a cladogram (see cladistics), or simply as a taxonomic reference.  

Main article: Cladistics

If a clade proves robust in alternate cladistic analyses using different sets of data, it may be adopted into taxonomy and become a taxon. Not all taxa, however, are considered to be clades. Reptiles, for example, are a paraphyletic group because they do not include aves (birds), which are thought to also have evolved from the common ancestor of the reptiles.

In cladistics, a clade that is located within another more inclusive clade is said to be "nested" within that clade. Nested clade analysis is beneficial in many ways. For instance, it enables the detection of range expansions in isolated geographic areas.

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Phylogenetic nomenclature

Traditional binomial nomenclature

In phylogenetics, binomial names are associated with the relationships of each described species. But this creates a problem because it makes assumptions about relationships about the description of the species identification. It suggests that species or genera are a unique category, and this contradicts the idea of recognizing only clades and lineages.

Relation to paraphyletic and polyphyletic groups

    Groups that do not include all the descendants of the most recent common ancestor are said to be paraphyletic. For example, as shown in the adjacent illustration, reptiles are paraphyletic because that group excludes birds. A group that does not contain the most recent common ancestor of its members is said to be polyphyletic (Greek polys = many). An example of a polyphyletic group is the warm-blooded animals.

Phylogenetic alternatives

To avoid the pitfalls of traditional Linnaean taxonomy in phylogenetic nomenclature, three new methods of phylogenetic naming have been proposed: node-, stem-, and apomorphy-based. In node-based naming, taxon name A might refer to the least inclusive clade containing X and Y. In stem-based naming, A would refer to the most inclusive clade containing X and Y but not Z. In apomorphy (derived feature)-based naming, A would refer to the clade identified by a feature synapomorphic (sharing a derivation) with a feature in specimen (taxon) X. Differences between a traditional approach and these phylogenetic alternatives become obvious when the phylogenetic hypothesis changes. Comparison between the traditional Linnaean approach to nomenclature and a phylogenetic alternative (node-based naming). Suppose that all we want to do is to give a name ("A") to a clade containing X and Y. In the Linnaean system this means that we have to introduce names for sister taxa, assigning all taxa to the categories species, genus, and family, and designate type species. No explicit reference to phylogeny is made. The phylogenetic alternative provides an explicit reference to evolutionary history, and nothing but the clade containing X and Y needs to be named. When the hypothesis of relationship changes, the phylogenetic alternative is cleaner and more explicit about what it refers to.