Clade



A clade (from ancient Greek, klados, "branch") is a term used in modern alpha taxonomy, the scientific classification of living and fossil organisms, to describe a monophyletic group, defined as a group consisting of a single common ancestor and all its descendants. The common ancestor of any reasonably-sized group, and most of its descendants, will usually be long dead. It is not necessary for a clade to contain any living representatives.

The context
Ever since Darwin showed that all organisms share common ancestry, taxonomy has consistently attempted to represent and reflect the evolutionary history of organisms. The DNA and RNA analysis used in modern molecular biology has greatly helped in illuminating this history, by providing large amounts of new phylogenetic information which was previously unavailable to taxonomists. These techniques of study are known as molecular phylogenetics, and they have given rise to the modern discipline of cladistics and phylogenetic systematics.

This new information and new insights have made very clear what the limitations of the old Linnaean system of taxonomy were and are. As a result, many taxonomists are gradually revising in radical ways the taxonomy of the groups that they study. For an example of a taxonomy (in this case a taxonomy of the gastropods) which has been partially revised in order to incorporate insights from molecular work, please see Taxonomy of the Gastropoda (Bouchet & Rocroi, 2005).

Updating taxonomy
The term "clade" did not exist in the older Linnaean taxonomy, which was by necessity based only on morphological similarities between organisms. The concept embodied by the word "clade" does not fit well into the rigid hierarchy that the Linnaean system of taxonomy uses; indeed, Cladistics and Linnean taxonomy are not really compatible.

Linnaean taxonomy demands that all organisms be placed neatly into a rigid, ranked, hierarchy of taxa, such that one individual kind of organism must belong in one of each of the categories: species, genus, family, order, class, phylum and kingdom. Because of this necessity to "file things away neatly", the Linnaean system is often very convenient indeed in organizing such things as large museum reference collections, however it does not represent well the process of change that actually happens over evolutionary time.

Because clades can be nested at any level, they do not have to be neatly slotted into a rank in an overall hierarchy. In contrast, the Linnaean taxa of "order", "class" etc must all be used when naming a new taxon. They cannot be avoided, and each one implies a certain (admittedly very poorly defined) level of diversity, which is supposed to be equivalent throughout the system.

Species arise by gradual modification, not sudden complete changes or jumps, (although also see "punctuated equilibrium"), thus there is no sound biological basis to make a distinction between a species and its "descendant" species. This is another important area where cladistics is more valuable to biologists than Linnaean taxonomy; intermediate taxa can be named according to their relationship to named taxa using the stem group terminology.

For example, the famous fossil organism Archaeopteryx has a lot of bird-like characteristics, but is not a true bird. It is, in effect, a 'great-aunt' of the group that contains all modern birds and their shared ancestors. Since modern birds are not descended from Archaeopteryx, it cannot fit into the Linnean taxon 'Aves' (birds). In cladistic terms, however, Archaeopterix can be considered a stem group to the bird clade - it branched off from the bird lineage before the first member of that lineage resembled a true bird.

Naming clades
Since taxonomy intends to reflect evolutionary relationships, in order to be valid in evolutionary terms a taxon must be monophyletic - that is, it must be a clade. The rankings (taxa) used in traditional Linnaean taxonomy do not function well within a cladistic framework: for instance, there is no ranking applicable to stem groups, thus some new terminology has been developed.

Three methods of naming clades have been proposed: node-, stem-, and apomorphy-based:
 * In node-based naming, taxon name A refers 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.

Here is an example comparing the traditional Linnaean approach to nomenclature with 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 also have to introduce names for sister taxa, and assign all taxa to the categories species, genus, and family, and then designate type species. No explicit reference to the actual phylogeny is made when these categories are used. 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.