Phylogeny and Systematics
A few definitions:
The science of organising living things into groups which reflect their natural, phylogenetic relationships, is called taxonomy. The groups are called taxa (sing. taxon, see below).
The published groups within each of the divisions in the phylogenetic hierarchy is known as a taxon. Like the relationships themselves, taxa fall into a hierarchy.
The lowest level taxon in most cases is the familiar species, which one can informally think of as a group of organisms which are so closely related that they can inter-breed freely. (This concept obviously fails for organisms which reproduce asexually, and in other circumstances also, but it is sufficient for now.)
Above the species level, grouping together similar species, is the genus (pl. genera). A familiar example of a genus is Pinus, to which several different but related species of pine tree belong. Above that again is the family, and so on.
From highest (most inclusive) to lowest (most specific), the major formal taxonomic units, or ranks are:
Intermediate divisions are often used, subspecies and variety being very commonly employed at the lower end.
To identify an organism is to determine which taxon it belongs to. An accurate identification is not only correct, but will identify an organism with a particular species.
However, it is not at all unusual, in practise, that an identification can only be made to genus or even higher level. There are many possible reasons. Perhaps the organism being identified is incomplete; some part (e.g. a flower) which is necessary for a completely accurate identification is not present. This problem is particularly acute when it comes to identifying fossils, which are more commonly fragmentary than not. In some cases, the species may not have been previously recognised, or even if recognised, not formally published.
In such cases, a relationship to a similar species which has been described might be indicated with an aff. indicating affinity to, or the less confident cf. meaning compare with.
In order to communicate biological information, it is essential to have universally understood name tags for the biological entities we are referring to. This labelling is theoretically possible by means of formulas or letters, though they are not euphonious and would be mnemonically difficult for most people. Instead, latinised names are employed.
The purpose of formal nomenclature is to provide a precise, simple, and stable system of unique names used by scientists in all countries. The system must allow for reasonable expansion and refinement to accommodate increasing knowledge. In other words, the stability must not become a straitjacket (Traverse 1996, p. 13). More
Homonyms are identical names for two different taxa.
Synonyms are different names for the same taxon.
Neither can be tolerated in a rational nomenclature. As a general rule, when these situations arise it is the first name to be published which is retained. However, the correct outcome is not always obvious because the distinction between taxa is often quite subjective. In fact, there are colloquial terms in common usage for scientists to tend to create inclusive taxa, with quite broad accommodation for variety (they are called lumpers) as opposed to those who subdivide very finely, creating taxa which accommodate very little variation at all (splitters). And, in fact, there is no right answer: man classifies; nature does not.
Although taxonomy has traditionally been associated with Linnaean nomenclature and classification, which was incorporated into evolutionary systematics, there is a tendency now to prefer to the cladistic system, and hence to create a cladistic taxonomy as an alternative to Linnaean. The problem here is the difference between the Linnaean and Cladistic systems is one of apples and oranges; one is a taxonomic, classification system, the other a means of constructing phylogenetic hypotheses; or in less jargonesque language, deciding which of a number of possible evolutionary trees is likely to be the more correct one (which doesn't mean it is the right one, as new discoveries can always overturn the current hypotheses). Trying to force Linnaean taxa into a cladistic mould creates endless confusion in the public mind, such as the statement "birds are dinosaurs". For this and other reasons, efforts to develop a formal, cladistic system of taxonomy and nomenclature to replace linnaean taxonomic methodology, while successful within certain specialised fields such paleoherpetology and "dinosaurology", has yet to catch on at a wider level.
Proceedings of a Mini-Symposium on Biological Nomenclature in the 21st Century — suggests replacing the Linnaean system with a cladistic phylogenetic system of nomenclature. However R. K. Brummitt in Quite Happy with the Present Code, Thank You — argues against the tendency to reduce the Linnaean system to the Cladistic one by eliminating paraphyletic taxa.
Dinosaurs and Evolution part 4 - by Jeff Polling, argues for the cladistic over the Linnaean scheme, with reference to Mononykus, a prehistoric animal that, like Archaeopteryx, was transitional between dinosaurs and birds (note: this page is part of a longer discussion regarding evolution and creationism).
page last modified MAK130330