About 1990 Carl Woese and colleagues proposed a radical new interpretation of the tree of life (evolutionary tree they called it). These scientists proposed three domains: eukaryotes, bacteria and archaea. Gone were the five kingdoms of R.H. Whittacker (1969): Monera (prokaryotes or bacteria); Protists (protozoans); Plants; Fungi; and Animals. Whittacker’s system was based on the shape and function of organisms as had all previous classification systems (such as Linnaeus’ separation of organisms into Plants and Animals). The new system however was to be based on phylogeny, the history of descent with modification as revealed in the genetic sequences.

Phylum among animals and division, among plants and fungi, are categories lower than domain and kingdom. At one time, a lot of divisions were recognized. In a textbook from 1973 for example, there were 28 divisions recognized among plants.  Now the number of divisions lies closer to 10. Nomenclature codes recognize 7 main taxonomic ranks: kingdom, phylum or division, class, order, family, genus and species. Domain is not mentioned in any nomenclature codes.

Nevertheless, domain is popularly considered to represent the highest level of separation and organization among organisms. All species in each domain are presumed to come from a line of descent separate from those taxa in the other two domains. However, as you can see from the discussion of Horizontal Gene Transfer (HGT), nobody is sure of any of this anymore. Since opinions change constantly concerning lines of descent, the taxonomic categories also change.

It is obvious that taxonomic categories are a very fluid system and cladistics (another system of classification) has thrown the whole issue further into disarray!