Current Best Guess
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The most recent high-level taxonomy of the protists is Cavalier-Smith & Chao (2003). Cavalier-Smith has probably written more often, and to more effect, in this area than anyone else; and one has to start somewhere. Then, too, we agree with his overall approach to eukaryote phylogeny. In particular, we concur in his partiality for discrete character states (where available) in preference to raw sequence homologies. An outline of this scheme might be shown as follows:
Lest anyone assume that the choice is entirely arbitrary, we offer another recent tree, produced using entirely different data, from Baldauf et al. (2000).
In fairness, we have cheated a good deal to get this result. A number of taxa, which appeared in only one of the studies, were eliminated. We were aggressive in synonymizing groups; and we imposed a root on the Baldauf tree which would not be acceptable to those authors. Nevertheless, the correspondence is startling. The trees differ in the position of exactly one taxon. The Discicristata are "promoted" to being the sister of the Chromalveolata in the Baldauf tree, rather than being the sister of the Parabasalia and Diplomonadida, as in the Cavalier-Smith & Chao tree. Unfortunately, the difference in root may be significant. Baldauf et al. do not specify an explicit root, thereby inviting the sort of abuse to which we have subjected their tree. However, they clearly believe, as do most workers, that the root lies within Archaea and falls about where we have placed the 'R' in the diagram above. Cavalier-Smith has a very different understanding. He asserts that both Archaea and Eukarya are derived from Eubacteria and that the root lies at the top of the dendrogram above.
Before developing that thought, we may, in a fit of dangerous optimism, combine the two trees, adding back several levels of additional detail, as well as most of the taxa from both trees which were previously omitted for the sake of comparability.
In this setting, the problem of the correct root becomes acute. If we are to accept the conventional root, we find that it falls in a rather peculiar location on the Cavalier-Smith & Chao tree. However, on closer inspection, this location is not entirely unreasonable. There is nothing intuitively wrong with a eukaryote story which begins with monads, then throws out successive branches of euglenoids, forams and radiolarians, plants and alveolates, then amoebas, and finally animals and fungi. Stechman and Cavalier-Smith (2002) argue their position for the root based on the existence of a particular gene fusion resulting in a single enzyme with two, very closely coupled, activities (dihydrofolate reductase and thymidylate synthase). While this is certainly an interesting and distinctive character, the possibilities for lateral gene transfer at this level of the tree cannot be completely ignored, nor can we suppose that the fusion, once acquired, could not be reversed. In fact, the duplication of a gene, with subsequent divergent specialization of the two copies, is a standard event in evolution. Thus, it ought to be easier to unfuse a gene than to fuse it in the first place. All things considered, then, the best supported tree might be the Cavalier-Smith & Chao tree, but with the conventional root, which is our current best guess. In addition, we have modified this tree with some extra branches and rearrangements based on our experience since this section of Palaeos opened. ATW041223.
For all its faults, this tree does not require anomalies like the early derivation of uniquely specialized groups, such as amoebae. We have taken the liberty of adding one taxon, the "Metabiotiformes", simply because it is convenient to have a name for the clade which unites plants, animals and fungi. Here, the 'R' represents the Stechman & Cavalier-Smith (2002) root. If Cavalier-Smith turns out to be right about the root, Metabiotiformes is more or less synonymous with Eukarya. ATW030529.