This tree comes from a summary that Alastair Simpson and Andrew Roger wrote, and shows our best estimate of the evolutionary relationships amongst eukaryotes as of mid-2004 (Simpson and Roger, 2004 - Current Biology 14: R693-R696). The question mark indicates a possible position of the root of the tree, based on the DHFR-TS fusion character (Stechmann and Cavalier-Smith, 2002, also Philippe et al., 2000). Note that all of the six major groups of eukaryotes shown here are disputed by at least some active researchers, with Chromalveolata and Excavata being particularly controversial.
As of 2009 this tree is still a reasonably good summary, however, some issues are worth comment. The group labelled above as 'Plantae' often now goes by the name 'Archaeplastida', to largely avoid the confusion caused by numerous different uses of the name 'Plantae'. Recent phylogenies suggest that Rhizaria is likely to be related specifically to stramenopiles and alveolates, forming a 'SAR' clade, and there is still no convincing evidence for a specific relationship between the SAR clade and the Haptophytes and Cryptophytes. It is controversial whether Chromalveolates can be considered a monphyletic group, albiet one that likely includes Rhizaria, or whether Chromalveolates are actually polyphyletic. Excavata remains controversial, but a series of recent molecular phlyogenetic studies tend to support its monophyly. A couple of recent phylogenomic analyses suggest that Plantae/Archaeplastida, Rhizaria and the chromalveolate lineages are related to the exclusion of Excavata. The Excavata issue, and to a lesser extent the Chromalveolate issue are discussed in our recent paper by Hampl et al. (2009) - which references several other important studies. Within supergroups: nucleariid amoebae are probably the sister group to fungi; Haptophytes and cryptophytes are closely related (this clade also includes Kathablepharids and Telonema); Stramenopiles and alveolates are likely closely related (this has in fact been quite well supported well prior to 2004). Interestingly, there has been no real, lasting progress on the position of the root of the tree of eukaryotes, nor the positions of the orphan lineages shown with dotted lines.