To minimise potential long branch attraction tree reconstruction artefacts, we discarded at this step the extremely fast evolving and or very partial sequences of Enterocytozoon bieneusi, Plasmodium spp. and B. hominis, all them having useful handbook 60% of miss ing data. We also discarded T. vaginalis because this species contained multiple copies of several APC C components and main targets. The resulting Bayesian and maximum likelihood trees recovered the monophyly of each eukaryotic phyla and most often supported by high Bayesian posterior probabilities and maximum likelihood bootstrap values, Discicristata, Het erokonta, Metazoa, Fungi, Choanoflagellata, Viridiplantae and Alveolata. The most remarkable result was the good support retrieved for the monophyly of Fungi, including the extremely fast evolving Microsporidia.

The APC C pro teins are therefore among the rare ones that sup port the correct phylogenetic placement of these parasites as members of the Fungi. Regarding the relationships among the main eukaryo tic groups, the sister grouping of the two choanoflagel lates and C. owczarzaki was supported both by the Bayesian and maximum likelihood trees, these two groups being closely related to Metazoa. This was in agreement with pre vious results, but not with those supporting the emergence of Capsaspora at the base of the group com posed of Choanoflagellata and Metazoa. The phylogenetic signal contained in APC C components and main targets also supported the monophyly of Opisthokonta.

Moreover, if we accept the putative unikont bikont rooting, our analyses also retrieved the Unikonta, including the apu sozoan Thecamonas trahens, albeit with a weaker sup port. Similarly, most of the relationships among bikont lineages were poorly resolved. In particular, the monophyly of Plantae was not recovered, green plants and algae appeared closely related to the haptophyte E. huxleyi, whereas the phylogenetic posi tion of red algae was not resolved. This agreed with other studies showing the difficulty to retrieve the monophyly of Plantae, even with much larger datasets. Finally, heterokonts formed the sister group of green plants and haptophytes. Taken together, our phylogenetic analyses showed that despite the relative small size of the supermatrix con structed with the APC C components and main targets, it contained an interesting phylogenetic signal that can be useful to infer part of the ancient evo lutionary history of eukaryotes.

However, the large size of most of the APC C subunits and GSK-3 main targets made difficult the use of the abundant body of sequence data coming from the analysis of expressed sequence tags because of their incomplete sequence coverage, which limited our taxonomic sampling. Nevertheless, our dataset can now be employed as a reference to enrich it with assembled EST sequences as well as with those from upcoming complete genome sequences from various protist species.