Critical analysis of eukaryotic phylogeny: A case study based on the HSP70family

Trichomonads, together with diplomonads and microsporidia, emerge at the ba se of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny . However, phylogenies based on protein sequences such as tubulin are marke dly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could he a reliable phylogenetic marker In eukaryotes. HSP70s are found in cytosol, endoplasmic reticulum, a nd organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly c omplete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitoch ondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters consid ered. Almost all the undoubtedly monophyletic groups, defined by ultrastruc tural characters, were recovered. However, due to the long branch attractio n phenomenon. the evolutionary rates were the main factor determining the p osition of species, even with the use of a close outgroup, which is an impo rtant advantage of HSP70 with respect to many other markers. Numerous varia ble sites are peculiar to Trichomonas and probably generated the artefnctua l placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of s pecies, and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.