The current paradigm of eukaryotic evolution is based primarily on comparative analysis of ribosomal RNA sequences. It shows several early-emerging lineages, mostly amitochondriate, which might be living relics of a progressive assembly of the eukaryotic cell. However, the analysis of slow-evolving positions, carried out with the newly developed slow-fast method, reveals that these lineages are, in terms of nucleotide substitution, fast-evolving ones, misplaced at the base of the tree by a long branch attraction artefact. Since the fast-evolving groups are not always the same, depending on which macromolecule is used as a marker, this explains most of the observed incongruent phylogenies. The current paradigm of eukaryotic evolution thus has to be seriously re-examined as the eukaryotic phylogeny is presently best summarized by a multifurcation. This is consistent with the Big Bang hypothesis that all extant eukaryotic lineages are the result of multiple cladogeneses within a relatively brief period, although insufficiency of data is also a possible explanation for the lack of resolution. For further resolution, rare evolutionary events such as shared insertions and/or deletions or gene fusions might be helpful.

Molecular phylogenetic analyses, based mainly on ribosomal RNA, show that three amitochondriate protist lineages, diplomonads, microsporidia, and trichomonads, emerge consistently at the base of the eukaryotic tree before groups having mitochondria. This suggests that these groups could have diverged before the mitochondrial endosymbiosis. Nevertheless, since all these organisms live in anaerobic environments, the absence of mitochondria might be due to secondary loss, as demonstrated for the later emerging eukaryoteEntamoeba histolytica. We have now isolated fromTrichomonas vaginalisa gene encoding a chaperone protein (HSP70) that in other lineages is addressed to the mitochondrial compartment. The phylogenetic reconstruction unambiguously located this HSP70 within a large set of mitochondrial sequences, itself a sister-group of α-purple bacteria. In addition, theT. vaginalisprotein exhibits the GDAWV sequence signature, so far exclusively found in mitochondrial HSP70 and in proteobacterial dnaK. Thus mitochondrial endosymbiosis could have occurred earlier than previously assumed. The trichomonad double membrane-bounded organelles, the hydrogenosomes, could have evolved from mitochondria.

The molecular phylogeny of eukaryotes was first based on the comparison of the small-subunit ribosomal RNA (SSU rRNA) and quickly became a paradigm (Sogin 1991<$REFLINK> ). However, serious criticisms have recently been raised against it. In particular, it has been suggested that the various protist lineages that emerged first (e.g., microsporidia, trichomonads, mycetozoans) were misplaced because of the long-branch attraction (LBA) artifact (Philippe and Adoutte 1998<$REFLINK> ; Philippe and Laurent 1998<$REFLINK> ; Germot and Philippe 1999<$REFLINK> ; Moreira, Le Guyader, and Philippe 1999<$REFLINK> ; Roger et al. 1999<$REFLINK> ; Stiller and Hall 1999<$REFLINK> ). Indeed, simulation studies (unpublished data) showed that when a distant outgroup was used, all the standard methods of phylogenetic reconstruction artifactually inferred a phylogeny with an asymmetrical base containing the fast-evolving lineages, leading to a tree shape very similar to the rRNA one.