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Evolution of Tubulins (dm)

Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondriate protists. They share ultrastructural similarities with other eukaryotes that occupy basal positions in molecular phylogenies. Their mitochondria genome architecture is also eubacteria-like, suggesting a close affinity with the ancestral alpha proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. Tubulin gene phylogenies are in general agreement with mitochondrial gene phylogenies and ultrastructural data, indicating that the “jakobids” may be polyphyletic. Relationships to the putatively deep-branching amitochondriate diplomonads remain uncertain.

Since the 1980s, diplomonads and their relatives retortamonads have been proposed as primitive eukaryotes that diverged before the acquisition of mitochondria. On this basis they became key organisms in attempts to understand the evolution of eukaryotic cells. Recent findings of mitochondrial-like genes in Giardia suggest that diplomonads may have lost mitochondria. However, the mitochondrial origins of some of these genes are highly questionable, and premitochondrial diplomonad scenarios are still advanced. In this phylogenetic examination we focus on a series of mostly poorly-known eukaryotes argued to be related to diplomonads on morphological grounds; the excavate taxa. Phylogenies of SSUrRNA genes, alpha tubulin, beta tubulin and concatenated alpha + beta tubulin all scatter the various excavate taxa across the diversity of eukaryotes. However all phylogenies place the excavate taxon Carpediemonas as a close relative of diplomonads (and with SSUrRNA, retortamonads), to the exclusion of all other eukaryotes. This novel relationship is recovered across phylogenetic methods and various taxon-deletion experiments and under different SSUrRNA alignments. Statistical support is strongest under maximum likelihood (when among-site rate variation is modelled) and when the most divergent diplomonad sequences are omitted, suggesting a true relationship rather than a long-branch attraction artefact. As Carpediemonas contains double membrane-bound organelles that are reminiscent of mitochondria, we speculate on the possible occurrence of mitochondria in the ancestors of diplomonads. The phylogenetic position of Carpediemonas suggests that it will be valuable in interpreting the evolutionary significance of many molecular and cellular biological peculiarities of diplomonads.