New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence

The phylum Euglenozoa consists of three distinct groups: the euglenoids, di plonemids and kinetoplastids. The phylogenetic position of the diplonemids within this phylum remains unsettled, since both morphological and molecula r data produce weak and contradictory results. It is shown here that taxono mic sampling, G+C content bias, mutational saturation and differences of ev olutionary rate among lineages are major factors affecting the topology of the small-subunit rRNA euglenozoan tree. When these problems are minimized by using a larger diplonemid sampling (including a sequence of environmenta l origin) and correcting for G+C bias (by using both paralinear distances o r an unbiased dataset), a diplonemids+euglenoids sisterhood is retrieved. B ootstrap support for this relationship is still moderate, but it is retriev ed by all analysis methods, overcoming previously reported disagreements. I n addition, the inclusion of a large number of euglenoid sequences in the a nalysis improves some phylogenetic relationships within this group. Some pr oblematic taxa, such as the species Khawkinea quartana, are now placed with high bootstrap support and monophyly is found for two interesting groups ( the photosynthetic genera Eutreptia+Eutreptiella and the loricate genera St rombomonas+Trachelomonas), although with weak statistical support.