Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater.

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Byline: Steven Godfrey Brian Kelly was hired to answer a question college football has stopped asking, and one LSU never needed to consider. For the better part of two decades, [...]

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Phylogenetic relationships in the genus Helvella were investigated using both LSU rDNA sequences and morphological features. The latter were coded and included in the analyses, resulting in better-supported clades. Helvella is monophyletic and Wynnella is its sister genus. Aporhynchous vs. pleurorhynchous asci are the synapomorphies for the 2 subgenera, Leucomelaenae and Helvella, which were confirmed as natural groups. Other recovered supported clades were section Leucomelaenae in the subgenus Leucomelaenae, and sections Elasticae, Helvella, and Lacunosae within the subgenus Helvella. Generic description, comments on taxonomically informative features, species complexes, and species that need typification are presented.

An increasing number of researchers have applied secondary-structure based multiple alignments of rDNA genes in phylogeny. These studies mostly depended on a few valuable divergent domains in LSU and SSU rDNA. Yet other divergent domains, e.g. D1, were poorly investigated and rarely used. However, these domains might contain additional evolutionary data and play a vital role in DNA-based phylogenetic study. Here, we investigated all available D1 sequences of Arachnida taxa and predicted corresponding secondary structures to help identify homologous positions in the D1 region. Long insertions were found exclusive to Eriophyoidea and folded into three newly proposed helices. Non-Acari taxa were all GC rich. In Acari, most Trombidiformes and all Mesostigmata (Parasitiformes) taxa were AT rich and Ixodida (Parasitiformes) GC rich; however there was no consistent base bias in Sarcoptiformes sequences. For Eriophyoid mites, genera Cecidophyopsis and Aceria were both well supported in MP, NJ, ME and ML tress based on D1 sequences, and clusters of Cecidophyopsis species were identical with former study. This demonstrated that the D1 region could act as a valuable molecular marker in phylogenetic reconstruction of Eriophyoidea. Additionally, D1 has been proven suitable in phylogenetic analysis at the family and genus level in Acari, but not in Opiliones.