Genus Ceratomyxa comprises coelozoic parasites of mainly marine and brackish water fish. This study describes a new Ceratomyxa species, Ceratomyxa schwanefeldii n. sp. which parasitizes the gall bladder of Barbonymus schwanefeldii collected from Sungai Tong in Setiu, Terengganu, Malaysia. The new species was described using morphological characteristics, and on nucleotide sequences of small subunit ribosomal DNA (SSU rDNA) and large subunit ribosomal DNA (LSU rDNA). Ceratomyxa schwanefeldii n. sp. exhibited vermiform shape plasmodia with slow undulatory motility, measuring 151.6 ± 86.0 (43.0–271.0) μm in length and 15.1 ± 4.8 (9.3–22.7) μm in width, with blunt poles at both ends. The mature spores were crescent-shaped, strongly arched in frontal view, with a sutural line between the two valves tapering to blunt ends. Formalin-fixed spores were 3.0 ± 0.4 (2.4–3.9) μm in length, 12.6 ± 1.2 (10.8–15.4) μm in thickness, with a concave posterior angle, 104.8° ± 10.2° (73.4–123.8). Two equal-sized spheroid polar capsules measured 1.5 ± 0.2 (1.2–1.8) μm in length and 1.3 ± 0.2 (0.9–1.7) μm in width. Phylogenetic analyses by Maximum likelihood and Bayesian Inference algorithms positioned C. schwanefeldii n. sp. as a sister species to Unicapsulocaudum mugilum and clustered within the clade of Amazonian freshwater Ceratomyxa species. The LSU rDNA phylogeny revealed that C. schwanefeldii n. sp. clusters within the marine Ceratomyxa clade and forms a sister relationship with C. leatherjacketi. This study represents the first description of a freshwater Ceratomyxa in Malaysia and the fourth recorded detection in the Asian region.

No summary available.

Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a “doublet” model for pairing sites (rRNA-helices) and compared our findings with the results of “standard” approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.

Although the taxonomy of oligotrich ciliates has been widely investigated, yet the species diversity remains poorly known. We newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region, and it was effective for detecting oligotrich species. Using the primers, we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China Sea. In total, 165 oligotrich sequences were obtained from five widely separated sampling sites. Sixty operational taxonomic units (OTUs) were obtained at 99% similarity threshold, and low-abundance OTUs with no more than two sequences contributed most of these (about 78%). Our findings are consistent with previous morphological studies, Strombidium was found the most abundant and widely distributed genus in this area. In addition, the BLAST search in the NCBI database resulted in 95% OTUs matching with named oligotrich species in similarity below 99%. Therefore, oligotrich morphospecies diversity has been underestimated as low-abundance species, and the LSU rDNA oligotrich sequence database needs to be better promoted.

No summary available.

Summary A detailed ultrastructural analysis of the type species of Gyrodinium, G. spirale, was made based on cells collected from Skagerrak and southern Kattegat (Denmark). This material is considered very similar to the type material studied by Bergh from southern Kattegat. The analysis revealed many characters typical for dinoflagellates as well as a number of previously undescribed features. Here, emphasis was given to a three-dimensional configuration of the flagellar apparatus, the surface ridges, and the nuclear capsule. The latter had a rather complex ultrastructure consisting of two wall-like layers surrounded by membranes, with nuclear pores restricted to globular invaginations of these layers. To overcome difficulties with culturing of many auto- and heterotrophic dinoflagellates, we designed a specific reverse primer to amplify ca. 1800 base pairs of nuclear-encoded LSU rDNA. Using this approach, LSU rDNA sequences were determined from three heterotrophic species of Gyrodinium, including the type species. Using other alveolates (i.e. ciliates and Apicomplexa) as outgroup species, phylogenetic analyses based on Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining supported Gyrodinium as a separate lineage. Unfortunately, the nearest sister group to Gyrodinium could not be established due to low bootstraps support for the deep branching pattern.