The ultrastructure of Placus striatus and a revision of the family Placidae (Ciliophora).

The first ultrastructural description of the genus Placus is presented. Each somatic kinetosome has a cone-shaped axosomal plate, nonoverlapping postciliary microtubules, an anteriorly directed kinetodesmal fiber, and a radial ribbon of transverse microtubules, which extend laterally under the ciliary furrow and insert in the cortical ridge. A closed ring of paired kinetosomes encircles the cytostome.

A molecular and ultrastructural description of Spathidiopsis buddenbrocki and the phylogenetic position of the family Placidae (Ciliophora).

Spathidiopsis and Placus are the only two genera within the family Placidae. The family has been placed in the class Prostomatea and order Prorodontida because its members have somatic monokinetids with a radial transverse ribbon, a straight non-overlapping postciliary ribbon, and anteriorly directed non-overlapping kinetodesmal fibril, an apical cytostome lacking specialized oral cilia, a brosse, and toxicysts. To confirm the stability of this placement, ultrastructural morphology and small subunit rRNA gene sequences of Spathidiopsis socialis, Spathidiopsis buddenbrocki, and Placus striatus were determined.

Phylogeny and systematic position of Zosterodasys (Ciliophora, Synhymeniida): a combined analysis of ciliate relationships using morphological and molecular data.

The Synhymeniida is characterized both by a band of somatic dikinetids, the synhymenium, extending across the surface of the cell and by a ventral cell mouth lacking specialized feeding cilia but subtended by a well-developed cyrtos. The synhymeniids have been hypothesized to be members of the class Nassophorea but our previous ultrastructural study of the synhymeniid genus Zosterodasys did not show any clear synapomorphies that would permit definitive placement in the Nassophorea or as a sister taxon to any of the other ciliate groups possessing a cyrtos. In the present study, simultaneous analysis of morphological and small subunit rDNA molecular data indicates that the Synhymeniida are sister to the class Phyllopharyngea and that this clade is, in turn, sister to the remaining Nassophorea, although this result is sensitive to dataset inclusion and alignment parameters.

Folliculinid ciliates: a new threat to Caribbean corals?

This is the first report of a putative pathogenic ciliate protozoan that has been associated with Caribbean corals. Previously, only 2 species of the phylum Ciliophora had been linked to coral diseases, and they were exclusive to the Indo-Pacific region. In this study, a ciliate of the genus Halofolliculina was found on 10 hard coral species at the National Parks of Los Roques and Morrocoy, Venezuela.

The misleading effects of composite taxa in supermatrices.

With the amount of available sequence data rapidly increasing, supermatrices are at the forefront of systematic studies. As an alternative to supertrees, supermatrices utilize a total evidence approach where different genes and other lines of data are merged into a single data matrix, which is then analyzed in an attempt to obtain the phylogeny that best explains the data. However, questions may arise when combining data sets in which one or more taxa do not have sequences available for each individual gene.

A simple test: evaluating explanations for the relative simplicity of the Edwardsiidae (Cnidaria: Anthozoa).

Many members of the cnidarian subclass Zoantharia (sea anemones, corals, and their allies) pass through a larval stage with eight complete mesenteries and without posterior musculature. This larva is usually transient, developing into an adult with 12 or more mesenteries. The adults of one family of sea anemones, the Edwardsiidae, bear the larval number and arrangement of mesenteries and lack the pedal disc seen in other sea anemones.

Character Coding and Inapplicable Data.

Inapplicable character states occur when character complexes are absent or reduced in some of the taxa. Several approaches have been proposed for representing such states in a character matrix so that the inapplicable condition has no effect on the placement of taxa and/or the applicable states are independent and not redundant. Here we examine each of these approaches and demonstrate that all have shortcomings.

Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes.

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most-parsimonious trees, and finding them all may be impossible using convential phylogenetic methods.

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING.

Abstract- Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor-joining bootstrapping.

PARSIMONY, HOMOLOGY AND THE ANALYSIS OF MULTISTATE CHARACTERS.

Abstract- The order of states in a transformation series describes an internested set of synapomorphies. States adjacent to each other in the transformation series thus share a degree of homology not found in the other states. Whether the level of homology is relatively apomorphic is determined by rooting the order with outgroup comparison.

PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET.

Abstract- When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious.

THE EUKARYOTIC KINGDOMS.

Abstract- Cladistic analysis of data from ultrastruetural and other cell biological studies indicates that neither the classical two kingdom nor the commonly accepted five kingdom classifications accurately represent the cellular diversity of eukaryotes. The resulting cladogram indicates instead that there are nine major groups of eukaryotes.