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.

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.

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, 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.