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Fig. 2 in What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora)

Fig. 2. Maximum Likelihood tree of the Oligotrichida inferred from small subunit ribosomal RNA (SSU rRNA) gene sequences (66 taxa and 1823 nucleotide positions) aligned with the Muscle algorithm (Edgar 2004) implemented in MEGA ver. 5.1 (Tamura et al. 2011). The alignment is available upon request. The tree was computed with RAxML (Stamatakis et al. 2008) and the datasets were bootstrap re-sampled 100 times. Support values are listed at the nodes. The second values at the nodes represent the posterior probability values of a Bayesian Inference analysis performed with MrBayes (Ronquist and Huelsenbeck 2003). Values below 50% and 0.5, respectively, are represented by a dash. * – initially published as Spirostrombidium sp.; ** – initially published as Parallelostrombidium sp.

Fig. 4 in What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora)

Fig. 4. Evolution of kinetid structures in the somatic ciliature of choreotrichid ciliates. The aloricate taxa have only one kinetid type, except for Leegaardiella elbraechteri and Lynnella. Tintinnids with ventral organelles have two (Tintinnidium, subgenus Tintinnidium), rarely one (Tintinnopsis cylindrata, Membranicola) or three (Tintinnidium, subgenus Semitintinnidium) kinetid types. Extant tintinnids with a ventral kinety have some dikinetids with two cilia and many monokinetids or some dikinetids with two cilia, some dikinetids with one cilium, and many monokinetids.

Fig. 1 in What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora)

Fig. 1. Hypothetical evolution of oligotrichid somatic ciliary patterns (0–IV, VI, VII, after Agatha 2011b; V, VIII–XIV, originals; protargol impregnation). Small arrows mark orientation of kineties (posterior to anterior). Arrowheads denote dorsal breaks in girdle kinety. Dotted arrows mark the tontoniid evolution. Dotted circles denote position of oral primordium in early dividers. Type 0 – dorsal kineties of hypotrich-like ancestor; Type I – strombidiid Parallelostrombidium; Type II – strombidiid Novistrombidium and tontoniid Tontonia; Type III – strombidiid Spirostrombidium; Type IV – strombidiid Omegastrombidium; Type V – strombidiid Strombidium, pelagostrombidiid Limnostrombidium, and tontoniid Pseudotontonia; Type VI – tontoniid Paratontonia; Type VII – tontoniids Laboea and Spirotontonia; Type VIII – strombidiid Foissneridium; Type IX – strombidiid Opisthostrombidium; Type X – cyrtostrombidiid Cyrtostrombidium; Type XI – strombi- diid Williophrya; Type XII – strombidiid Apostrombidium; Type XIII – hypothetic stage; Type XIV – strombidiid Varistrombidium. EX – extrusome attachment sites, GK – girdle kinety, OP – oral primordium, VK – ventral kinety.

Fig. 3 in What Morphology and Molecules Tell Us about the Evolution of Oligotrichea (Alveolata, Ciliophora)

Fig. 3. Maximum Likelihood tree of the Choreotrichida inferred from small subunit ribosomal RNA (SSU rRNA) gene sequences (138 taxa and 1859 nucleotide positions) aligned with the Muscle algorithm (Edgar 2004) implemented in MEGA ver. 5.1 (Tamura et al. 2011). The alignment is available upon request. The tree was computed with RAxML (Stamatakis et al. 2008) and the datasets were bootstrap re-sampled 100 times. Support values are listed at the nodes. The second values at the nodes represent the posterior probability values of a Bayesian Inference analysis performed with MrBayes (Ronquist and Huelsenbeck 2003). Values below 50% and 0.5, respectively, are represented by dashes. Branches with unambiguously clustered taxa are collapsed, species of the genus Tintinnopsis grouped in 5 different clades numbered I–V. Most common lorica structures: – hyaline; – entirely agglomerated; – composed of hyaline collar and agglomerated bowl; * – after Kofoid and Campbell (1929) a synonym of Codonella cratera; ** – does not correspond with the redescription of Agatha and Riedel-Lorjé (2006); *** – possibly incorrectly identified, might be Dadayiella acutiformis; **** – invalid taxon, very likely a replacement lorica (see text).

Fig. 12 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 12. Neoformation organelles in dividers of Limnostrombidium viride in the transmission electron microscope. (A) Oblique section of the organelle's distal (asterisk) and proximal portions with the outgrowing cilia of the oral primordium. The axonemes (arrowheads) are very short, lack the central pair of microtubules, and are bulbous because being embedded in many vesicles. (B) Cross section of cilia. Their axonemes already possess the "9×2+2" ultrastructure (arrowheads). (C) Tangential section of the neoformation organelle showing cross sections of cilia (arrowheads) and vesicles with electron-dense content of unknown function. (D) Longitudinal section of the posterior cell portion. Both the unciliated (arrowhead) and ciliated (double arrowhead) portions of the organelle are shown twice in cross section. MB, cell membrane; PE, perilemma; V, vesicles. Scale bars: 1 µm (A–C), 5 µm (D).

Fig. 11 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 11. Ring-canal of Limnostrombidium viride in the transmission electron microscope. The transverse section of the organelle shows its position between the anterior furrow (asterisk) and the stripe of extrusome attachment sites (arrow denotes the electron-dense cap of an empty "extrusome chamber"). Vesicles are adjacent to the irregular anterior membrane portion of the canal, while the posterior portion is underlain by two layers of perpendicularly orientated microtubules. ML, two layers of microtubules; PE, perilemma; RC, lumen of ringcanal; V, vesicles of unknown function. Scale bar: 1 µm.

Fig. 10 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 10. Extrusome attachment sites (A) and immature extrusomes (B, C) of L. viride in the TEM. (A) Freeze-fracture replica showing the extrusome attachment rosettes. (B, C) Transverse and longitudinal sections; white lines mark corresponding section planes. The extrusome shows in longitudinal section an electron-dense fusiform wall and an electron-light lumen with indistinct transverse stripes. The apical portion of the extrusome is surrounded by an electron-dense structure; both are enclosed by a membrane (arrowheads). The transverse section shows the extrusome to be composed of six electron-dense trapeziums arranged around a bright lumen. 1, attachment rosette with one central and eight peripheral particles; 2, first ring; 3, second ring; ED, electron-dense structure; EX, extrusomes. Scale bars: 1 µm.

Fig. 3 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 3. Oral ciliature of Limnostrombidium viride in the scanning (A) and transmission electron microscopes (B–D). (A) Proximal portion of the adoral zone of membranelles. The endoral membrane is usually covered by a cytoplasmic fold and a membranous sheet (probably perilemma). (B) Longitudinal section of the buccal lip and endoral membrane in ventral view. Note the numerous vesicles with fluffy content of unknown nature in the anterior cell half and especially in the buccal lip. The perilemma forms stacks in the buccal cavity, while it otherwise covers the cell only with a single layer. (C) Longitudinal section of the buccal vertex near the cytostome. The distal ends of the endoral cilia have modified axonemes (arrowhead), i.e., they have a reduced number of peripheral microtubular doublets. Some cilia of the buccal membranelles and the multiple membranes are also recognisable. (D) Transverse section of the basal bodies of the endoral membrane (seen from inside the buccal cavity). BL, buccal lip; BM, buccal membranelles; CM, collar membranelles; E, endoral membrane; ED, electron-dense bodies; LM, bifurcated left microtubular ribbons; NE, possibly nematodesmata; PE, perilemma; RM, right microtubular ribbons. Scale bars: 10 µm (A), 1 µm (B–D).

Fig. 9 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 9. Extrusomes of Limnostrombidium viride in the SEM (A, B) and TEM (C, D). (A) Lateral view of a cell. Arrowheads mark just ejected extrusomes. (B) Extrusome cluster. (C) Cross section of extrusome stripe. (D) Longitudinal section. One extrusome is just ejected (arrow), four are in the resting state, and three "empty chambers" (asterisks) are the remains of previously ejected extrusomes. CSL, concentric sheet layers; CT, curved tubules; EC, extrusome cores; ED, electron-dense bodies; EM, extrusome membranes; EX, extrusomes; GK, girdle kinety; MT, separating microtubules; PE, perilemma. Scale bars: 20 µm (A), 1 µm (B–D).

Fig. 7 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 7. Hemitheca of Limnostrombidium viride in the transmission electron microscope. (A) Tangential section showing the seams (arrow) between the polygonal cortical platelets, which are covered by the layer of longitudinal microtubules. (B) Freeze-fracture replica showing the seams between the polygonal platelets, the layer of longitudinally orientated microtubules, the alveoli, and remnants of the cell membrane with its densely arranged particles (arrows). (C) Transverse section showing the perilemma with its electron-dense bodies, the alveoli, the layer of longitudinal microtubules, and the polygonal cortical platelets. The arrowhead marks the cell membrane. AL, alveoli; CP, cortical platelets; MT, cortical microtubular layer; PE, perilemma. Scale bars: 1 µm.

Fig. 2 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 2. Transmission electron micrographs of collar membranelles in Limnostrombidium viride. Their anterior ends are directed to the left. (A–C) Transverse sections at different planes showing the various connections between the basal bodies of an individual membranelle and the microtubules extending into the cytoplasm. (D) The axonemes of the individual cilia are enclosed by the cell membrane, while all cilia of a membranelle are additionally surrounded by the perilemma. (E) Transverse sections of two polykinetids at the level of the basal bodies. The last file of the upper adoral membrane has associated short ciliary stubs only (arrowhead). 1–3, rows 1–3; ED, electron-dense bodies; IMF, intermembranellar fibre; M1, microtubular ribbons at row 1; M3, microtubular ribbons at row 3; PE, perilemma. Scale bars: 1 µm (A–C), 0.5 µm (D, E).

Fig. 6 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 6. Ventral kinety of Limnostrombidium viride in the transmission electron microscope. (A) Longitudinal section of a dikinetid showing the diverging basal bodies. A perilemma covers the cell surface. (B) Transverse section showing a dikinetid in the longitudinal furrow later- ally bordered by the cortical platelets of the hemitheca. CP, cortical platelets; ED, electron-dense bodies; ML, cortical microtubular layer; PE, perilemma; SC1, anterior dikinetidal cilium; SC2, posterior dikinetidal cilium. Scale bars: 1 µm.

Fig. 1 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 1. Limnostrombidium viride (A, schematic line drawing combining data from scanning and transmission electron microscopy; B, C, scanning electron micrographs). (A) General morphology. Note that the polygonal platelets of the hemitheca are only depicted in the cell periphery to show the more centrally located organelles. For the sake of clarity, the course of the neoformation organelle is somewhat stretched. (B, C) Ventral view and detail of ventral side. The arrowhead (C) marks the opening of the neoformation organelle in the stripe of extrusome attachment sites. BL, buccal lip; BM, buccal membranelles; CM, collar membranelles; EX, stripe of extrusome attachment sites; GK, girdle kinety; HT, hemitheca; MA, macronucleus; MI, micronucleus; NF, neoformation organelle; VK, ventral kinety. Scale bars: 30 µm (A), 20 µm (B), 10 µm (C).

Fig. 8 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 8. Nuclear apparatus of Limnostrombidium viride in the transmission electron microscope. (A) Interphase state showing the micronucleus in an indentation of the macronucleus, which has an irregular surface and contains numerous electron-dense inclusions, probably nucleoli. (B) A macronucleus showing the replication band. The arrow indicates the migration direction of the replication band. 1, zone of typical macronuclear structure; 2, zone characterised by protein and RNA production; 3, bright zone with beginning biosynthesis and DNA replication; MA, macronucleus; MI, micronucleus. Scale bars: 2 µm.

Fig. 4 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa

Fig. 4. Girdle kinety of Limnostrombidium viride (A, scanning electron micrograph; B, scheme of dikinetid). (A) Detail of kinety showing the two alternating types of girdle cilia. (B) Dikinetid with the associated structures; the presence of a transverse ribbon is uncertain. Numbering of the triplets (1–9) follows the "Grain convention", but is somewhat uncertain, as the triplets are difficult to identify. The scheme bases on numerous transmission electron micrographs (not shown). DS, desmose; KD, kinetodesmal fibril; PC, postciliary microtubular ribbon; SC1, club-shaped cilia of left dikinetidal basal bodies (originally anterior ones); SC2, condylocilia of right dikinetidal basal bodies (originally posterior ones). Scale bar: 2 µm.

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Fig. 3 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)

Fig. 3. Illustration of the morphology of Colpodella, Perkinsus, and Parvilucifera which is indicated to be the plesiomorphic condition for the Alveolata. Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.

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Fig. 1 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)

Fig. 1. Consenses of optimal trees found from parsimony analysis of SSU rDNA aligned with MALIGN using all aligned sites (A), only conservative sites (B), and excluding outgroup taxa for all sites (C) and conservative sites only (D). Branches are drawn proportional to amount of change. Values at internodes for groups of interest are parsimony jackknife support indices (asterisk indicates not supported with this method). Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.

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Fig. 2 in Molecular Determination of the Phylogenetic Position of a Species in the Genus Colpodella (Alveolata)

Fig. 2. Consenses of optimal trees found from parsimony analysis of combined 18S rDNA and actin nucleotide sequences (SSU rDNA data were only available for 24 taxa) for all available sites (A) and for conservative SSU rDNA sites (B); values at internodes are Bremer support indices. Optimal tree (C) found for combined analyses using only those taxa for which both genes are available; values at internodes are Bremer support indices for the 18S rDNA data (above nodes) and for the actin data (below nodes). Thickened branches indicate implied retention of the Colpodella/Perkinsus morphology.

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Fig. 4 in Hyaloklossia Labb´e, 1896 (Alveolata: Apicomplexa) in frogs: Description of a new species and proposing a new subfamily to accommodate these enigmatic parasites

Fig. 4. Mature sporocysts of Hyaloklossia in the kidney of Pelophylax porosus porosus. (A) Light microscopy of a mature sporocyst in homogenized kidney tissue. (B) Nomarski interference contrast microscopy of a mature sporocyst in squash preparation of renal tubular tissue showing the presence of four spindle-shaped sporozoites. (C) Composite line drawing. Bar = 10 μm. Asterisk: sporocyst residuum.