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Fig. 1 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea

Fig. 1. Pseudocyrtohymenides lacunae nov. gen., nov. spec. (A, B), living specimens and (C–E), after protargol impregnation. (A, B), ventral (A) and dorsal (B) views of representative specimens; arrow denotes contractile vacuole. (C, D), ventral (C) and dorsal (D) views of the holotype specimen. (E), ventral views showing the variation of frontal-ventral-transverse cirri. AZM, adoral zone of membranelles; DK1, dorsal kinety 1; EM, endoral membrane; G, cortical granules; LMR, left marginal cirral row; Ma, macronuclear nodules; Mi, micronuclei; PM, paroral membrane; RMR, right marginal cirral row; TC, transverse cirri. Scale bars: 50 µm.

Fig. 3 in Morphology and Phylogeny of Four Marine Scuticociliates (Protista, Ciliophora), with Descriptions of Two New Species: Pleuronema elegans spec. nov. and Uronema orientalis spec. nov.

Fig. 3. Pleuronema grolierei Wang et al., 2008 (A–H) and P. setigerum Calkins, 1902 (I–M) in vivo (A–D, I–K) and after protargol (E–H, L, M). A, I – ventral views of typical individuals, arrow in (A) shows contractile vacuole, arrowheads in (I) mark paroral membrane; B – ventral view, arrowheads mark oral cilia; C, K – ventral views, arrowheads point to caudal cilia; D – ventral view, arrow marks ingested algae, arrowhead shows irregularly-shaped crystals; E – anterior region, arrow shows the anterior part of membranelle 2; F – detailed structure of the buccal area; G – posterior region, arrowhead points to membranelle 3; H – macronucleus; J – ventral view, arrowheads show irregularly-shaped crystals; L – posterior region, arrowhead indicates the ring-like posterior end of M2a; M – detailed structure of the buccal area, arrow marks membranelle 3, arrowheads show preoral kineties. M1 – membranelle 1; M2a – the anterior part of membranelle 2; M2b – the posterior part of membranelle 2; Ma – macronucleus. Scale bars: A, I = 20 μm, M = 5 μm.

Fig. 1 in Morphology and Phylogeny of Four Marine Scuticociliates (Protista, Ciliophora), with Descriptions of Two New Species: Pleuronema elegans spec. nov. and Uronema orientalis spec. nov.

Fig. 1. Map and photographs of biotopes (A–D) in which the samples were collected. A – no. 1 swimming beach, Qingdao (36°06′N; 120°32′E); B – beach near Sculpture Garden, Qingdao (36°4′N; 120°29′E); C – coastal area of no. 1 swimming beach, Qingdao (36°06′N; 120°32′E), the site that is further into the sea than that of (A); D – a mangrove wetland in Shenzhen, Guangdong Province (22°30′N; 114°37′E).

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Fig. 1. a in On the Enigmatic Hook of the Metaradiophryids (Alveolata, Ciliophora)

Fig. 1. a – ventral view of a medium-sized Metaradiophrya asymmetrica (135 µm × 55 µm) fixed in Schaudinn's fluid and stained in Mallory's anilin blue-orange G-acid fuchsin; b – right lateral view showing the normal shape of the ciliate; cv – contractile vacuole, h – hook, manu – macronucleus, minu – micronucleus (after Beers 1938).

Fig. 5 in Morphology and Phylogeny of Four Marine Scuticociliates (Protista, Ciliophora), with Descriptions of Two New Species: Pleuronema elegans spec. nov. and Uronema orientalis spec. nov.

Fig. 5. Phylogenetic tree inferred from the small subunit ribosomal RNA (SSU rRNA) gene sequences, showing the positions of Pleuronema elegans spec. nov., P. grolierei, P. puytoraci, and Uronema orientalis spec. nov. (in bold). Numbers at nodes represent the bootstrap values of maximum likelihood (ML) out of 1,000 replicates and the posterior probability of Bayesian analysis (BI). The scale bar corresponds to five substitutions per 100 nucleotide positions.

Fig. 2 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea

Fig. 2. Pseudocyrtohymenides lacunae nov. gen., nov. spec. (A–E), living specimens; (F–K), after protargol impregnation. (A, D), ventral views of representative specimens. (B, C, E), dorsal views showing cortical granules and dorsal bristles. (F–K), dorsal (F, J) and ventral (G–I, K) views showing infraciliature and nuclear apparatus. AZM, adoral zone of membranelles; CV, contractile vacuole; DB, dorsal bristle; DK1–4, dorsal kineties 1–4; EM, endoral membrane; FC, frontal cirrus; G, cortical granules; LMR, left marginal cirral row; Ma, macronuclear nodules; Mi, micronuclei; PM, paroral membrane; RMR, right marginal cirral row; TC, transverse cirri; VC, ventral cirri. Scale bars: 100 µm in A–D and 50 µm in F–G.

Fig. 3 in Morphology and Molecular Phylogeny of Pseudocyrtohymenides lacunae nov. gen., nov. spec. (Ciliophora: Oxytrichidae) from South Korea

Fig. 3. Phylogenetic tree of SSU rRNA gene sequences, showing the position of Pseudocyrtohymenides lacunae nov. spec. on the basis of Maximum Likelihood (ML) and Bayesian Inference (BI). Bootstrap values of ML and posterior probabilities of BI were denoted on each interior branch. If the values of the bootstrap and the posterior probability were less than 50% and 0.50, respectively, they were excluded. The scale bar represents one nucleotide substitution per 100 nt.

Fig. 5 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Fig. 5. Maximum likelihood (ML) tree inferred from SSU rDNA sequences, showing the position of Uronema nigricans and Lembadion lucens (red arrows). Numbers near branches denote ML bootstrap value/BI posterior probability. Asterisks (*) indicate topologies that differ between the ML and BI analyses. Fully supported (100%/1.00) branches are marked with solid circles. Question marks (?) in red color indicate that the two sequences are possibly misidentified. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. All branches are drawn to scale. Systematic classification mainly follows Lynn (2008).

Fig. 4 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Fig. 4. Photomicrographs of Lembadion lucens from life (A–D, with A in bright field illumination and others in DIC microscopy) and after protargol staining (E–K). (A, B) Ventral views of representative individuals, cell in B was slightly depressed. Arrow shows caudal cilia. (C) Dorsal view, arrowhead points to the contractile vacuole. (D) Apical view, revealing the shape of cross section. Arrow shows oral cilia. (E) Ventral view of a stained cell, showing the silverline system. (F, G) Ventral (F) and dorsal (G) view of a representative individual, to show the ciliature and nuclear apparatus. (H) Micronucleus (arrow) and macronucleus. (I) Ventral view of posterior portion. Arrows depict two basal body rows of caudal cilia. (J) Mid portion of dorsal view, illustrating the monokinetids and dikinetids. (K) Detailed view, arrows show the two separated pairs of basal bodies and arrowheads indicate the posterior ends of four gradually shortened outer rows of adoral membranelle. Scale bars: 30 μm.

Fig. 6 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Fig. 6. Sequence comparison of the small subunit ribosomal RNA gene determined by BioEdit 7.0.5.2 (Hall 1999), showing the unmatched nucleotides of Uronema nigricans MF072399 and Lembadion lucens MF072398 with their sister sequences in the same clades, respectively (see Fig. 5). Nucleotide positions are given at the top of each column. Insertions and deletions are compensated by introducing alignment gaps (–). Numbers of unmatched sites (n) and sequence similarity percentages (%) compared with Uronema nigricans MF072399 and Lembadion lucens MF072398 are also supplied. The two sequences with question marks (?) are possibly misidentified. ID, identical; n, numbers of unmatched sites; %, sequence similarity percentages.

Fig. 3 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Fig. 3. Photomicrographs of Uronema nigricans from life (A–E, in bright field illumination) and after protargol (F–M) staining. (A–C) Right ventrolateral views of representative individuals, with cell in C slightly depressed. Arrow in A shows contractile vacuole, while in C indicates macronucleus. (D) View of caudal portion of another cell, arrow points to caudal cilium. (E) Different body sizes, showing conspicuous apical plate. (F, G) Ventral views of stained individuals, indicating the structure of scutica. (H, I) Portion views of oral apparatus, revealing the number of kinety rows in M2 (two rows in H and three rows in I). (J, K) Ventral (J) and dorsal (K) view of a representative individual to show the ciliature and nuclear apparatus. Arrow in J points to basal body of caudal cilium, arrow in K indicating the apical plate. (L, M) Left ventrolateral (L) and right dorsolateral (M) view of another stained individual to show the ciliature and oral apparatus. Scale bars: 15 μm (A, B); 30 μm (E).

Fig. 1 in Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Fig. 1. Map and sampling site. The yellow dots on the map and two corresponding photographs (A, B) show the collecting sites. (A) Fresh- water river in Shenzhen, southern China (22°32'19"N; 114°06'45"E). (B) Huguangyan Lake, an oligotrophic lake in Zhanjiang, southern China (21°08'38"N; 110°16'20"E).

Fig. 2 in Morphology and Phylogeny of Four Marine Scuticociliates (Protista, Ciliophora), with Descriptions of Two New Species: Pleuronema elegans spec. nov. and Uronema orientalis spec. nov.

Fig. 2. Pleuronema elegans spec. nov. in vivo (A, B, D, H–L), after protargol (E–G, M–Q) and silver nitrate staining (C). A, H – ventral view of a representative individual; B – detailed view of cortex to demonstrate arrangement of extrusomes; C – part of silverline system; D – swimming trace; E, F – ventral (E) and dorsal (F) views of the same specimen, showing infraciliature and nuclear apparatus; G – detailed structure of the buccal area, arrow shows the straight posterior end of M2a; I – ventral view, arrow marks paroral membrane and arrowhead shows ingested algae; J – ventral view, arrow shows membranelle 1, arrowheads mark the anterior part of membranelle 2; K – ventral view, arrowheads point to caudal cilia; L – ventral view, arrowheads mark somatic cilia; M – infraciliature of ventral side, arrow indicates membranelle 1, arrowhead refers to paired basal bodies; N – posterior region, arrow shows V-shaped posterior part of membranelle 2, arrowheads point to preoral kineties, double-arrowhead indicates membranelle 3; O – anterior region, arrowhead shows the anterior part of membranelle 2; P – macronucleus; Q – detailed view of membranelle 3 (arrowhead). M1, 3 – membranelles 1 and 3; M2a – the anterior part of membranelle 2; M2b – the posterior part of membranelle 2; Ma – macronucleus; PK – preoral kinety; PM – paroral membrane. Scale bars: A, E, F, H, I = 50 μm, J = 20 μm.

Fig. 7 in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 7. Reconstruction of ancestral morphologies in pleurostomatids. Schematic drawings are based on the results of the likelihood method in combination with the Markov evolutionary model implemented in the computer program Mesquite. aE – apical group of oral extrusomes, B – dorsal brush, CV – contractile vacuoles, MA – macronucleus, MI – micronucleus, oE – extrusomes attached along the whole length of the oral bulge, PeK1–3 – preoral kineties 1–3, sE – extrusomes attached to the somatic cortex.

Fig. 3 in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 3. Phylogenetic analysis of the combined molecular and morphological dataset comprising 26 haptorian taxa and 1492 characters. The tree was constructed with Bayesian inference using mixed models and with the maximum parsimony analysis implemented in PAUP*. Nodal support is indicated by posterior probabilities for Bayesian inference and the bootstrap values for the maximum parsimony. A dash indicates MP bootstraps below 50%. The scale bar indicates two changes per one hundred characters.

Fig. 5. Split support spectrum for the 18S in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 5. Split support spectrum for the 18S rRNA gene alignment used to construct the phylogenetic network in Fig. 4. Column height represents the number of clade-supporting positions, i.e., putative primary homologies. Column parts above the y-axis represent the in-group partition, while those below the axis correspond to the out-group partition.

Fig. 2 in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 2. Small subunit rRNA gene phylogeny based on 1462 nucleotide characters from 26 haptorian taxa. The tree was constructed using three methods (Bayesian inference, maximum likelihood, and maximum parsimony) with the GTR + I + Γ evolutionary model and the gamma shape parameter at 0.4970, the proportion of invariable sites at 0.6150, and a rate matrix for the model as suggested by jModeltest. Nodal supports are indicated as follows: posterior probabilities for the Bayesian inference / bootstrap values for maximum likelihood / bootstrap values for maximum parsimony. A dash indicates MP bootstraps below 50%. The scale bar indicates two substitutions per one hundred nucleotide positions. Sequences in bold were obtained during this study.

Fig. 1. Weighted 50 in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 1. Weighted 50% majority-rule consensus tree (length = 66, consistency index = 0.83, retention index = 0.93) inferred from 30 characters of 26 haptorian taxa. Tree was computed with the maximum parsimony algorithm using PAUP*. Nodal supports are indicated as follows: % of occurrence in the 1185 equally most parsimonious trees / bootstrap values in % for maximum parsimony / posterior probabilities for the Bayesian inference. A dash indicates support below 50% in the maximum parsimony analyses or 0.50 for the Bayesian inference.

Fig. 4 in Reconstruction of Evolutionary History of Pleurostomatid Ciliates (Ciliophora, Litostomatea, Haptoria): Interplay of Morphology and Molecules

Fig. 4. Phylogenetic network based on 1462 nucleotide characters from 26 haptorian taxa. The split graph was constructed using the neighbornet algorithm and the uncorrected distances. Numbers along edges are bootstrap values coming from 1000 replicates. Values <50% are not shown. The scale bar indicates one substitution per one hundred nucleotide positions.