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Fig. 4 in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 4. Comparisons among different buccal apparatus patterns of Paramesanophrys gen. nov. and some related genera; arrows in A–J show different positions to which PM extends anteriorly and highlighted structures in A–J mark M2. A. Paramesanophrys typica gen. et sp. nov. (from the present work). B. Mesanophrys carcini (Grolière & Léglise, 1977) Small & Lynn in Aescht, 2001 (from Song & Wilbert 2000). C. Uronema marinum Dujardin, 1841 (from Song et al. 2009). D. Uronemella filificum (Kahl, 1931) Song & Wilbert, 2002 (from Song & Wilbert 2002). E. Metanophrys sinensis Song & Wilbert, 2000 (from Song & Wilbert 2000). F. Anophryoides haemophila Cawthorn et al., 1996 (from Cawthorn et al. 1996). G. Philasterides armatalis Song, 2000 (from Song 2000). H. Paranophrys marina Thompson & Berger, 1965 (from Song et al. 2002). I. Paralembus digitiformis Kahl, 1931 (from Song & Wilbert 2000). J. Cohnilembus verminus (Müller, 1786) Kahl, 1933 (from Song 2000). Abbreviations: M1–3 = membranelles 1, 2 and 3; PM = paroral membrane; Sc = scutica.

Fig. 7 in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 7. Metanophrys similis Song et al., 2002, in vivo (A–F) and after protargol staining (G–J). A. Ventral view of a typical individual. B–D. Ventral views of three individuals; arrowheads in D mark somatic cilia. E. Food vacuole (arrow). F. Posterior region; arrow shows caudal cilium. G, I. Ventral views, to show detailed structure of the buccal area. H. Dorsal view; arrow shows monokinetids, arrowhead marks dikinetids. J. Macronucleus. Abbreviations: M1–3 = membranelles 1, 2 and 3; Ma = macronucleus; PM = paroral membrane. Scale bars: A–D = 30 μm.

Fig. 6 in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 6. Metanophrys sinensis Song & Wilbert, 2000, in vivo (A–D, G) and after protargol (E–F, I–J) or silver nitrate (H) staining. A. Ventral view of a typical individual. B. Ventral view of another individual; arrowheads mark somatic cilia. C. Ventral view; arrowhead exhibits buccal field. D. Notched pellicle (arrowhead). E. Detailed structure of buccal area. F. Individual in morphogenesis, to show buccal apparatus. G. Ventral view, showing bar-shaped crystal (arrowhead). H. Detail of somatic kinetids. I. Dikinetids of scutica (arrowheads). J. Posterior region; arrowheads show monokinetids of somatic kineties. Abbreviations: M1–3 = membranelles 1, 2 and 3; PM = paroral membrane. Scale bars: A–B = 15 μm.

Fig. 5 in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 5. Mesanophrys carcini Small & Lynn in Aescht, 2001, in vivo (A–D) and after protargol staining (E–G). A. Ventral view of a representative individual; arrow shows contractile vacuole. B–D. Ventral views of four individuals; arrow in B shows caudal cilium and arrow in D marks food vacuole. E–F. Ventral views, detailed structure of buccal area. G. Dorsal view; arrow indicates somatic kinety. Abbreviations: M1–3 = membranelles 1, 2 and 3; Ma = macronucleus; PM = paroral membrane; Sc = scutica. Scale bars: A–D = 30 μm; E–G = 5 μm.

Fig. 2 in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 2. Paramesanophrys typica gen. et sp. nov., from life (A–F) and after protargol staining (G–I). A. Ventral view of a representative individual. B. Different body shapes. C. Changing shapes of buccal field of the same individual. D. Movement trace. E. Food granules. F. Part of pellicle, to show extrusomes. G–H. Ventral (G) and dorsal (H) views of the same specimen (holotype), showing infraciliature and nuclear apparatus. I. Detailed structure of the buccal area. Abbreviations: M1–3 = membranelles 1, 2 and 3; Ma = macronucleus; PM = paroral membrane; Sc = scutica. Scale bars: A = 30 μm; B = 40 μm.

Fig. 1. Sampling sites. A in Taxonomy and morphology of four "ophrys-related" scuticociliates (Protista, Ciliophora, Scuticociliatia), with the description of a new genus, Paramesanophrys gen. nov.

Fig. 1. Sampling sites. A. Coastal waters of the Yellow Sea at Qingdao, Shandong province. B. A coastal mariculture-region in Zhanjiang, Guangdong province. C. Coastal waters of Daya Bay, Guangdong province.

Fig. 5 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 5. Clevelandella hastula (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A, F–H) and after protargol impregnation (B–E). A–E. Ventral view of specimens with well-preserved body shape. Arrows mark the proximal end of the peristomial opening, black arrowheads mark the proximal end of the adoral zone of membranelles. F. Ventral view, showing general organization of body. G–H. Ciliary pattern of ventral and dorsal sides. Conspicuous cilia of adoral membranelles emerge out of the peristomial opening in (G). Asterisks indicate the position of the ciliary whorl (posterior suture), arrow marks the proximal end of the peristomial opening. Scale bars = 30 μm.

Fig. 10 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 10. Clevelandella parapanesthiae (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 30 μm.

Fig. 1 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 1. Clevelandella constricta (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 120 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. Black double arrowhead marks densely packed, oval, refractile bodies (probably paraglycogen platelets). M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). O. Prokaryotes freely scattered throughout the cytoplasm posterior to the macronucleus. P. Detail of oval, refractile bodies (probably paraglycogen platelets) anterior to the macronucleus. Scale bars = 50 μm.

Fig. 3 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 3. Clevelandella constricta (Kidder, 1937). Vietnamese (A, E–G) and Cambodian (D) specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969, as well as Thai I specimens (B– C) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, D–G) and after protargol impregnation (B–C). A–C. Ventral view of specimens with well-preserved body shape. D–E. Ventral view, showing the general body organization. Arrows mark oval, refractile bodies anterior to the macronucleus, black arrowheads mark the proximal end of the adoral zone of membranelles, white arrowheads denote the karyophore attached to the right and left body margins and black double arrowhead marks the canal leading from the contractile vacuole to the cytopyge. F–G. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture), white double arrowhead denotes the right suture. Scale bars: A–C, E–G = 50 μm; D = 20 μm.

Fig. 11 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 11. Clevelandella parapanesthiae (Kidder, 1937). Vietnamese specimens (A–B, E–G) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 and Thai I specimens (C–D) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, E–G) and after protargol impregnation (B–D). A–D. Ventral views of specimens with well-preserved body shape. Black arrowheads mark the proximal end of the adoral zone of membranelles. E–G. A strongly squeezed specimen by pressure of the cover slip, causing the body to become markedly wider and the notch at the base of the peristomial projection to be lost. The general body organization is shown in (E), the ciliary pattern of ventral and dorsal sides is shown in (F) and (G). Asterisks mark the position of the ciliary whorl (posterior suture), white arrowhead denotes the karyophore attaching to right body margin, white double arrowhead denotes the right suture. Scale bars = 30 μm.

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Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium – M. rubrum, M. major, and M. chamaeleon - being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination - particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate – requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.

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Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

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Fig. 4. A–E. Uronemita filificum Kahl, 1931. F–I. Uronema marinum Dujardin, 1841. J–N. Pleuronema setigerum Calkins, 1902. A–C, F–H, J–L in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus

Fig. 4. A–E. Uronemita filificum Kahl, 1931. F–I. Uronema marinum Dujardin, 1841. J–N. Pleuronema setigerum Calkins, 1902. A–C, F–H, J–L. In vivo. D–E, M–N. After silver impregnation. A, F, J. Ventral views of typical individuals. B–C, G–H, K–L. Different individuals, showing variation in body shape, arrow in (B) shows the conspicuous apical plate, arrows in (C, H) mark contractile vacuoles. D, I, M–N. Detailed structures of buccal area, arrow in (M) indicates the ring-like posterior end of M2a, arrowheads in (M) mark preoral kineties. E. Ventral view, arrowheads show somatic kineties. Abbreviations: M1, 2, 3 = membranelle 1, 2 and 3; M2a = the anterior part of membranelle 2; M2b = the posterior part of membranelle 2; Ma = macronucleus; PM = paroral membrane. Scale bars: A–B = 20 μm; F, H, N = 10 μm; G = 5 μm, J–L = 30 μm.

Fig. 3. A–D in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus

Fig. 3. A–D. Pseudocohnilembus hargisi Evans & Thompson, 1964. E–J. Parauronema cf. longum Song, 1995. A–C, E–I. In vivo. D, J. After silver impregnation. A, E. Ventral views of typical individuals, arrow in (A) shows caudal cilia. B–C, F–G. Different individuals, showing varying body shapes, arrowheads in (F) mark somatic kineties. D, J. Detailed structure of the buccal area. H. Ventral view, arrow refers to dumbbell-shaped crystals. I. Posterior end, arrow marks caudal cilium. Abbreviations: M1, 2, 3 = membranelle 1, 2 and 3; PM = paroral membrane; Sc = scutica. Scale bars: A–B = 15 μm; C, E = 40 μm; G = 60 μm.

Fig. 5. All reported populations for the following species. A. Uronema marinum Dujardin, 1841. B in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus

Fig. 5. All reported populations for the following species. A. Uronema marinum Dujardin, 1841. B. Pseudocohnilembus hargisi Evans & Thompson, 1964. C. Metanophrys similis Song et al., 2002. D. Pleuronema setigerum Calkins, 1902. E. Uronemita filificum Kahl, 1931.

Fig. 2. A–D in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus

Fig. 2. A–D. Mesanophrys cf. carcini Small & Lynn in Aescht, 2001. E–G. Metanophrys similis Song et al., 2002. A–C, E–F. In vivo. D, G. After silver impregnation. A, E. Ventral views of typical individuals, arrow in (E) shows caudal cilia. B, F. Different individuals, showing different body shapes. C. Individual in morphogenesis. D, G. Detailed structure of the buccal area. Abbreviations: M1, 2, 3 = membranelle 1, 2 and 3; Ma = macronucleus; PM = paroral membrane. Scale bars: 30 μm.

Fig. 1. Sampling map. A in Seven scuticociliates (Protozoa, Ciliophora) from Alabama, USA, with descriptions of two parasitic species isolated from a freshwater mussel Potamilus purpuratus

Fig. 1. Sampling map. A. Chewacla Creek, Auburn, Alabama (32º36′56″ N, 85º28ʹ58″ E). B. Orange Beach, Alabama (30º16′44″ N, 87º33′35″ E).

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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.