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11. Kinetal maps showing the evolution of the somatic ciliary patterns in tintinnids with a ventral kinety (8, original; 9, modified from in Snyder and Brownlee 1991; 10; modified from c in Choi et al. 1992; 11; modified from 3 in Kim S. Y. et al. 2010; protargol impregnation). 8. Hypothetical tintinnid ancestor. 9. Nolaclusilis. A ventral kinety was created and the dikinetids, except for the anteriormost ones, transformed into monokinetids. 10. Eutintinnus. Dorsal kineties developed. 11. Favella ehrenbergii. A monokinetidal lateral ciliary field was introduced. BM, buccal membranelle; CM, collar membranelles; DK, dorsal kineties; LA, lateral ciliary field; LF, left ciliary field; OP, oral primordium; RF, right ciliary field; VK, ventral kinety.
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Fifty-six features of halteriid, oligotrichid, and choreotrichid ciliates are cladistically analysed, including an updated hypothesis about the evolution of the somatic ciliary patterns. Based on its morphology, Lynnella clusters with Parastrombidinopsis, Parastrombidium, and Strombidinopsis, while it is basal to the other choreotrichids in the mol...
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... characters cell shape (Character 1), position of the adoral zone of membranelles (Character 3), number of somatic kineties (Character 14), nuclear apparatus (Character 28), and polysaccharide cortical platelets (Character 35) were Table 1. Character numbers, character states, and coding used for the construction of the traditional cladogram (Fig. 17). The coding is mainly based on the outgroup comparison with the stichotrichs. If not stated otherwise, the characters are additive (ordered; Wagner/Farris ...
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... separate (coded 0) 28 a One ellipsoidal macronucleus nodule (coded 1), one C-shaped macronucleus (coded 2), or more than two macronucleus nodules (coded 3) AGATHA & STRU¨DERSTRU¨STRU¨DER-KYPKE-EVOLUTION OF CHOREOTRICHIDS Table 2. Distribution of character states over the taxa cladistically analysed with the computer programs PAUP* and Hennig86 (Fig. 18). Note that the character state trees of Character 8 (bipartition of adoral zone of membranelles), Character 18 (oligotrichid girdle kinety), Character 26 (structure of somatic kinetids), and Character 41 ...
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... model (Kimura 1980), and the distance trees were constructed with NEIGHBOUR (NJ; Saitou and Nei 1987). The data were re-sampled 500 (PhyML) and 1,000 (MP, NJ) times, respectively. The MP analysis was performed, using 438 parsimony-informative characters and a random addition (n = 5) of the species with the TBR branch-swapping algorithm in effect. Fig. 1-7. Kinetal maps showing the early evolution of the choreotrichid somatic ciliary patterns (originals; protargol impregnation). 1. Ancestor's dorsal side with 3-9 longitudinal somatic kineties composed of dikinetids, each having a distinct cilium associated only with the anterior basal body. This pattern is still found in recent ...
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... (e.g. Fig. 4b in Berger 2011 and Fig. 54b in Petz et al. 1995). 2. In a "dorsalization" process, the ancestor's ventral side was reduced and the dorsal side extended across the whole posterior cell por- tion. The posterior dikinetidal basal bodies became ciliated, producing the pattern of Strombidinopsis and Leegaardiella sol (inferred from Fig. 1 ...
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... the anteriormost ones, trans- formed into ciliated monokinetids, producing the pattern of Nolaclusilis Snyder and Brownlee, 1991 ( Fig. 9). Next, two dorsal kineties evolved, creating the pattern of Eutintinnus Kofoid and Campbell, 1939 (Fig. 10). Subsequently, a lateral ciliary field was introduced, generating the pattern of F. ehren- bergii ( Fig. 11) and F. panamensis (Fig. 28, ...
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... the pattern of Tintinnopsis brasiliensis Kofoid and Campbell, 1929 was produced. The ventral kinety developed a dikinetidal posterior portion and separated from the right ciliary field in F. arcuata (Fig. 12, 32, 37-43; see below), while the most complex tintinnid ciliary pattern so far known was created by the introduction of a posterior kinety (Fig. 13). It occurs with minute deviations in Codonella and the remaining Tintinnopsis species with agglom- erated loricae, Codonellopsis and Stenosemella Jo¨rgensenJo¨rgensen, 1924 whose loricae are composed of agglomerated bowls and hya- line collars, and Cymatocylis Laackmann, 1910 with hyaline loricae. Thus, this kinety pattern (Fig. 13) is ...
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... kinety (Fig. 13). It occurs with minute deviations in Codonella and the remaining Tintinnopsis species with agglom- erated loricae, Codonellopsis and Stenosemella Jo¨rgensenJo¨rgensen, 1924 whose loricae are composed of agglomerated bowls and hya- line collars, and Cymatocylis Laackmann, 1910 with hyaline loricae. Thus, this kinety pattern (Fig. 13) is associated with different lorica structures. All these species are marine, with the exception of the freshwater species Codonella cratera (Lei- dy, 1877) Imhof, 1885 and Stenosemella lacustris Foissner and O'Donoghue, 1990, whose generic affiliations are doubtful (Agatha 2010a;Agatha and Tsai ...
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... buccal membranelles can usually be distinguished from larger and longer collar membranelles; in the oligotrichid (14), Favella arcuata (15), and a marine Tintinnidium species (16) from life (origi- nals). Clavate or pin-shaped tentaculoids (arrowheads) insert between the collar membranelles. CM, collar membranelles; L, lorica. Scale bars 10 lm (Fig. 14), 30 lm (Fig. 15), and 20 lm (Fig. 16). ...
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... can usually be distinguished from larger and longer collar membranelles; in the oligotrichid (14), Favella arcuata (15), and a marine Tintinnidium species (16) from life (origi- nals). Clavate or pin-shaped tentaculoids (arrowheads) insert between the collar membranelles. CM, collar membranelles; L, lorica. Scale bars 10 lm (Fig. 14), 30 lm (Fig. 15), and 20 lm (Fig. 16). ...
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... distinguished from larger and longer collar membranelles; in the oligotrichid (14), Favella arcuata (15), and a marine Tintinnidium species (16) from life (origi- nals). Clavate or pin-shaped tentaculoids (arrowheads) insert between the collar membranelles. CM, collar membranelles; L, lorica. Scale bars 10 lm (Fig. 14), 30 lm (Fig. 15), and 20 lm (Fig. 16). ...
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... 21. Structure of tintinnid ventral kinety. The tin- tinnid ventral kineties are monokinetidal, except for those of F. arcuata (Fig. 12, 37-43) and Favella sp. (Fig. 72 in LavalPeuto 1994), which comprise a monokinetidal anterior and a dikinetidal posterior portion (for details, see "Taxonomic ...
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... 22. Unciliated ventral stripe. Usually, the distance between the ventral kinety and the right ciliary field is similar to that found between kineties of the right and left ciliary fields; only in F. arcuata (Fig. 12, 32, 37, 39-42) and Favella sp. (Fig. 72 in Laval-Peuto 1994), both structures are sepa- rated by a conspicuous unciliated stripe. Possibly, this feature is connected with the extraordinary structure of the ventral kinety (Character ...
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... of a usu- ally dikinetidal kinety posterior to the left or lateral ciliary field is considered the derived state ( Agatha and Stru¨derStru¨der-Kypke 2007). Based on the published data, the posterior kinety evolved after the reduction of one dorsal kinety in tintinnids with a monokinetidal ventral kinety close to the right ciliary field (Fig. 13, 17, 18). However, Brownlee (1982) described in his unpublished PhD Thesis a Favella species that is similar to F. arcuata in having an extraordinary ventral kinety (Charac- ter 21) separated from the right ciliary field by an unciliated stripe (Character 22), but possesses additionally a posterior kinety. If these observations were correct, a ...
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... that is similar to F. arcuata in having an extraordinary ventral kinety (Charac- ter 21) separated from the right ciliary field by an unciliated stripe (Character 22), but possesses additionally a posterior kinety. If these observations were correct, a posterior kinety would have already been present in the ancestor of F. arcuata- like tintinnids (Fig. 12) and those with the most complex cili- ary pattern (Fig. 13), and F. arcuata would have later lost the posterior kinety. Further investigations are needed to properly determine where the posterior kinety ...
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... kinety (Charac- ter 21) separated from the right ciliary field by an unciliated stripe (Character 22), but possesses additionally a posterior kinety. If these observations were correct, a posterior kinety would have already been present in the ancestor of F. arcuata- like tintinnids (Fig. 12) and those with the most complex cili- ary pattern (Fig. 13), and F. arcuata would have later lost the posterior kinety. Further investigations are needed to properly determine where the posterior kinety ...
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... studies on tin- tinnids revealed five types of capsules (Laval-Peuto and Barrıá de Cao 1987), which are assumed to be always associated with striae, accessory combs, and/or tentaculoids. One or more of these organelles were found in Climacocylis Jo¨rgensenJo¨rgensen, 1924 (Type III), Codonaria Kofoid and Campbell, 1939, Codonella, Codonellopsis (Fig. 14), 1909;Schweyer 1909). In the species anal- ysed here, only Types I and II occasionally occur. Observa- tions concerning the presence of capsules, striae, accessory combs, and tentaculoids are occasionally contradictory, possi- bly because their occurrence is correlated with food availabil- ity ( Capriulo et al. 1986;Entz ...
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... distal portions insert directly posteriorly to the collar membranelles (Skovgaard and Legrand 2005). In tintinnids, potentially contractile cytoplasmic extensions, the tentaculoids containing capsules (Character 31), were found in marine Codonella species (Haeckel 1873;Schweyer 1909), Codonellop- sis schabi (Brandt, 1906) Kofoid andCampbell, 1929 (Fig. 14), Dictyocysta lepida Ehrenberg, 1854 (see pin-shaped structures in Fig. 23 in Agatha 2010a), Eutintinnus species (Schweyer 1909), F. arcuata (Fig. 15), Rhabdonella species (Schweyer 1909), Stenosemella pacifica Campbell, 1929 (Agatha and, marine Tintinnidium species (Fig. 16), and marine Tintinnopsis species (Agatha 2010b; Haeckel 1873; ...
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... extensions, the tentaculoids containing capsules (Character 31), were found in marine Codonella species (Haeckel 1873;Schweyer 1909), Codonellop- sis schabi (Brandt, 1906) Kofoid andCampbell, 1929 (Fig. 14), Dictyocysta lepida Ehrenberg, 1854 (see pin-shaped structures in Fig. 23 in Agatha 2010a), Eutintinnus species (Schweyer 1909), F. arcuata (Fig. 15), Rhabdonella species (Schweyer 1909), Stenosemella pacifica Campbell, 1929 (Agatha and, marine Tintinnidium species (Fig. 16), and marine Tintinnopsis species (Agatha 2010b; Haeckel 1873; Schweyer 1909), while they are at least temporarily absent in some other tintinnids, e.g. in F. ehrenbergii (not mentioned by ) and F. panamensis ...
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... 1909), Codonellop- sis schabi (Brandt, 1906) Kofoid andCampbell, 1929 (Fig. 14), Dictyocysta lepida Ehrenberg, 1854 (see pin-shaped structures in Fig. 23 in Agatha 2010a), Eutintinnus species (Schweyer 1909), F. arcuata (Fig. 15), Rhabdonella species (Schweyer 1909), Stenosemella pacifica Campbell, 1929 (Agatha and, marine Tintinnidium species (Fig. 16), and marine Tintinnopsis species (Agatha 2010b; Haeckel 1873; Schweyer 1909), while they are at least temporarily absent in some other tintinnids, e.g. in F. ehrenbergii (not mentioned by ) and F. panamensis (Agatha S., pers. observ.). As the alternative is less parsimonious, the tentacles and the tentaculoids are regarded as ...
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... and often has a spiralled or annulated epilorica 2.5- 11 lm long ( x = 5.5 lm; n = 80; Fig. 23). The opening mea- sures 60-100 lm ( x = 81 lm; n = 104) in diameter. The pos- terior process is 20-90 lm long ( x = 57 lm; n = 80) and has dextrally spiralled ribs (Fig. 23, 25, 26). The lorica wall is monolaminar with alveoli and has a smooth surface (Fig. 21, 23, 24). The paralorica has a spiralled structure and a broadly rounded posterior end; a posterior process is absent (Fig. 27). The somatic ciliary pattern comprises a right, left, and lateral ciliary field, as well as two dikinetidal dorsal kineties and a monokinetidal ventral kinety abutting on the right ciliary field (Fig. 22, 28, 29). The ...
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... of Favella arcuata. In scanning electron micro- graphs, the lorica is 150-200 lm long ( x = 182 lm; n = 43) and has a ring-shaped subapical bulge and often a spiralled or annulated epilorica 3-10.5 lm long ( x = 6 lm; n = 37; Fig. 30, 31). The opening measures 55-75 lm ( x = 67 lm; n = 46) in diameter. The posterior process is 20-50 lm long ( x = 35 lm; n = 43) and lacks ribs (Fig. 31, 35). The lorica wall is monolaminar with alveoli, pores, and occasionally some subapical windows; its outer surface has reticulate ridges ( Fig. 31-35). The paralorica has a spiralled ...
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... electron micro- graphs, the lorica is 150-200 lm long ( x = 182 lm; n = 43) and has a ring-shaped subapical bulge and often a spiralled or annulated epilorica 3-10.5 lm long ( x = 6 lm; n = 37; Fig. 30, 31). The opening measures 55-75 lm ( x = 67 lm; n = 46) in diameter. The posterior process is 20-50 lm long ( x = 35 lm; n = 43) and lacks ribs (Fig. 31, 35). The lorica wall is monolaminar with alveoli, pores, and occasionally some subapical windows; its outer surface has reticulate ridges ( Fig. 31-35). The paralorica has a spiralled structure and a broadly rounded posterior end; a posterior process is absent (Fig. 36). The somatic ciliature comprises a dikinetidal dorsal kinety ...
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... epilorica 3-10.5 lm long ( x = 6 lm; n = 37; Fig. 30, 31). The opening measures 55-75 lm ( x = 67 lm; n = 46) in diameter. The posterior process is 20-50 lm long ( x = 35 lm; n = 43) and lacks ribs (Fig. 31, 35). The lorica wall is monolaminar with alveoli, pores, and occasionally some subapical windows; its outer surface has reticulate ridges ( Fig. 31-35). The paralorica has a spiralled structure and a broadly rounded posterior end; a posterior process is absent (Fig. 36). The somatic ciliature comprises a dikinetidal dorsal kinety occasionally plus some kinety fragments, a left and lat- eral ciliary field, and a right ciliary field separated by a con- spicuous unciliated stripe from ...
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... process is absent (Fig. 36). The somatic ciliature comprises a dikinetidal dorsal kinety occasionally plus some kinety fragments, a left and lat- eral ciliary field, and a right ciliary field separated by a con- spicuous unciliated stripe from the ventral kinety, which is composed of a monokinetidal anterior and a dikinetidal pos- terior portion (Fig. 12, 32, 37-45). The ciliary rows of the right and left ciliary fields are composed of monokinetids and one anterior dikinetid. The lateral ciliary field is composed of densely spaced monokinetids. Tentaculoids insert between the collar membranelles on the peristomial rim (Fig. ...
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... of a monokinetidal anterior and a dikinetidal pos- terior portion (Fig. 12, 32, 37-45). The ciliary rows of the right and left ciliary fields are composed of monokinetids and one anterior dikinetid. The lateral ciliary field is composed of densely spaced monokinetids. Tentaculoids insert between the collar membranelles on the peristomial rim (Fig. ...
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... analyses. In the cladogram based on the Hennigian argumentation method, the Leegaardiellidae Lynn and Mon- tagnes, 1988 are the most basal choreotrichid taxon followed by the cluster of Strombidinopsis, Parastrombidium, Para- strombidinopsis, and Lynnella and a cluster of the Lohmanniel- lidae and Strobilidiidae (Fig. 17). Although the tintinnids are monophyletic mainly based on characters 19-1 and 38-1 (Table 1), the suborder Strobilidiina comprising the aloricate choreotrichids is paraphyletic. Here, we follow Mayr and Bock (2002) and Ho¨randlHo¨randl and Stuessy (2010) in recognizing the para- phyletic suborder Strobilidiina. Within the tintinnids, ...
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... the 76 characters used in the Hennig86 and PAUP* computer analyses (Table 2), 61 were parsimony informative. The trees created by Hennig86 are shorter (L = 164) and have lower consistency (Ci = 75) and retention indices (Ri = 93) than those established with PAUP* (L = 205, Ci = 80, Ri = 97), but the consensus tree (Fig. 18) has more polytomies than that calculated by PAUP* (not ...
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... contrast to the Hennigian argumentation scheme (Fig. 17), the Leegaardiellidae do not form a monophylum based on their bipartite collar membranelles in the computed trees (Fig. 18). While the secondarily opened adoral zone of membranelles represents the synapomorphy of Lynnella, Para- strombidinopsis, and Parastrombidium in the Hennig86 and hand-made trees (Fig. 17, 18), Lynnella falls into ...
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... contrast to the Hennigian argumentation scheme (Fig. 17), the Leegaardiellidae do not form a monophylum based on their bipartite collar membranelles in the computed trees (Fig. 18). While the secondarily opened adoral zone of membranelles represents the synapomorphy of Lynnella, Para- strombidinopsis, and Parastrombidium in the Hennig86 and hand-made trees (Fig. 17, 18), Lynnella falls into a cluster formed by Lohmanniella and the Strobilidiidae ( Pelagostrobilidium Petz et al. 1995;Strobilidium;Rimostrombidium) ...
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... the Hennigian argumentation scheme (Fig. 17), the Leegaardiellidae do not form a monophylum based on their bipartite collar membranelles in the computed trees (Fig. 18). While the secondarily opened adoral zone of membranelles represents the synapomorphy of Lynnella, Para- strombidinopsis, and Parastrombidium in the Hennig86 and hand-made trees (Fig. 17, 18), Lynnella falls into a cluster formed by Lohmanniella and the Strobilidiidae ( Pelagostrobilidium Petz et al. 1995;Strobilidium;Rimostrombidium) in the PAUP* ...
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... clear separation of tintinnids with two ventral organelles from those with a ventral kinety as revealed by the argumen- tation scheme (Fig. 17) is not recognizable in the consensus trees (Fig. 18). The synapomorphic character of the extrusome types (Characters 31, 32) for Codonella, Codonellopsis, and Stenosemella (excluding S. lacustris with doubtful generic affili- ation) is not shown by the PAUP* and Hennig86 analyses, while the introduction of a lorica sac (Character 39) ...
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... clear separation of tintinnids with two ventral organelles from those with a ventral kinety as revealed by the argumen- tation scheme (Fig. 17) is not recognizable in the consensus trees (Fig. 18). The synapomorphic character of the extrusome types (Characters 31, 32) for Codonella, Codonellopsis, and Stenosemella (excluding S. lacustris with doubtful generic affili- ation) is not shown by the PAUP* and Hennig86 analyses, while the introduction of a lorica sac (Character 39) in Codo- nella and Codonellopsis is at least ...
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... of the extrusome types (Characters 31, 32) for Codonella, Codonellopsis, and Stenosemella (excluding S. lacustris with doubtful generic affili- ation) is not shown by the PAUP* and Hennig86 analyses, while the introduction of a lorica sac (Character 39) in Codo- nella and Codonellopsis is at least recognizable in the hand- made and Hennig86 trees (Fig. 17, ...
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... all trees, the most highly derived tintinnids share the most complex ciliary pattern (Fig. 13) composed of a right, left, and lateral ciliary field as well as a ventral, dorsal, and posterior kinety. The genera Codonella, Codonellopsis, Cymat- ocylis, Stenosemella, and Tintinnopsis demonstrate this pattern with the exceptions of T. brasiliensis studied by Cai et al. (2006), whose pattern is similar to that of F. ehrenbergii, and ...
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... sequences. The GenBank accession number, length, and GC content of the new SSU rRNA gene sequences are as follows: Favella panamensis (FeFL10-9)-JQ837817, 1,758 nu- cleotides, GC 47.0%; F. panamensis (FeMD10-46)-JQ837818, 1,748 nucleotides, GC 46.9%; F. panamensis (FeMD10-52)- AGATHA & STRU¨DERSTRU¨STRU¨DER-KYPKE-EVOLUTION OF CHOREOTRICHIDS Fig. 19. Maximum likelihood tree inferred from SSU rRNA gene sequences, computed with PhyML ( Guindon et al. 2010), based on the general-time-reversible (GTR) model with gamma distribution and an estimate of invariable sites. The first numbers at the nodes represent the bootstrap supports (of 500 replicates) for PhyML (ML), whereas the second ...
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... trees and signature nucleotides. All phyloge- netic analyses result in trees with comparable topologies (Fig. 19). As in previous analyses, the aloricate choreotrichids are not monophyletic and are basal to the loricate tintinnids. Within the monophyletic tintinnids, the families Tintinnidiidae Kofoid and Campbell, 1929 and TintinnidaeClaparè de and Lachmann, 1858 branch successively, followed by a well-sup- ported cluster of Favella species, ...
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... de and Lachmann, 1858 branch successively, followed by a well-sup- ported cluster of Favella species, which comprises the Korean F. ehrenbergii sensu Kim S. Y. et al. (2010), F. campanula sequenced by Gao et al. (2009), F. panamensis analysed by Stru¨derStru¨der-Kypke and Lynn (2003), and F. panamensis from the present study (see below; Fig. 21-29). This group of Favella species has a relatively long branch, indicating many nucleo- tide changes and a high mutation rate. Actually, many signa- ture positions exist that separate this cluster from the other tintinnid taxa (Fig. ...
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... the genetic divergences range between 0.65% for Codonellopsis americana Campbell, 1929 andC. nipponica Hada, 1964 and 2.55% for Stenosemella nivalis (Meunier, 1910) Campbell, 1929 andS. ventricosa Claparè de andLachmann, 1858) Jo¨rgensenJo¨rgensen, 1924. The four genera form two well-supported groups, each with some signature nucleotides (Fig. 19, 20): one comprises Dicty- ocysta and Codonella (97% ML, 1.0 BI, 90% MP, 98% NJ), the other Codonellopsis and S. nivalis (with full support). Stenosemella ventricosa and Tintinnopsis fimbriata Meunier, Note the smooth surface of the whorls. K2, first kinety of right ciliary field; L, lorica; LA, lateral ciliary field; P, peduncle; VK, ...
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... ocysta and Codonella (97% ML, 1.0 BI, 90% MP, 98% NJ), the other Codonellopsis and S. nivalis (with full support). Stenosemella ventricosa and Tintinnopsis fimbriata Meunier, Note the smooth surface of the whorls. K2, first kinety of right ciliary field; L, lorica; LA, lateral ciliary field; P, peduncle; VK, ventral kinety. Scale bars 100 lm (Fig. 21), 50 lm (Fig. 23, 27), 20 lm (Fig. 22, 25, 26), and 10 lm (Fig. 24). 340 basally to these two ...
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... alveoli in the wall, the other caused by the ridges on the outer surface. 34. Outer lorica surface showing reticulate ridges and pores. 35. Posterior lorica process showing a reticulate surface. L, lorica; LA, lateral ciliary field; OP, oral primordium; P, peduncle; RF, right ciliary field; VK, ventral kinety. Scale bars 100 lm (Fig. 30), 50 lm (Fig. 31), 20 lm (Fig. 33), 10 lm (Fig. 32, 35), and 5 lm (Fig. ...
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... coastal waters. These authors investigated for the first time the somatic ciliary pattern, but did not mention the lorica ultrastructure (texture) and omitted to discuss the species identification in detail. Favella panamensis collected by us in the North Atlantic matches the Korean specimens in the ciliary pattern (cf. Fig. 22, 28, 29 with Fig. 11) and both have a genetic similarity of 99.89%. As they are thus at least cong- eners, we transfer our observations of the monolaminar lorica wall and the posterior process to the Korean specimens. Our findings agree with the original and authoritative lorica descriptions (Fig. 21, 23-26; Brandt 1906Brandt , 1907;Claparè de and Lachmann ...
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... Korean specimens in the ciliary pattern (cf. Fig. 22, 28, 29 with Fig. 11) and both have a genetic similarity of 99.89%. As they are thus at least cong- eners, we transfer our observations of the monolaminar lorica wall and the posterior process to the Korean specimens. Our findings agree with the original and authoritative lorica descriptions (Fig. 21, 23-26; Brandt 1906Brandt , 1907;Claparè de and Lachmann 1858). Since the Korean and Norwegian specimens also have similar lorica dimensions (length: 94- 330 lm vs. 230-290 lm; opening diameter: 88-94 lm vs. 83104 lm;Brandt 1906Brandt , 1907, the identification by seems to be correct. Their redescription of the type species F. ehrenbergii and ...
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... 1907, the identification by seems to be correct. Their redescription of the type species F. ehrenbergii and the SSU rRNA gene sequence provided are thus regarded as authoritative. Accordingly, the diagnosis of the genus Favella is improved by including the descriptions by Brandt (1906Brandt ( , 1907 and as well as our own data from F. panamensis (Fig. 21- 29). For the morphologically and genetically deviating Favella species clustering with Metacylis and Rhabdonella, a new genus is established (see ...
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... variability dur- ing the cell cycle in a Favella species and discovered a huge phenotypic plasticity. While the generic affiliation seems to be correct due to the apparently smooth lorica surface (Fig. 29 in Laval-Peuto 1981), the identification with F. ehrenbergii is questionable as the posterior process is more slender and apparently lacks ribs (Fig. 2, 11, 30-32 in Laval-Peuto 1981). The population produced not only typical Favella loricae, but also loricae that were identified with Coxliella annulata (Daday, 1887) Brandt, 1907and Coxliella decipiens Jo¨rgensenJo¨rgensen, 1924. Likewise, Kim S. Y. et al. (2010 found Coxliella loricae in their monoclonal cultures, but omitted to identify ...
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... (Imhof, 1886Favella campanula (Schmidt, 1901Favella elongata Roxas, 1941;Favella markusovszkyi (Daday, 1887Favella philippinensis Roxas, 1941;and Favella septentrionalis Campbell, 1942 probably belong to the genus Favella due to the structure of their lorica walls. The affiliation of F. campanula is supported by its SSU rRNA gene sequence ( Fig. 19; Gao et al. 2009). The assignment of Favella amoyen- sis Wang and Nie, 1932;Favella gracilicauda Strelkow, 1953;and Favella hainanensis Nie and Ch'eng, 1947 is, however, uncertain. Favella panamensis illustrated by Small and Lynn (1985) and Lynn and Small (2002) apparently differs from our specimens in the presence of a posterior ...
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... Fehr99ssu_1) sensu Snoeyenbos-West et al. (2002), F. taraikaensis, Favella sp. (McManus andKatz 2009), and F. arcu- ata from this study form a cluster with Metacylis and Rhabdonella distinctly apart from the Favella species men- tioned above ( Gao et al. 2009;McManus and Katz 2009;Lynn 2003, 2008). Differences in the somatic ciliary pattern (cf. Fig. 12, 32, 37-43 in this study and Fig. 72 in Laval-Pe- uto 1994 with Fig. 11, 22, 28, 29 in this study and Fig. 15, 16 in Kim S. Y. et al. 2010) and lorica ultrastructure (cf. Fig. 30-35 with Fig. 23-26) support the separation of F. arcuata from the "true" Favella cluster (see above). These morphologic and genetic discrepancies justify the ...
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... sp. (McManus andKatz 2009), and F. arcu- ata from this study form a cluster with Metacylis and Rhabdonella distinctly apart from the Favella species men- tioned above ( Gao et al. 2009;McManus and Katz 2009;Lynn 2003, 2008). Differences in the somatic ciliary pattern (cf. Fig. 12, 32, 37-43 in this study and Fig. 72 in Laval-Pe- uto 1994 with Fig. 11, 22, 28, 29 in this study and Fig. 15, 16 in Kim S. Y. et al. 2010) and lorica ultrastructure (cf. Fig. 30-35 with Fig. 23-26) support the separation of F. arcuata from the "true" Favella cluster (see above). These morphologic and genetic discrepancies justify the establish- ment of a new genus with Favella arcuata (Brandt, 1906) ...
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... first glance, it seems that a dikinetidal posterior kinety abuts on the posterior end of the monokinetidal ventral kinety in S. arcuata (Fig. 12, 37-43) and Favella sp. (Fig. 72 in Laval-Peuto 1994). During ontogenesis, individual divisions of the monokinetidal and dikinetidal ciliary rows associated with substantial migration processes are thus expected. However, only a single break occurs ( Fig. 44, 45; Fig. 72 in Laval-Peuto 1994), indicating a single kinety with a monokinetidal ...
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... Lynn (2008), especially, in the ultrastructure of the lorica wall (i.e. alveoli enclosed by an inner and outer layer, low surface ridges, and pores). The surface ridges probably cause the whit- ish appearance of S. arcuata in the light microscope at low magnification, and these are not visible in F. panamensis with its smooth lorica surface (cf. Fig. 30, 31, 34 with Fig. 21, 23, 26). The affiliation of Schmidingerella with the Rhabdonellidae is not only supported by ultrastructural studies on Rhabdonel- la spiralis (Fol, 1881) Brandt, 1906 (Agatha S., unpubl. observ.), but also by the rather close relationship of the two genera in the SSU rRNA phylogenies ( Fig. 19; Gao et al. 2009;Lynn 2003, ...
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... in the ultrastructure of the lorica wall (i.e. alveoli enclosed by an inner and outer layer, low surface ridges, and pores). The surface ridges probably cause the whit- ish appearance of S. arcuata in the light microscope at low magnification, and these are not visible in F. panamensis with its smooth lorica surface (cf. Fig. 30, 31, 34 with Fig. 21, 23, 26). The affiliation of Schmidingerella with the Rhabdonellidae is not only supported by ultrastructural studies on Rhabdonel- la spiralis (Fol, 1881) Brandt, 1906 (Agatha S., unpubl. observ.), but also by the rather close relationship of the two genera in the SSU rRNA phylogenies ( Fig. 19; Gao et al. 2009;Lynn 2003, 2008) and the shared ...
Context 51
... its smooth lorica surface (cf. Fig. 30, 31, 34 with Fig. 21, 23, 26). The affiliation of Schmidingerella with the Rhabdonellidae is not only supported by ultrastructural studies on Rhabdonel- la spiralis (Fol, 1881) Brandt, 1906 (Agatha S., unpubl. observ.), but also by the rather close relationship of the two genera in the SSU rRNA phylogenies ( Fig. 19; Gao et al. 2009;Lynn 2003, 2008) and the shared signature nucleotides (Fig. 20). Metacylis angulata falls into the same cluster. The specimens sequenced by Stru¨derStru¨der-Kypke and Lynn (2003) were collected from Buzzards Bay, Massachusetts, which is rather close to the type locality of Great South Bay, Long Island, New York, at the ...
Citations
... Whether the stalked structure attached to the lorica bottom in Amphorides (Claparède and Lachmann 1858) and the aggregation of particles in the openings of Stenosemella loricae (Laackmann 1908;Meunier 1910) represent encysted tintinnids is uncertain. Anecdotal observations demonstrated a peculiar type of resting cyst in Schmidingerella species (Table 1; Agatha and Strüder-Kypke 2012): they are roughly flask-shaped with a broadened anterior portion directed to the lorica opening and an emergence pore closed by a skull cap-shaped structure (papula) directed towards the bottom of the lorica. ...
... However, the lorica ultrastructure and the somatic ciliary pattern along with 18S rRNA sequence data distinctly differ between both genera. Accordingly, the genus Schmidingerella was placed in the family Rhabdonellidae (Agatha and Strüder-Kypke 2012). The genus with its type species S. arcuata currently contains six species and has been suggested as a model for tintinnids because various aspects have already been studied. ...
Resting cysts protect ciliates against adverse environmental conditions. The morphology and ultrastructure of resting cysts has been described in very few Oligotrichea, a group of mainly marine planktonic ciliates. The present study provides the first ultrastructural data for loricate choreotrichids, applying light and electron microscopy on the cysts of the tintinnid Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012. The morphology of live cysts and the wall ultrastructure of cryofixed cysts were morphometrically analysed. The resting cyst is roughly flask-shaped, broadening to a slightly concave, laterally protruding anterior plate. An emergence pore closed by a skull cap-shaped papula is directed to the bottom of the lorica on the opposite side of the cyst. The cyst wall consists of an ectocyst, mesocyst, and endocyst differing in thickness, structure, and nitrogen concentration as revealed by conventional transmission electron microscopy, electron energy loss spectroscopy, and electron spectroscopic imaging. The cysts of S. meunieri belong to the kinetosome-resorbing type, which also occurs in the majority of hypotrich ciliates. Two main features (flask-shape and presence of an emergence pore) are shared with the closely related aloricate choreotrichids and oligotrichids, distinguishing the Oligotrichea from the hypotrich and the more distantly related euplotid ciliates.
... While the majority of the ~1000 tintinnid descriptions are based primarily on lorica morphology, the detection of widespread crypticity and intraspecific variability (Jung et al., 2018;Santoferrara et al., 2013Santoferrara et al., , 2015Xu et al., 2012) necessitates the use of additional methods to delineate species. The use of DNA barcode sequences-in particular the small subunit ribosomal RNA gene (SSU rRNA), the D1-D2 region of the large subunit rRNA gene (LSU rRNA) and the 5.8S rRNA gene with the internally transcribed spacer regions (ITS rRNA)-initiated the revision of tintinnid relationships that now include the redescription and reclassification of multiple species, genera and families (Agatha & Strüder-Kypke, 2012, 2014Bachy et al., 2012;Santoferrara et al., 2017). However, it remains problematic that the combination of morphology and DNA barcode data in species identification sometimes reveals a discordant relationship, including divergent lorica morphologies that have identical barcode sequences, as well as indistinguishable morphologies with divergent barcode sequences . ...
... Together, lorica morphology, DNA barcodes and ecophysiological data can provide a useful platform to differentiate many distinct genera and species. These characters are of particular importance in lieu of the gold standard of ciliate taxonomy, cytological and ultrastructural data, which are seldom available due to the expertise and cultivation required for staining techniques (Agatha & Strüder-Kypke, 2012, 2014Laval-Peuto & Brownlee, 1986). However, even an integration of these characters can still fail to separate cryptic taxa . ...
... The process of gene duplication, loss of MDS within paralogues and reconstruction of fully functional genes through scrambling may rapidly lead to reproductively incompatible individuals, as they would be incapable of creating functional MAC loci post-conjugation (Gao et al., 2015). This study incorporates lorica morphology, DNA barcoding, ecophysiology and single-cell 'omics to compare two cultivated cryptic tintinnid ciliates in the genus Schmidingerella: Schmidingerella arcuata (Brandt, 1906) Agatha & Strüder-Kypke, 2012, and Schmidingerella meunieri (Kofoid, 1929) Agatha & Strüder-Kypke, 2012. The purpose of this study is to explore how minor differences in the common indices of tintinnid species discrimination (i.e., lorica morphology, DNA barcodes and ecophysiology) correspond to genetic compatibility, inferred by using single-cell omics to compare the genomic architecture between the two tintinnids. ...
The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes, and ecophysiological traits. In addition, single-cell 'omics analyses (single-cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. Results include a highly similar lorica that is larger in S. meunieri, a 0 to 0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among eleven prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e. lorica morphology, DNA barcode sequences, and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species-specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co-occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification.
... However, some variations of lorica features were not verified in the phylogenetic analysis based on gene sequences (Santoferrara et al., 2017). Therefore, it is necessary to find more comprehensive morphological features and combine them with molecular phylogeny in order to improve the specific resolution of tintinnids (Agatha and Strüder-Kypke, 2012;Santoferrara et al., 2016). ...
... This study reveals that the ciliary pattern of the genus Leprotintinnus is attributed to the most complex type, which consists of a ventral, a dorsal, and a posterior kinety as well as a right, a left, and a lateral ciliary field (Agatha and Strüder-Kypke, 2007). This type of ciliary pattern has been reported in many other genera, such as Codonlla (affiliation doubtful) (Foissner et al., 1999), Codonellopsis (Petz et al., 1995;Kim et al., 2013), Laackmanniella (Kim et al., 2013), Cymatocylis (Wasik and Mikolajczyk, 1994;Petz et al., 1995), Stenosemella (Agatha and Tsai, 2008), Tintinnopsis (Gruber et al., 2018), and Schmidingerella (Agatha and Strüder-Kypke, 2012). The differences in the ciliary patterns of these species are very slight, except for the position of the posterior kinety is shifty. ...
... At present, it is still difficult to distinguish different families or genera by this type of ciliary pattern. We can only help future taxonomic revise by reporting more cell features that reveal new patterns of somatic ciliature or some subtle but very important features in the most complex ciliature pattern (Agatha and Strüder-Kypke, 2012;Gruber et al., 2018). Tintinnopsis radix (Imhof, 1886) Brandt, 1907and Rhizodomus tagatzi Strelkow and Wirketis, 1950 are the most similar tintinnid species to L. nordqvisti and L. simplex based on their common ciliary pattern, i.e., the ventral kinety curving drastically to the right and extending anterior to the right ciliary field, and the posterior kinety positioned below the left ciliary field Saccà et al., 2012). ...
Tintinnid ciliates are a highly diverse and essential group in the marine planktonic microbial loop. However, most of the known tintinnids were recorded only by the lorica characters and very few of them had been studied on their cytological features. In this study, the morphological characters of the lorica, ciliary pattern, nuclear apparatus, ontogenesis, and the molecular phylogeny of two poorly known tintinnid ciliates, Leprotintinnus nordqvisti (Brandt, 1906) Kofoid and Campbell (1929) and L. simplex Schmidt (1902), isolated from coastal waters of southern China, were investigated based on living observation, silver staining, three nuclear ribosomal DNA markers (18S, ITS1-5.8S-ITS2, and 28S genes) and one mitochondrial DNA marker (CO1 gene). For the first time, the somatic ciliary pattern of the genus Leprotintinnus was disclosed, viz., comprising a ventral, a dorsal, and a posterior kinety as well as a right, a left, and a lateral ciliary field. The diagnoses of both Leprotintinnus species were improved and the neotype was assigned. The ontogenesis of L. nordqvisti was in enantiotropic division mode with the new dorsal and posterior kineties generated de novo. The molecular phylogeny confirmed that Leprotintinnus species are closely related to some species of Tintinnopsis, Stylicauda, Rhizodomus, and Climacocylis. The anterior extending of the ventral kinety together with some of the lateral kinety is likely to be a distinguishing feature to determine their systematic relationships. This study also revealed that (i) the lorica of L. nordqvisti is polymorphic or plastic; (ii) Leprotintinnus tubulosus Roxas (1941) might be a synonym of L. nordqvisti; (iii) Leprotintinnus neriticus sensu Yoo et al. (1988) might be a misidentification of L. simplex.
... In some studies, signature characters were added only descriptively, while in others they were included in diagnoses. For instance, signature characters and their positions in the respective nuclear and/or plastidencoded gene sequence alignments were visually identified in ciliates (Agatha and Strüder-Kypke, 2012;Hirt et al., 1995;Sun et al., 2012;Wang et al., 2020;Zhang et al., 2014). In other studies, the signature characters were included in diagnoses of, e.g., unicellular chlorophytes at different hierarchical ranks (Marin and Melkonian, 2010), euglenids (Marin et al., 2003), fungi (Rosling et al., 2011), and metazoans (Churchill et al., 2014;Delić et al., 2017;Grosse et al., 2021;Johnson et Schematic representation of phylogenetic relationships as inferred from rRNA gene sequences (see the full trees in Supplementary Data S1). ...
... Family Favellidae Kofoid and Campbell, 1929 Remarks: Data on signature characters are added to the improved diagnosis published by Agatha and Strüder-Kypke (2012). The family comprises a single genus, for which the given diagnosis is thus also applicable. ...
... Marine and brackish habitats. Discussion: At first glance, Favella resembles Schmidingerella in lorica shape; yet, they differ in the subapical bulge (absent vs. present), the wall (smooth and without windows vs. with reticulate surface ridges and windows), and the somatic ciliary pattern (e.g., ventral kinety monokinetidal vs. bipartite in monokinetidal anterior and dikinetidal posterior portion; broad unciliated stripe separating ventral kinety and right ciliary field absent vs. present; Agatha and Strüder-Kypke, 2012). Regarding the 18S rRNA gene, the ITS1-5.8S ...
Traditionally, taxa following the botanical or zoological codes of nomenclature are diagnosed mainly by morphological characters, although integrative taxonomy advocates including additional features. While many taxonomic studies include DNA sequence analyses, a systematic integration of diagnostic molecular characters (signature characters) is still rare. Here, we suggest a practical guideline for the detection and evaluation of signature characters that provides the means necessary to complement diagnoses and facilitates identifications. The guideline comprises generally applicable criteria exemplified by a case study on an ecologically important group of planktonic protists, the Oligotrichea. The detection of signature characters and their discrete states in multiple sequence alignments is facilitated by the recently developed tool DeSignate. Moreover, we introduce a novel bioinformatic approach to test the influence of different alignment programs on the consistency of signature characters. Our workflow enabled detection of consensus signature characters for most tested taxa and inclusion of such characters in the diagnoses of three orders, eight families, and two genera in the Oligotrichea. The suggested approach is a step towards an integrative taxonomy linking reliable molecular sequence data to organisms’ traits.
... We propose the lorica sac to originate from an additional secretion cycle of compact material which is not attached to the inner lorica surface. The most parsimonious assumption is its development in the last common ancestor of the two families with a partial loss in Codonellopsis and a complete reversal in the Stenosemellidae, Laackmanniella, and possibly Wangiella (Agatha, 2010b;Agatha & Strüder-Kypke, 2012). The generic affiliation of Dictyocysta species with hyaline lorica walls (e.g., D. mitra; this study) is questionable; genetic data and further ultrastructural studies for confirming that the observed reticulate texture is actually generated by tubules and not by irregular alveoli are required. ...
... data on Epirhabdonella and Protorhabdonella; Abboud-Abi Saab, 2008;Balech, 1968;Burns, 1983;Gold & Morales, 1977;Jörgensen, 1924;Kršinić, 2010;Lackey & Balech, 1966); in Epicancella (Epiplocylididae), light microscopy has not revealed windows (Brandt, 1906(Brandt, , 1907Fernandes, 2004). Spiraled structures are restricted to the collars of the rhabdonellid genera Metacylis, Pseudometacylis, and Schmidingerella and to the paraloricae in Schmidingerella (Agatha & Strüder-Kypke, 2012;Jörgensen, 1924;Lackey & Balech, 1966). ...
Tintinnid ciliates build loricae, whose structure, shape, and size still largely represent the basis for taxonomy and classification, although genetic analyses demonstrated their limited utility for inferring evolutionary relationships. The textures of the lorica walls, however, result from the chemical and physical properties of the forming material, which is supposed to be rather conserved in closely related taxa, viz., congeners and confamilial genera. Within a particular texture, small deviations in the chemical composition might affect the wall’s stickiness and accordingly its capability to adhere foreign particles, explaining the intertwining of tintinnids with hyaline and agglutinated loricae in phylogenetic inferences. In a comprehensive comparative study, the lorica textures were electron microscopically and morphometrically analysed in 21 species from 17 genera and more than nine families together with literature data. Most species were investigated for the first time, and the taxa cover a substantial portion of the molecular genealogy. The phylogeny-aware analysis of the lorica-related features provides a preliminary hypothesis on lorica evolution. Eventually, this conspectus suggests the dominance of hard lorica walls with an alveolar texture and proposes different modes of lorica formation.
... Nevertheless, lorica-based approaches alone are now thought to be inadequate for species identification and discrimination, since the lorica could be polymorphic owing to the influence of environmental conditions or physiological state of the cell itself [23,28]. Recently, a few tintinnine species were studied using integrative techniques (live observation, silver staining, electron microscopy, and gene sequencing), which resulted in new insights into their systematics [29][30][31]. There is increasing evidence of lorica plasticity and cryptic species diversity among tintinnines [24,25,[32][33][34]. ...
... Previous molecular phylogenetic studies have revealed that Tintinnopsis is polyphyletic [51,52], most of its members being distributed among at least eleven lineages with some species clustering with taxa that have either a sparsely agglomerated lorica (Leprotintinnus, Rhizodomus, Stylicauda) or a particle-free lorica (Climacocylis, Helicostomella) [52]. These stable and well-supported clades indicated that these unique and ambiguous Tintinnopsis-like species may belong to several distinct genera and families as indicated by their divergent cell features, lorica ultrastructure, and, especially, synapomorphies of the somatic ciliary pattern, which have been confirmed as key diagnostic trait at genus level in other well-known genera [29,52]. ...
... Historically, lorica features have been the main diagnostic character used to delineate genera in Tintinnina owing to their ease of collection and observation. In recent decades, however, the application both of cytological characters based on live and stained specimens and phylogenetic analyses based on sequence data has led to the traditional lorica-based classification being challenged [e.g., 29,30,53]. Hence, detailed investigations of cytological features of cell are necessary in order to distinguish among forms with a similar lorica. In the present study we revealed that the complex ciliary pattern in T. karajacensis and T. gracilis, is sufficiently distinct to distinguish these from most other tintinnines as follows: i. kinetids in the ventral kinety conspicuously densely arranged in the middle portion as compared with anterior and posterior portions (vs. ...
Background
The taxonomic classification of the suborder Tintinnina Kofoid & Campbell, 1929, a species-rich group of planktonic ciliated protistans with a characteristic lorica, has long been ambiguous largely due to the lack of cytological and molecular data for most species. Tintinnopsis is the largest, most widespread, and most taxonomically complex genus within this group with about 170 species occurring in nearshore waters. Previous molecular phylogenetic studies have revealed that Tintinnopsis is polyphyletic.
Results
Here we document the live morphology, infraciliature, gene sequences, and habitat characteristics of three poorly known tintinnine species, viz. Tintinnopsis karajacensis Brandt, 1896, Tintinnopsis gracilis Kofoid & Campbell, 1929, and Tintinnopsis tocantinensis Kofoid & Campbell, 1929, isolated from the coastal waters of China. Based on a unique cytological feature (i.e., an elongated ciliary tuft with densely arranged kinetids) in the former two species, Antetintinnopsis gen. nov. is erected with Antetintinnopsis hemispiralis (Yin, 1956) comb. nov. (original combination: Tintinnopsis hemispiralis Yin, 1956) designated as the type species. Moreover, A. karajacensis (Brandt, 1896) comb. nov. (original combination: Tintinnopsis karajacensis Brandt, 1896) and A. gracilis (Kofoid & Campbell, 1929) comb. nov. (original combination: Tintinnopsis gracilis Kofoid & Campbell, 1929) are placed in a highly supported clade that branches separately from Tintinnopsis clades in phylogenetic trees based on SSU rDNA and LSU rDNA sequence data, thus supporting the establishment of the new genus. One other species is assigned to Antetintinnopsis gen. nov., namely A. subacuta (Jörgensen, 1899) comb. nov. (original combination Tintinnopsis subacuta Jörgensen, 1899).
Conclusions
The findings of the phylogenetic analyses support the assertion that cytological characters are taxonomically informative for tintinnines. This study also contributes to the broadening of our understanding of the tintinnine biodiversity and evolution.
... These sequences caused a change of paradigm in tintinnid taxonomy (for example, revealing the non-monophyly of hyaline and hard-agglomerated taxa), although the heterogeneous quality of the obtained data and interpretations have also caused confusion (see examples noted by Strüder-Kypke 2014, Santoferrara et al. 2017). More reliably but sparsely, recent descriptions and redescriptions have incorporated lorica, cell and DNA sequencing data , Agatha and Strüder-Kypke 2012, Saccà et al. 2012, Ganser and Agatha 2018, Gruber et al. 2018, Smith et al. 2018). ...
... 4C-D) and a different family(Agatha and Strüder-Kypke 2012). ...
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... These sequences caused a change of paradigm in tintinnid taxonomy (for example, revealing the non-monophyly of hyaline and hard-agglomerated taxa), although the heterogeneous quality of the obtained data and interpretations have also caused confusion (see examples noted by Strüder-Kypke 2014, Santoferrara et al. 2017). More reliably but sparsely, recent descriptions and redescriptions have incorporated lorica, cell and DNA sequencing data (Kim et al. 2010, Agatha and Strüder-Kypke 2012, Saccà et al. 2012, Ganser and Agatha 2018, Gruber et al. 2018, Smith et al. 2018. ...
... 4C-D) and a different family(Agatha and Strüder-Kypke 2012). ...
... Here we use single-cell 'omics (genomics and transcriptomics) to study the MIC genome and the transcriptome (a proxy for the gene-sized chromosomes of the macronuclear genome) of Schmidingerella arcuata, a marine ciliate (class Spirotrichea, order Tintinnida). Long-used as an ecological model in planktonic food web studies, S. arcuata is ubiquitous in coastal waters, where it periodically dominates the ciliate community (Dolan and Pierce 2013;Santoferrara et al. 2018;Agatha and Strüder-Kypke 2012;Echevarria et al. 2014). S. arcuata is also one of the few marine ciliates amenable to culture and thus represents a ciliate that is both ecologically relevant and cultivable (Echevarria et al. 2016;Montagnes et al. 2008Montagnes et al. , 2013Dolan 2012;Jung et al. 2016;Cobb 2017;Gruber et al. 2019). ...
... Schmidingerella arcuata was collected from the surface waters of northeastern Long Island Sound, CT cycle. Morphology and 18S rDNA sequences (see Santoferrara et al. 2013) confirmed the taxonomic identification of S. arcuata (Agatha and Strüder Kypke, 2012). ...
Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long-served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new non-model genome resource for the study of ciliate ecology and genomic biology, and provides a detailed functional counterpart to ecological research on S. arcuata.
... However, data from (potentially) related taxa for comparison with the type species are often lacking or difficult to obtain [9]. Furthermore, available data is frequently not added consistently to formal diagnoses [10,11], due to problems in, for instance, the definition of diagnostic molecular characters and the designation of their positions, as well as the lack of suitable tools. For a standardized designation of the position of diagnostic molecular characters in taxon diagnoses, a reference sequence alignment and/or a reference sequence are recommended, facilitating comparability and reproducibility [1]. ...
... Currently, time-consuming inspections of the alignments by eye yield characters distinguishing the query group from the reference group, e.g., by Agatha and Strüder-Kypke [10]. Previous software solutions like the workbench utility in BOLD [12] and CAOS [13] are rarely employed. ...
Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort.
DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced.
DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at (https://designate.dbresearch.uni-salzburg.at/) and is open source (https://github.com/DatabaseGroup/DeSignate/).
