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& Seravin, 1976; Seravin & Gerassimova, 1978); and for the oral cortex \u2013 the presence of transverse microtubular ribbons supporting the cytopharynx in the Subphylum Rhabdophora and the presence of postciliary microtubular ribbons supporting the cytopharynx in the Subphylum Cyrtophora (Small, 1976) (Table 1.3). However, Huttenlauch and Bardele (1987) demonstrated in an ultrastructural study of oral development that the supposed oral transverse ribbons of the prostomate rhabdophoran Coleps were in fact postciliary microtubules that Table 1.3. Classifications systems proposed by Small and Lynn (1981, 1985).a Small & Lynn (1981) Small & Lynn (1985) Phylum Ciliophora Phylum Ciliophora Postciliodesmatophora Postciliodesmatophora KARYORELICTEA KARYORELICTEA SPIROTRICHEA SPIROTRICHEA Rhabdophora Heterotrichia PROSTOMEA Stichotrichia LITOSTOMEA Choreotrichia Haptoria Rhabdophora Vestibuliferia PROSTOMATEA Cyrtophora LITOSTOMATEA PHYLLOPHARYNGEA Haptoria Phyllopharyngia Trichostomatia Chonotrichia Cyrtophora Suctoria PHYLLOPHARYNGEA NASSOPHOREA Phyllopharyngia Hypostomia Chonotrichia Polyhymenophoria Suctoria COLPODEA NASSOPHOREA OLIGOHYMENOPHOREA Nassophoria Hymenostomia Hypotrichia Peritrichia COLPODEA Astomia OLIGOHYMENOPHOREA Apostomia Hymenostomatia Peritrichia Astomatia Apostomatia Plagiopylia a Classes are indicated in bold capital letters; subclasses, in italics. became twisted during division morphogenesis, making them appear to be transverse microtubules. So, this rhabdophoran was really a cyrtophoran ! This undercut our confidence that these characters had deep phylogenetic significance, and led Lynn and Corliss (1991) to abandon the subphyla, retaining only the eight classes of Small and Lynn. Later, de Puytorac et al. (1993) suggested three different subphyla, also based on signifi- cant cortical ultrastructural features proposed by Fleury, Delgado, Iftode, and Adoutte (1992): the Subphylum Tubulicorticata \u2013 a microtubular cor- tex; the Subphylum Filicorticata \u2013 a micro fibrillar cortex; and the Subphylum Epiplasmata \u2013 an epi- plasmic cortex (Table 1.4). Fleury et al. (1992) had used molecular phylogenies derived from large subunit rRNA gene sequences to support these morphology-based subdivisions. Nevertheless, Lynn and Small (1997) argued that given the variability of cortical ultrastructures in ciliates it was extremely difficult to circumscribe the limits of these subphyla. For example, virtually Fig. 1.4. Colpodeans and their somatic kinetids as a demonstration of the more conservative nature of the somatic kinetid and its \u201cdeeper\u201d phylogenetic signal over the oral structures and general morphology of a group of ciliates. Sorogena was a gymnostome; Colpoda was a vestibuliferan; Cyrtolophosis was a hymenostome; and Bursaria was a spirotrich 1.3 The Age of Ultrastructure (1970\u20131990) 9 10 1. Introduction and Progress in the Last Half Century all ciliates could be described as having a \u201ccorti- cal cytoskeleton of superficial microtubules associ ated, or not, with cortical kinetosomes\u201d \u2013 the major feature distinguishing ciliates in the Subphylum Tubulicorticata (de Puytorac et al., 1993). This reduced emphasis on oral structures as being of great phylogenetic significance extended to the homology of \u201c membranelles \u201d or oral polykinetids , used to establish the Classes Kinetofragminophora , Oligohymenophora , and Polyhymenophora . De Puytorac and Grain (1976) and Grain (1984) had demonstrated the variety of \u201cmembranelles\u201d or oral polykinetids in their reviews of the diversity of cortical ultrastructures of ciliates. This variety Table 1.4. A comparison of the macrosystems of the Phylum Ciliophora of de Puytorac (1994a) and the system proposed herein. Authorships for names will be found in Chapter 17.a de Puytorac (1994a) Proposed system Phylum Ciliophora Phylum Ciliophora Tubulicorticata Postciliodesmatophora POSTCILIODESMATOPHORA KARYORELICTEA KARYORELICTEA HETEROTRICHEA Trachelocercia Intramacronucleata Loxodia SPIROTRICHEA Protocruziidia Protocruziidia Protoheterotrichia Phacodiniidia HETEROTRICHEA Hypotrichia Heterotrichia Oligotrichia Clevelandellidia Choreotrichia SPIROTRICHA Stichotrichia HYPOTRICHEA Licnophoria Euplotia ARMOPHOREA Oxytrichia LITOSTOMATEA OLIGOTRICHEA Haptoria Oligotrichia Trichostomatia Strobilia PHYLLOPHARYNGEA TRANSVERSALA Cyrtophoria COLPODEA Rhynchodia Colpodia Chonotrichia Bryometopia Suctoria PLAGIOPYLEA NASSOPHOREA Filicorticata COLPODEA LITOSTOMATEA PROSTOMATEA VESTIBULIFEREA PLAGIOPYLEA Epiplasmata OLIGOHYMENOPHOREA CILIOSTOMATOPHORA Peniculia PHYLLOPHARYNGEA Scuticociliatia Cyrtophoria Hymenostomatia Chonotrichia Apostomatia Rhynchodia Peritrichia Suctoria Astomatia MEMBRANELLOPHORA NASSOPHOREA Prostomatia Nassulia OLIGOHYMENOPHOREA Peniculia Scuticociliatia Peritrichia Hysterocinetia Astomatia Hymenostomatia Apostomatia *Superclasses are indicated in capital letters; classes, in bold capital letters; subclasses, in italics. lead to a proliferation of names to capture some of these differences. Oral polykinetids in kinetof- ragminophorans could be pseudomembranelles , in oligohymenophorans could be membranoids or membranelles , and in polyhymenophorans could be paramembranelles or heteromembranelles (see definitions in Chapter 2 ). This diversity suggested that these different complex oral structures were probably not homologues. In fact, what they undoubtedly illustrate are diverse solutions to the \u201cproblem\u201d of filter feeding that had arisen through convergent evolution in a much larger number than three independent lineages or classes. Small and Lynn (1981, 1985) recognized these lineages as eight classes, established primarily on the basis of the ultrastructure of the somatic cortex, applying the principles of \u201cstructural conservatism\u201d and \u201csomatic over oral\u201d (Fig. 1.4). 1.4 The Age of Refinement (1990\u2013Present) Greenwood et al. (1991a) suggested that 1990 might be designated as the beginning of the next age in ciliate systematics , the Age of Refinement , for it is in this period that tremendous advances have been made in confirming our basic notions derived from research on ciliate ultrastructure. As with the other ages, the technological roots of this age precede its formal beginning, and are based in the molecular phylogenetic work of Sogin\u2019s lab on small subunit rRNA gene sequences (Elwood, Olsen, & Sogin, 1985; Lynn & Sogin, 1988) and Adoutte\u2019s lab on large subunit rRNA gene sequences (Adoutte, Baroin, & Perasso, 1989; Baroin, Perasso, Qu, Brugerolle, Bachellerie, & Adoutte, 1988). Thus, it might also be called the Age of Genetic Diversity , since the sequences of these highly conserved genes (see Chapter 16 ), enabled us to test the structural conservatism of the ciliate somatic cortex , using the \u201cmolecular skel- etons\u201d of the ribosomal subunits \u2013 the small and large subunit rRNAs. These early papers demonstrated tremendous genetic diversity within the phylum, a level of genetic diversity similar to differences among the \u201ckingdoms\u201d of multicellular organisms, like the plants , animals , and fungi . Further, the major clades established on the basis of ultrastructural research were generally confirmed, indicating that the somatic kinetid was a generally reliable feature to establish common descent (Lynn, 1991, 1996a; Lynn & Small, 1997). However, the molecular data suggested the need for further separation of clades, both at the \u201cclass\u201d level and higher (Lynn, 1996b; Lynn & Small). De Puytorac (1994a) had presaged this by elevating to class rank two groups that molecular genetic data confirmed to be distinct \u2013 the Class PLAGIOPYLEA and the Class HETEROTRICHEA