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, removing heterotrichs from the spirotrich assemblage (cf. Table 1.3, 1.4). However, de Puytorac (1994a) elevated sev- eral groups to class rank (e.g., HYPOTRICHEA , OLIGOTRICHEA , VESTIBULIFEREA ) for which there is as yet no strong molecular genetic evidence (see Chapter 16 ). Two new clades differentiated by small subunit rRNA gene sequences and now rec- ognized as classes are the Class ARMOPHOREA (see Affa\u2019a, Hickey, Strüder-Kypke, & Lynn, 2004; van Hoek, Akhmanova, Huynen, & Hackstein, 2000a) and the Class PLAGIOPYLEA (see Embley & Finlay, 1994; Lynn & Strüder-Kypke, 2002) (Fig. 1.5, Table 1.4). Lynn (2004) highlighted a diffi- culty with each of these so-called \u201c riboclasses \u201d: the Class ARMOPHOREA associated genera, such as Metopus and Nyctotherus , whose somatic kinetids were dissimilar, while the Class PLAGIOPYLEA separated some genera, such as Plagiopyla and Trimyema , whose kinetids were quite similar to those of the Class OLIGOHYMENOPHOREA to which the plagiopyleans had been transferred as a subclass by Small and Lynn (1985) (Table 1.3). Thus, somatic kinetid structure seems not to be highly conserved in armophoreans and to be more highly conserved in some plagiopyleans! We have appar- ently reached the limits of structural conservatism of the somatic cortex as a principle, and we can only say that these are the exceptions that prove the rule! By the mid-1990s there was ample evidence from a variety of independent phylogenetic analy- ses of both small subunit and large subunit rRNA gene sequences to demonstrate a fundamental bifurcation in the phylum (Baroin-Tourancheau, Tsao, Klobutcher, Pearlman, & Adoutte, 1995; Hammerschmidt, Schlegel, Lynn, Leipe, Sogin, & Raikov, 1996; Hirt et al., 1995) (Fig. 1.5). One branch, which separates the ciliates with postciliodesmata sensu stricto , corresponds to 1.4 The Age of Refinement (1990\u2013Present) 11 Fig. 1.5. A molecular phylogeny of the Phylum Ciliophora based on small subunit rRNA gene sequences. Several representatives of each class have been chosen to demonstrate the genetic diversity within the phylum and the dis- tinctness of the different clades that are considered to be of class rank in the classification proposed herein (see Table 1.4) (see Chapter 16 for further discussion of molecular phylogenetics) the Subphylum POSTCILIODESMATOPHORA , a concept proposed by Gerassimova and Seravin (1976). This subphylum now includes only the Classes KARYORELICTEA and HETEROTRICHEA ; it excludes the spirotrich clade, which was included by Small and Lynn (1985) (cf. Tables 1.3, 1.4). While karyorelicteans do not have dividing macronuclei, the heterotrichs do, apparently relying primarily on extramacronuclear microtubules for this proc- ess (Diener, Burchill, & Burton, 1983; Jenkins, 1973). Lynn (1996a) named the other branch, the Subphylum INTRAMACRONUCLEATA , because all ciliates in this clade have a dividing macronu- cleus that relies predominantly on intramacronu- clear microtubules for completion of division. The suggestion that macronuclear division has arisen separately twice during the evolution of ciliates is not unreasonable, considering that at least two kinds of nuclear division, using both extranuclear and intranuclear microtubules also occur in the dinoflag- ellates (Perret, Albert, Bordes, & Soyer-Gobillard, 1991), the sister clade to the ciliates (Leander & Keeling, 2003; Van de Peer, Van der Auwera, & De Wachter, 1996). 1.5 Major Differences in the New Scheme Corliss (1979) noted in his discussion of the major differences of schemes that an obvious trend has been the inflation of taxa as our discovery and understanding of diversity have changed from the 1880s until the present. As discussed above, approaches have been influenced both by techno- logical advances \u2013 light microscopy , cytological staining, electron microscopy , molecular biology \u2013 and by new conceptual views. With respect to the latter, the emphasis on the somatic cortex by Small and Lynn (1981) caused a major revision in our understanding of relationships between the mid-1970s and the mid-1980s. Currently, there are two recent classification systems of ciliates seeking adherents; one proposed by de Puytorac (1994a) and his colleagues in the second volume of the Traité de Zoologie and the other proposed most recently by Lynn (2004) and presented in a slightly revised version herein (Table 1.4). Since various differences between these views have been discussed above, this section will serve to summarize these. 1. The subphyletic divisions in the two systems are different: three by de Puytorac (1994a) and two here (Table 1.4). Data on genetic diversity support a major division into two subphyla, the Subphylum POSTCILIODESMATOPHORA and the Subphylum INTRAMACRONUCLEATA . 2. De Puytorac (1994a) recognizes five super- classes, one essentially equivalent to our Subphylum POSTCILIODESMATOPHORA , while we provide no such subdivisions (Table 1.4). It is the case in molecular phylogenies that there is substructure within the Subphylum INTRAMACRONUCLEATA . For example, six classes (i.e., PHYLLOPHARYNGEA , NASSOPHOREA , COLPODEA , PLAGIO- PYLEA , PROSTOMATEA , and OLIGOHYM- ENOPHOREA ) are often consistently supported as a clade (Fig. 1.5). This grouping may repre- sent a natural assemblage, and therefore repre- sent a superclass assemblage. However, there is no obvious shared derived morphological feature uniting these taxa, and at this time we do not recognize it as a taxonomic category. 3. De Puytorac (1994a) recognizes 11 classes as does the system proposed here (Table 1.4). However, the classes are different. De Puytorac (1994a) includes the prostomates in the Class NASSOPHOREA . Differences in the somatic kinetid (Eisler, 1989; Lynn, 1991), stomatogenesis (Eisler; Huttenlauch & Bardele, 1987), and small subunit rRNA gene sequences (Stechmann, Schlegel, & Lynn, 1998) between nassophoreans and prostomate- ans argue against uniting them in the same class (Fig. 1.5). While both systems recognize the spirotrichs as a larger assemblage, the eleva- tion of the oligotrichs to class rank, equivalent to hypotrichs , is not justified by the molecular data, which suggest at least seven separate lineages in the Class SPIROTRICHEA , here recognized as subclasses (Strüder-Kypke & Lynn, 2003). Finally, we cannot agree with de Puytorac (1994a) that elevation of the vestibuliferians to class rank is warranted. We prefer to refer to this clade by the Bütschlian moniker, Trichostomatia (Table 1.4). The trichostomatians in this sense and the haptorians share virtually identical somatic kinetid patterns (Lynn, 1981, 1991). This varies only in the entodiniomorphids where Lynn (1991) has 1.5 Major Differences in the New Scheme 13 14 1. Introduction and Progress in the Last Half Century interpreted the appearance of a transient micro- tubule during kinetid replication (see Furness & Butler, 1986) to be the homologue of the T2 transverse microtubular ribbon of litostomes . Moreover, extensive analyses of litostome small subunit rRNA gene sequences consistently group the haptorians and trichostomes (Wright & Lynn, 1997b; Strüder-Kypke, Wright, Foissner, Chatzinotas, & Lynn, 2006). De Puytorac (1994a) elevated a considerable number of taxa to subclass and ordinal ranks, totalling 25 subclasses and 70 orders. Comparison with the scheme presented here will demonstrate considerable agreement in the basic groups or clades, despite possible differences in rank (Table 1.4 and the original references). While Small and Lynn (1981, 1985) established 15 subclasses and 48 orders, our revised scheme has 19 subclasses and 59 orders. Many of these changes have been influenced by genetic data obtained in the last few years, and these are discussed both by Lynn (1996b,