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and his group (Fauré- Fremiet, 1948a, 1950a, 1950b). Corliss (1968) Fig. 16.7. Character evolution in the ciliates using a phylogenetic tree whose deep topology is based on the consensus of gene sequences, primarily from the small subunit rRNA and histone H4 genes (cf. Figs. 16.3, 16.5). A Presence of polytene chromo- somes and chromosal fragmentation during macronu- clear development . B Presence of replication bands during S phase of macronuclear DNA synthesis. Note that the genus Protocruzia does not have this feature although it clusters with the Class SPIROTRICHEA (cf. Figs. 16.3, 16.5). C Presence of somatic monoki- netids . D Presence of buccokinetal (black), parakinetal (dark grey), telokinetal (grey), apokinetal (white), and mixokinetal (half black: half grey) modes of stoma- togenesis . KA , Class KARYORELICTEA ; HE , Class HETEROTRICHEA ; SP , Class SPIROTRICHEA ; AR , Class ARMOPHOREA ; LI , Class LITOSTOMATEA ; PH , Class PHYLLOPHARYNGEA ; CO , Class COL- PODEA ; NA , Class NASSOPHOREA ; PL , Class PLAGIOPYLEA ; PR , Class PROSTOMATEA ; OL , Class OLIGOHYMENOPHOREA 16.3 Character State Evolution 337 338 16. Deep Phylogeny, Gene Sequences, and Character State Evolution affirmed this view, and presented the basis of the current classification of stomatogenetic types (Corliss, 1979). Foissner (1996b) has updated and refined the classification of types, and provided a phylogenetic scenario for the evolution of these sto- matogenetic types , assuming that the buccokinetal mode was ancestral or plesiomorphous. Foissner (1996b) noted that evidence for this assumption is weak, but he used as support the model proposed by Eisler (1992) for the evolution of the ciliate cortex. Distribution of all buccokinetal modes on the tree is not consistent with this view (Fig. 16.7D). Instead, the most broadly distributed mode is the telokinetal mode (Fig. 16.7D). Thus, Eisler’s model (Eisler, 1992; Schlegel & Eisler, 1996) may be incorrect. Alternatively, soon after the ancestral cortex evolved by this “paroral model” of evolution (Eisler, 1992), a telokinetal mode of stomatogen- esis may have evolved as the cell division process. As we have argued elsewhere, and is confirmed by this analysis, modes of stomatogenesis should be used only as descriptive features at this deep level. The usefulness of stomatogenetic characters is highest when characterizing and comparing genera and species. It is also useful in broadly associating ciliates into different clades based on the details of the stomatogenetic process rather than the mode itself (e.g. phyllopharyngean merotelokinetal vs. colpodean merotelokinetal ; see Foissner, 1996b). A final feature that we have not mapped on the tree, but which has been discussed by several research groups, is the evolution of hydrogeno- somes from mitochondria (Embley et al., 1995; van Hoek et al., 2000b). Hydrogenosomes have been found in all species so far examined of the Classes ARMOPHOREA and PLAGIOPYLEA , which are not closely related (Figs. 16.6, 16.7), and in select members of the Classes LITOSTOMATEA and OLIGOHYMENOPHOREA . The latter evidence – origin within a class – demonstrates unambigu- ously the adaptive nature of the hydrogenosome (Fenchel & Finlay, 1990b, 1991a). 16.4 Summary We have provided this discussion as an approach to demonstrating how to rationalize morphologi- cal and molecular features of the ciliates. This approach can also serve as the basis for provid- ing evidence of the robustness of a classification or suggesting deeper subdivisions, which may not be inspired immediately by morphology (e.g., Subphylum Intramacronucleata ; see Lynn, 1996a). As the species sampling for our gene sequence database expands, this approach may be productively extended “higher” in the tree, testing relationships among subclasses within classes and orders within subclasses. For exam- ple, the increased species sampling of SSUrRNA genes of suctorians provided very preliminary genetic evidence that the Orders Exogenida , Endogenida , and Evaginogenida may capture the evolutionary diversification of the suctorians (Snoeyenbos et al., 2004). Extensive sampling within the Class OLIGOHYMEN-OPHOREA has confirmed the monophyly of the major sub- classes classically based on morphology (Affa’a, Hickey, Strüder-Kypke, & Lynn, 2004; J.C. Clamp et al., 2008; Greenwood et al., 1991a; Lynn & Strüder-Kypke, 2005; Strüder-Kypke et al., 2000b). Yet, clearly, much work remains to be done!