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structures, even at the ultrastructural level, have found their limits. Lynn (1991) noted that genera such as Transitella , Phacodinium , Plagiopyla , Lechriopyla , and Schizocaryum exhibit cortical features that cannot be used to confidently assign them to a major class. In fact, the latter four genera have now been assigned to a class based only on gene sequences! 3.2.2 Morphogenetic Patterns The analysis of developmental patterns in revealing phylogenetic relationships has its roots in the 19th century in the work of Haeckel and von Baer (see Gould, 1977). While this approach must be applied with caution, Corliss (1968, 1979) noted that application of the Biogenetic Law to ciliate development \u2013 similarities in the ontogenies of different major groups of ciliates \u201crecapitulating\u201d their phylogeny \u2013 had provided important insights. Sewertzoff (1931) discussed a number of other principles, such as oligomerization and polymeri- zation , which have been applied to the evolution of protozoan lineages (von Gelei; 1950; Poljansky & Raikov, 1976; Raabe, 1971a). Oligomerization and polymerization , and the related principle of auxo- morphy (Fauré-Fremiet, 1968), have been used to explain the origin of new types, primarily at the genus and species levels, but have not provided insights relating major groups of ciliates. Ontogenetic patterns that have been the most illuminating in relating higher taxa are those exhibited by ciliates at asexual reproduction Fig. 3.4. A demonstration of the structural diversity of the oral region among ciliate genera from the class COLPODEA. When examined, all of these genera have the same basic somatic kinetid pattern (bottom right). However, prior to the Age of Ultrastructure, they were placed in different higher taxa: Colpoda and Bryophrya were trichostomes; Cyrtolophosis was a hymenostome; Platyophrya was a gymnostome; Bryometopus and Bursaria were heterotrichs (see Corliss, 1961). Sorogena and Grossglockneria were described during the Age of Ultrastructure. (Modified from Foissner, 1993a.) 3.2 Above the Genus-Species Level 83 84 3. Characters and the Rationale Behind the New Classification during which new mouthparts are formed and the somatic region of the parent is partitioned for the progeny. These two related processes are termed cortical stomatogenesis and cortical somatogen- esis , respectively (Lynn & Corliss, 1991). As noted in Chapter 1, similarities in oral structures and division morphogenesis of hymenostomes , thigmotrichs , and peritrichs lead Fauré-Fremiet (1950a) to conclude these groups shared a common ancestry, while Guilcher (1951) used developmental patterns to infer the common ancestry of cyrto- phorians , suctorians , and chonotrichs (Fig. 1.1). In addition to uniting major groups, stomatogenetic patterns can be used to separate major groups. For example, Small (1967) recognized a pattern of stomatogenesis among the hymenostomes in which the scutica or scutico-hook was formed, now called scuticobuccokinetal stomatogenesis , and this formed the basis for his distinguishing the Order Scuticociliatida within the oligohy- menophorean clade. Bardele (1989) has described a research program devoted to the careful analysis of morphogenesis using electron microscopy , arguing that this will enable us to identify with certainty the true devel- opmental origin of the microtubular associates of kinetosomes and so determine homologies. In fact, Huttenlauch and Bardele (1987) proved the impor- tance of this approach when they demonstrated that the microtubular ribbons supporting the cytophar- ynx of the prostome Coleps were in fact postciliary microtubular ribbons . These postciliary ribbons change their orientation during stomatogenesis to appear like transverse microtubular ribbons , an interpretation previously given to them based on morphostatic ultrastructure (e.g., see Lynn, 1985; de Puytorac & Grain, 1972). Furness and Butler (1986) examined somatic kinetosomal replication in entodiniomorphids and revealed the transient appearance of a second transverse microtubular ribbon microtubule, providing support for align- ment of entodiniomorphids to the litostome clade (Lynn, 1991; Lynn & Nicholls, 1985). Patterns of oral kinetid assembly can involve the joining and rotation of kinetosomes and the appearance and disappearance of fibrillar structures in predictable sequences (Eisler, 1989; Jerka-Dziadosz, 1980, 1981a, 1981b, 1982), and these features may ultimately prove useful to systematists when the database becomes sufficiently large. Finally, brief mention should be made of the ultrastructure of the nuclear apparatus. Nuclear dimorphism \u2013 the micronucleus and macronucleus \u2013 is a synapomorphy for the Phylum Ciliophora . The inability of the macronucleus to divide has long been considered a \u201c karyological relict \u201d character (Corliss, 1979; Raikov, 1969, 1982, 1996). Related to this, Orias (1991a) has suggested that differences in the use of extra-macronuclear and intra-macronuclear microtubules during macronuclear division argue that macronuclear division evolved twice in the phylum. Lynn (1996a) used this feature to estab- lish the Subphylum Intramacronucleata , uniting all ciliates that primarily use intra-macronuclear microtubules during macronuclear division. Thus, morphogenetic patterns at a variety of levels of biological organization and of a variety of structures have proved useful in revealing com- mon descent among major groups of ciliates. These will continue to be useful at these higher levels, in addition to providing subtle differences that may distinguish species and genera. 3.2.3 Gene and Protein Sequences The distinctive nature of the major groups of ciliates revealed both by light and electron micro- scopy means that relatively few characters can be used to assemble them into larger groups. As noted above and in Chapter 1, features of the somatic kinetid , similar patterns of division mor- phogenesis , and nuclear features have been most useful. Sequences of genes and proteins provide a large number of characters, either as nucleotides or amino acids, and many of these may evolve independently of each other. This structural con- servation with variation, at yet a lower level of biological organization , is presumed to signal deep common ancestry , and therefore permits us to test relationships established using morpho- logical criteria, such as the ultrastructure of the somatic kinetid . The earliest studies used sequences of the 5S and 5.8S rRNAs, but their shorter lengths and conserved nature were not helpful in resolving deep relationships (Van Bell, 1985). Initial studies to sequence cloned small subunit ribosomal RNA (SSrRNA) genes (Elwood, Olsen, & Sogin, 1985; Sogin, Swanton, Gunderson, & Elwood, 1986b) and reverse transcripts of both SSrRNA and large subunit rRNA (LSUrRNA) (Baroin et al., 1988; Lynn & Sogin, 1988; Nanney et al., 1989; Preparata et al., 1989) provided clear evidence that these data would prove useful in elucidating deep phylogeny. Analyses were enabled by powerful sets of phy- logenetic inference packages. Recent updates are found in Felsenstein (2004) and Swofford (2002). The application of PCR using universal eukary- ote primers provided both a rapid alternative to cloning genes and the potential to obtain sequence information from small numbers of cells, even a single cell (Medlin, Elwood, Stickel, & Sogin, 1988). The PCR sequencing approach has been extended to other genes, including histones (Bernhard & Schlegel, 1998), tubulins (Baroin-Tourancheau, Villalobo, Tsao, Torres, & Pearlman, 1998; Israel, Pond, Muse, & Katz, 2002), actins (Hogan, Hewitt, Orr, Prescott, & Müller, 2001), and translation factors (Moreira, Kervestin, Jean-Jean, & Philippe,