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327 Abstract Our understanding of the evolutionary diversi\ufb01 cation of ciliates in the past two decades particularly has depended upon the interaction between conceptual views and technological advanc- es. Transmission electron microscopy precipitated a revolution in our views of what characters might be signi\ufb01 cant in inferring deep phylogenetic relation- ships. The \ufb01 brillar patterns of somatic kinetids were considered crucial, based on the notion of the struc- tural conservation of these cortical components. Molecular phylogenetic analyses have been used to test the conclusions based on electron microscopy. In the main, phylogenetic relationships inferred from sequences of the small subunit and large subunit rRNA genes have con\ufb01 rmed the major class- es, and suggested several new ones (i.e., Classes ARMOPHOREA and PLAGIOPYLEA). In addi- tion, the rRNA genes demonstrated a fundamental subphyletic division \u2013 now named the Subphyla Postciliodesmatophora and Intramacronucleata. Protein gene sequences (e.g., elongation factor 1\u3b1, \u3b1-tubulin, and histone H3 and H4) provide con\ufb01 r- mation for some clades. Using the rRNA phylogeny, the evolution of some major character states, particularly nuclear ones, can be assessed. Keywords Phosphoglycerate kinase, intramem- branous particles, ciliary necklace The progress in our understanding of the evolution- ary diversification of ciliates has depended upon an interaction between conceptual views and techno- logical advances . On the conceptual side, our views of which characters or features of ciliates were most important in revealing common ancestry have changed ( see Chapter 1 ). Briefly, in the 18th and 19th centuries, overall ciliation patterns and the dominance of the \u201c spirotrich \u201d oral region divided the ciliates into \u201cholotrichs\u201d and \u201c spirotrichs \u201d. In the first half of the 20th century, ontogenetic patterns , particularly revealed by silver-staining organisms at cell division, received greater weight and aligned taxa that had previously been distantly separated (e.g., chonotrichs and suctoria were related to the cyrtophorines ). In the latter half of the 20th century, transmission electron microscopy revealed a whole new set of cytoskeletal charac- ters, particularly the somatic kinetid patterns. The diversity of these somatic kinetid patterns initially suggested eight major clades or classes (Small & Lynn, 1981, 1985). In the 1970s, microbiologists studying prokaryo- tes had been successfully using small subunit (SSU) rRNA genes to resolve relationships among this group whose members were not rich in mor- phological features (Stackebrandt & Woese, 1981). By the mid-1980s, several research groups began sequencing SSUrRNA genes of ciliates (Elwood, Olsen, & Sogin, 1985; Sogin & Elwood, 1986; Sogin, Swanton, Gunderson, & Elwood, 1986a), demonstrating that ciliates, even with this small sampling of species, appeared to be monophyletic and yet showed very deep divergences, equivalent to the genetic distances between the classical plant and animal \u201ckingdoms\u201d. The first denser samplings of species, using both the SSUrRNA (Lynn & Sogin, 1988; Sogin & Elwood) and the large subunit (LSU) rRNA (Baroin et al., 1988), provided enough taxon density to demonstrate Chapter 16 Deep Phylogeny, Gene Sequences, and Character State Evolution \u2013 Mapping the Course of Ciliate Evolution 328 16. Deep Phylogeny, Gene Sequences, and Character State Evolution utility in testing the deeper relationships predicted by ultrastructural research. The molecular phylogenetic approach is now a recognized method for testing and establishing phylogenetic relationships among organisms, and has been particularly fruitful in revealing the broad lines of evolutionary descent among eukaryotes. However, it rests on the basic assumption that phylogenetic trees based on genes truly represent the phylogeny of the organisms. Ultimately, our confidence in so-called \u201cgene trees\u201d increases when multiple and unlinked genes show patterns congruent with each other and with organismal phylogenies constructed on other features, such as morphology. It is the purpose of this chapter to briefly review the deep phylogeny of ciliates as inferred from features of cortical ultrastructure , primarily, and then to examine how this topology is congruent with gene tree topologies derived from rRNA genes and several protein coding genes. This will provide a consensus phylogenetic tree of the currently recognized classes of ciliates, which will provide the basis for a final discussion of the evolution of character states in the phylum. It is this distribution of character states that, in part, forms the rationale for the higher classification presented in Chapter 17 . 16.1 Deep Phylogeny and Ultrastructure The transmission electron microscope provided a technical approach that opened up literally a vast array of detailed character information with which to investigate the cellular morphology of protists. Initially, there was a preoccupation with cortical fibrillar systems, an approach pioneered by Pitelka (1969). Later, comparative analyses of these cortical patterns, especially of somatic kinetids , suggested eight major clades or classes of ciliates: (1) Class KARYORELICTEA ; (2) Class SPIROTRICHEA ; (3) Class LITOSTOM- ATEA ; (4) Class PHYLLOPHARYNGEA ; (5) Class COLPODEA ; (6) Class NASSOPHOREA ; (7) Class PROSTOMATEA ; and (8) Class OLIGOHYMENOPHOREA (Lynn, 1981; Small & Lynn, 1981, 1985). As discussed in Chapter 1 , arrangement of these classes into subphyla based on morphology has not been supported by molec- ular analyses (see below). While divided into subphyla by Small and Lynn (1985), the classes emerged \u201cbush-like\u201d from the common ancestor (Fig. 16.1). Bardele (1981) analyzed the arrays of intramem- branous particles of cilia in 68 genera, representing a broad diversity of ciliates. These particle array patterns were classified into a ciliary necklace that ringed the base of the cilium, ciliary plaques , ciliary rosettes , single- and double-stranded longitudinal rows, and orthogonal arrays covering most of the cilium. His analysis suggested six major assem- blages: (1) SPIROTRICHA , corresponding to the Class SPIROTRICHEA ; (2) GYMNOSTOMATA , which included representatives of the Classes LITOSTOMATEA and PROSTOMATEA ; (3) TRICHOSTOMATA , which included representatives from the Classes LITOSTOMATEA and COLPODEA ; (4) ENTO- DINIOMORPHA , which included repre- sentatives from the Class LITOSTOMATEA ; (5) HYPOSTOMATA + SUCTORIA , corresponding to the ClassPHYLLOPHARYNGEA ; and (6) HYMEN- OSTOMATA + PERITRICHA + ASTOMATA , corre- sponding to the Class OLIGOHYMENOPHOREA . Bardele\u2019s \u201cciliate bush\u201d was anchored in a gymnos- tome -like form and radiated out from there. While there was some broad agreement with the clades based on cortical ultrastructure, the particle array character set was not rich enough to tease out the details of this diversification (Fig. 16.2). Bardele (1987, 1989) turned his \u201cciliate bush\u201d upside down as he reviewed the data arising from his laboratory on the ultrastructure of ontogeny , and particularly stomatogenesis , in ciliates. These observations, coupled with the conception that the ciliate ciliature arose by proliferation from the paroral (Eisler, 1989, 1992), suggested that gym- nostomy \u2013 a simple, anterior oral region \u2013 may have arisen repeatedly as a derived and secondary feature of oral apparatus evolution and not as a pri- mary feature. Bardele (1989) concluded by doubt- ing that many of the major groups suggested by Small and Lynn (1981, 1985) would be confirmed to be monophyletic, and he strongly argued that a research program in ontogeny would reveal this view to be true. By the early 1990s, there was general agree- ment among morphologists