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Abstract The history of ciliate systematics has been divided into \ufb01 ve periods: (1) the Age of Discovery; (2) the Age of Exploitation; (3) the Age of Infraciliature; (4) the Age of Ultrastructure; and (5) the Age of Re\ufb01 nement. Progress in each of these periods arose through an interaction of technology and conceptual views. For example, re\ufb01 ned silver staining techniques revealed the law of desmodexy of the ciliate cortex and enabled the development of comparative morphogenetics in the Age of Infraciliature. Electron microscopy was essential for the conceptual notion of levels of organization below the cell and provided the impetus for the structural conservatism hypothesis in the Age of Ultrastructure. In this latter age, the foundations for the current classi\ufb01 cation system have been laid. Gene sequencing has provided the next techno- logical innovation, which has enabled testing and revising our views on relationships in the current Age of Re\ufb01 nement. Major differences between the scheme presented herein with its two subphyla and 11 classes and other competing schemes are brie\ufb02 y discussed. Keywords Kinetid, cortex, rRNA gene, molecular phylogeny, organic design Systematics as a discipline was defined by Simpson (1961) as \u201cthe scientific study of the kinds and diversity of organisms and of any and all relation- ships among them\u201d (p. 7). One aim of modern systematics is to represent these relationships among organisms by natural classifications : these are hierarchical and reflect as closely as possible the true phylogeny of a group of organisms. The approach to establishing a hierarchical classifica- tion is influenced by the conceptual views of how significant particular characters are in inferring relationships, and these conceptual views, in their turn, are influenced by the technical approaches in vogue. In this context, Corliss (1974a) discussed the historical development of ciliate systematics in four periods: (1) the Age of Discovery (1880\u2013 1930), exemplified by Bütschli; (2) the Age of Exploitation (1930\u20131950), exemplified by Kahl; (3) the Age of the Infraciliature (1950\u20131970), exemplified by Chatton, Lwoff, and Fauré-Fremiet, and during which Corliss (1961) published the first edition of \u201cThe Ciliated Protozoa\u201d; and (4) the Age of Ultrastructure , whose beginnings around 1970 were summarized in the review chapter by Pitelka (1969). The zenith of the Age of Ultrastructure (1970\u20131990) was at the time of the second edition of \u201cThe Ciliated Protozoa\u201d by Corliss (1979), and its ending might be established around 1990, at the appearance of the first reports on gene sequences of ciliates. Indeed, Greenwood, Sogin, and Lynn (1991a) suggested this criterion as the beginning of a fifth age \u2013 the Age of Refinement (1990\u2013present), during which the major lines of evolution and our closest approach yet to a natural classification for the phylum might be possible. It is therefore useful to briefly review this history, especially empha- sizing the last 50 years to understand how ciliate systematics has indeed progressed. Chapter 1 Introduction and Progress in the Last Half Century 1 2 1. Introduction and Progress in the Last Half Century 1.1 The Ages of Discovery (1880\u20131930) and Exploitation (1930\u20131950) Bütschli (1887\u20131889) and Kahl (1930\u20131935), exem- plifying the Ages of Discovery and Exploitation, respectively, primarily used light microscopic observations of living ciliates, without the use of sophisticated stains. From the Age of Discovery to the Age of Exploitation, the number of higher taxa doubled as our understanding of diversity exploded (Table 1.1). The conceptual approach focused on the character of the somatic and oral ciliature and on a consideration that evolution proceeded from simpler forms to more complex forms. This is reflected in the characterization of the higher taxa by Bütschli as Holotricha \u2013 evenly covered by somatic cilia \u2013 and Spirotricha \u2013 with a prominent spiralling adoral zone of membranelles (Table 1.1). The suctorians with their bizarre ten- tacled appearance and absence of external ciliature were given equivalent stature to all other ciliates by both Bütschli and Kahl. Other specialized and \u201ccomplex\u201d sessile forms, like the chonotrichs and peritrichs , were also segregated to a higher rank by Kahl, equivalent to Holotricha and Spirotricha (Table 1.1). Within these higher taxa, oral features, indicated by the suffix \u201c-stomata\u201d, were major characters to indicate common descent (Table 1.1). It is interesting to note that the opalinid \u201cflagel- lates\u201d were considered \u201cprotociliates\u201d during the Kahlian period based on the views of Metcalf (1923, 1940) among others (Table 1.1). 1.2 The Age of the Infraciliature (1950\u20131970) Five scientists \u2013 Chatton and Lwoff, Klein, von Gelei, and Fauré-Fremiet \u2013 stand out as the pioneers of this period, which Corliss (1974a) suggested extended from about 1950 to 1970. Yet, the roots of this age originated earlier in the 20th century in descriptions of the different technical approaches to using silver to stain the cortex and other struc- tures of ciliates \u2013 the dry silver method of Klein (1929) and the wet silver method of Chatton and Lwoff (1930). The observations made by these pioneers culminated in seminal conceptual papers attributing a variety of causal relationships to various infraciliary structures (Chatton & Lwoff, 1935b; Klein, 1928, 1929; von Gelei, 1932, 1934b; von Gelei & Horváth, 1931). Chatton and Lwoff\u2019s (1935b) law of desmodexy stands out as one of the \u201crules\u201d emerging from this period that has stood the test of time: true kinetodesmata and/or kinetodesmal fibrils, when present, lie to or extend anteriad and/or to the organism\u2019s right of the kinety with which they are associated (see Chapter 2 ). With this rule, one can not only identify a ciliate, but also one can deduce the polarity of the cell. The developmental autonomy and \u201cgenetic\u201d continuity Table 1.1. Major systems of ciliate classification popular prior to 1950.a Bütschlian Erab Kahlian Era (1880\u20131930)a (1930\u20131950) INFUSORIA Subphylum Ciliophora Ciliata CILIATA Holotricha Protociliata Gymnostomata Opalinata Trichostomata Euciliata Astomata Holotricha Spirotricha Gymnostomata Heterotricha Prostomata Oligotricha Pleurostomata Hypotricha Hypostomata Peritricha Trichostomata Suctoria Apostomea Hymenostomata Thigmotricha Stomodea Rhynchodea Astomata Spirotricha Heterotricha Ctenostomata Oligotricha Tintinnoinea Entodiniomorpha Hypotricha Peritricha Mobilia Sessilia Chonotricha SUCTORIA a Classes are indicated in bold capital letters; subclasses, in ital- ics; orders, in bold; suborders and \u201ctribes\u201d, further indented in Roman type. b It should be noted that Bütschli (1887\u20131889) originally pro- posed a scheme that differed slightly from that shown (see Corliss, 1962a; Jankowski, 1967a). Later workers in the period re-arranged it so that it came to resemble the form presented here. In all cases, the number of major groups remained essen- tially the same. of the infraciliature was summarized at the begin- ning of this period by Lwoff (1950) in his book entitled \u201cProblems of Morphogenesis in Ciliates\u201d. Fauré-Fremiet and his students applied these conceptual views of the developmental impor- tance of infraciliary patterns to resolving phyloge- netic problems within the phylum. Fauré-Fremiet\u2019s (1950a) discussion of comparative morphogenesis of ciliates rested on the conceptual presumption that similarities in pattern of the ciliature during divi- sion morphogenesis revealed the common ancestry of lineages (see Corliss, 1968). These similarities in division morphogenesis were particularly important in establishing the phylogenetic affinities of polymorphic