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75 Abstract Classi\ufb01 cation of a group of organisms typically begins \u201cat the bottom\u201d with an examina- tion of the variation in characters of species \u2013 the genus-species level. A variety of methods have been used to determine species of ciliates from the interbreeding criterion of the biological species to a variety of features related to the morphology and ecology of a species, including life history traits, behavior, and size and shape of a variety of struc- tures revealed by observation of living or stained cells. Genetic approaches are becoming increas- ingly more popular, especially molecular genetic ones. These have included the use of isoenzymes , randomly ampli\ufb01 ed polymorphic DNA ( RAPD ), and restriction fragment length polymorphisms ( RFLP ). The current cutting edge approaches are the sequencing of genes, such as small and large subunit rRNA , histone , actin , heat shock proteins , tubulins , and translation factors . Most recently, the mitochondrial cytochrome c oxidase 1 ( cox1 ) gene has been chosen by some as a species \u201c barcode \u201d. Above the genus-level, establishing groups is more problematic, but should always rely on the establishment of monophyly using synapomor- phies or shared-derived characters . These charac- ters can be ultrastructural features of the somatic and oral kinetids , patterns of morphogenesis , and gene sequences . Taxonomy ultimately uses nomen- clature and its rules to establish priority, ensure consistency, and maintain stability. Keywords Biological species, morphological species, holotype, priority, synonym As noted in Chapter 1, Simpson (1961) defined systematics as \u201cthe scientific study of the kinds and diversity of organisms and of any and all relationships among them\u201d (p. 7). Systematists uncover patterns of variation in natural popula- tions, discover the mechanisms by which spe- cies originate, and determine the phylogenetic history of organisms. These activities often lead systematists to establish a classification system to reflect the evolutionary history of a group. Ciliate systematists are no less concerned with these issues, and a variety of approaches have been discussed (e.g., Berger, 1978; Corliss, 1974a, 1976, 1979; Gates, 1978a; Lynn, 1996b). This diversity of approaches in philosophy and methodology, coupled with the technological advances of the discipline, from cytology to electron microscopy to molecular phylogenetics, has deepened our understanding of the processes of ciliate evolution (see Chapter 1 ). While the main approach of this book is to discuss variation at a suprafamilial level, our systematic approach must begin \u201cat the bot- tom\u201d, so to speak, at the level of species and genera. By first understanding the breadth of variation in characters at these levels, we can begin to assemble groups into larger and larger sets, ultimately establishing a hierarchical clas- sification of the phylum. Since there are fairly clear differences in approach as one proceeds up the hierarchy (Corliss, 1980), it is appropriate to discuss ciliate systematics at two different \u201clevels\u201d \u2013 at the genus-species level and above the genus- species level. Chapter 3 Characters and the Rationale Behind the New Classification 76 3. Characters and the Rationale Behind the New Classification 3.1 At the Genus-Species Level The perennial question for biologists is \u201cWhat is a species?\u201d The criterion of interbreeding as an operational definition of species \u2013 the biological species concept (see Mayr, 1970) \u2013 has been one of the most popular definitions of a species. We have known for many years that, in principle, it likely applies to ciliates, ever since the discovery of con- jugation by Maupas (1889). To complicate matters, Sonneborn (1937, 1938) and Jennings (1938) rec- ognized in the genus Paramecium that there were also cryptic or sibling species complexes (i.e., spe- cies that are morphologically extremely similar but yet separated into genetically distinct reproductive units). Gruchy (1955) discovered a similar species complex in the genus Tetrahymena . Thus, if a species is known to be sexual, one could in principle apply this methodological approach. Of course, one must first maintain in culture or in some preserved state ready to be cultured, representatives of all known isolates. Then, each time a new isolate is discovered, one must conduct all possible mating tests with known isolates to determine whether or not it is indeed new (see 3.1.3 GENETICS). This genetic approach is undoubtedly the most definitive. Nevertheless, conjugation is rarely observed in natural populations of ciliates, many of which might be permanently asexual (Lucchesi & Santangelo, 2004). Moreover, it is practically impossible to maintain in culture all isolates of spe- cies as a set of \u201cstandards\u201d against which to assess new isolates. Furthermore, it is often not easy to ensure that isolates have been treated perfectly so that one can confidently conclude that they are mating-incompatible. Thus, most taxonomists use morphology to describe new species, and assume that if the morphology of the new isolate is differ- ent in significant ways from the morphology of all previously described species, it is certain that the new isolate is a valid new species. Increasingly, as discussed below, molecular genetic approaches are being used as reliable substitutes for the interbreed- ing criterion to establish the genetic and taxonomic distinctness of new isolates. An approach to the description of a new genus- species level taxon should begin with a search of the recent literature, which will provide direction as to the characters considered to be important for the taxonomy of the group. Below, we discuss in general terms some broad categories of descrip- tive characters: life history, ecology, and cultiva- tion; morphology and multivariate morphometrics; genetics; isoenzymes and biochemistry; and gene sequences. 3.1.1 Life History , Ecology , and Cultivation Corliss (1976, 1979) argued that a multiplicity of characters is essential for a complete description of a new species \u2013 his \u201c constellation of charac- ters \u201d principle. Some of the first and possibly least problematic characters are those associated with life history and ecology. What habitat is the ciliate found in \u2013 freshwater, brackish, marine or terres- trial? What is its biogeography in these habitats \u2013 endemic or ubiquitous? What habitat variables appear to be important \u2013 temperature, pH, oxygen concentration, saprobic index (see Bick, 1972; Foissner, Berger, & Kohmann, 1994; Foissner, Blatterer, Berger, & Kohmann, 1991)? If possible, features of its life cycle should be determined (Fig. 3.1). Has conjugation been observed? If so, how do the partners pair \u2013 anteri- orly, laterally, ventrally? A common polymorphism is encystment . Have cysts been observed and are there any distinguishing characteristics of the cysts \u2013 wall ornamentation, wall layers, pigmentation? If the ciliate is free-living, is the life cycle also poly- morphic in terms of ciliated forms \u2013 macrostome or cannibal forms, microstome forms? On what do these stages feed \u2013 bacteria, algae and other pro- tists, other ciliates? If the ciliate is parasitic, is the life cycle polymorphic in other ways \u2013 trophont , protomont , tomont , tomite , theront (Fig. 3.1)? If possible, it is very helpful to establish the ciliate in culture. This enables more detailed morphological observations to be made, includ- ing the analysis of biochemical and genetic fea- tures (see below). Culture methods will vary with the group. Various approaches are described in Protocols in Protozoology (Lee & Soldo, 1992), and an older paper published by the Society of Protozoologists has helpful directions focused on different taxa (Committee on Cultures, 1958). Reference to literature