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Abstract Classifi cation of a group of organisms 
typically begins “at the bottom” with an examina-
tion of the variation in characters of species – 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 amplifi 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 “ barcode ”. 
 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 “the scientific study of the kinds 
and diversity of organisms and of any and all 
relationships among them” (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 “at the bot-
tom”, 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 “levels” 
– 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 “What is 
a species?” The criterion of interbreeding as an 
operational definition of species – the biological 
species concept (see Mayr, 1970) – 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 “standards” 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 
 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 – his “ constellation of charac-
ters ” 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 – freshwater, brackish, marine or terres-
trial? What is its biogeography in these habitats 
– endemic or ubiquitous? What habitat variables 
appear to be important – 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 – anteri-
orly, laterally, ventrally? A common polymorphism 
is encystment . Have cysts been observed and are 
there any distinguishing characteristics of the cysts 
– wall ornamentation, wall layers, pigmentation? If 
the ciliate is free-living, is the life cycle also poly-
morphic in terms of ciliated forms – macrostome 
or cannibal forms, microstome forms? On what do 
these stages feed – bacteria, algae and other pro-
tists, other ciliates? If the ciliate is parasitic, is the 
life cycle polymorphic in other ways – 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