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2001; Kusch, Welter, 
Stremmel, & Schmidt, 2000; Mollenbeck, 1999). Since 
 RAPD fingerprinting depends upon PCR , large 
numbers of cells are, in principle, not required. 
However, the technique does have significant problems, 
including variation introduced due to inefficiencies in 
the PCR and due to variations in band intensity. For 
these reasons, more predictable approaches are to be 
 The techniques discussed so far have all assessed 
variation based on nuclear genetic variation, which 
may be more constrained both within and between 
species. A promising new approach is the “ bar-
code ” gene, mitochondrial cytochrome c oxidase 
1 ( cox 1 ), which has been successfully applied to a 
variety of animal groups (Hajibabaei, Janzen, Burns, 
Hallwachs, & Hebert, 2006; Hebert, Cywinska, Ball, 
& DeWaard, 2003; Hebert, Stoeckle, Zemlak, & 
Francis, 2004). Barth, Krenek, Fokin, and Berendonk 
(2006) demonstrated that cox 1 could be effectively 
used to separate out several Paramecium species, with 
interspecific divergences ranging from 12–27%, while 
Lynn and Strüder-Kypke (2006) and Chantangsi, 
Lynn, and Brandl (2007) have demonstrated simi-
lar levels of divergence in cox 1 between species of 
Tetrahymena that are identical based on the SSrRNA 
gene sequence. Barth et al. (2006) showed signifi-
cant intrahaplogroup variation within Paramecium 
caudatum and Paramecium multimicronucleatum , 
suggesting that these species may, in fact, be sibling 
species complexes , while Chantangsi et al. (2007) 
have demonstrated that isolates of Tetrahymena iden-
tified to species on the basis of isozyme patterns have 
apparently been misclassified. 
 3.1.6 Summary 
 The approaches presented above provide different 
methods of assessing variation within species and 
between species within genera. We cannot recom-
mend one of these approaches over another. Rather, a 
modern description of a new species of ciliate should, 
where possible, include data provided by observa-
tion of living organisms, stained organisms, and 
gene sequence data (e.g. see Agatha, Strüder-Kypke, 
Beran, & Lynn, 2005; Modeo, Petroni, Rosati, & 
Montagnes, 2003; Rosati, Modeo, Melai, Petroni, 
& Verni, 2004). Comparison of these datasets with 
previous descriptions should then enable one to 
conclude whether an isolate is indeed new. As our 
databases of gene sequences increase, it has been 
demonstrated that fluorescence in situ hybridiza-
tion can be used to identify species (Fried, Ludwig, 
Psenner, & Schleifer, 2002), and environmental gene 
sequences can be linked to morphology using both 
light and scanning electron microscopy (Stoeck, 
Fowle, & Epstein, 2003). 
 While body size is important, body size on its 
own is seldom sufficient to distinguish a species. 
Indeed, there are many other quantitative traits not 
correlated with size that may ultimately be dis-
criminatory. Just as there are no hard and fast rules 
for determining whether an isolate is a new spe-
cies, it is also difficult to provide any for the genus 
level. In general, one can say that genera should be 
differentiated on the basis of significant qualitative 
characters. And one may reasonably ask – what is 
a significant qualitative character? Again, there are 
no hard and fast rules, and what characters are con-
sidered important may depend upon whether the 
taxonomist is a “ lumper ” or a “ splitter ” – what is a 
significant qualitative character for a “splitter” may 
3.1 At the Genus-Species Level 81
82 3. Characters and the Rationale Behind the New Classification
not be so for a “lumper” (Corliss, 1976). In general, 
it is our view that “significant” at the generic level 
should at least included qualitative differences in 
body shape, pattern of the somatic kineties, and 
organization of the oral structures . As noted in 
Chapter 1, oral variations are likely to directly 
affect growth and reproductive rates, enhancing 
the relative fitness and fixation of new oral variants 
(Lynn, 1979b). Thus, it is often the case that new 
genera are distinguished on the basis of variations 
in oral features, as well as qualitative variations in 
somatic features. 
 3.2 Above the Genus-Species 
 Above the level of genus and species, it is even 
more difficult to provide guidance on what fea-
tures can be used to generally distinguish a family, 
an order, a class, or a subphylum. Corliss (1976, 
1979) discussed the “ gap size of distinctness ” as a 
conceptual way to identify the discontinuities that 
separate these higher taxa. As he noted, “one should 
be able to recognize a gap of ‘sufficient’ (how 
defined?!?) magnitude between any two groups of 
species before proposing their formal separation 
into different higher taxa” (p. 59, Corliss, 1979). 
Indeed, it is often the case that higher taxa show 
these discontinuities with respect to each other, 
and they often exhibit what Corliss (1979) termed 
a shared “ constellation of characters ”, which fur-
ther supports their separation. While a ‘sufficient’ 
gap size of distinctness and a shared constellation 
of characters often characterize higher taxa, there 
must be at least one synapomorphic or shared 
derived character that can be used to establish the 
 monophyly of the group. 
 Thus, to identify major monophyletic clades, we 
must ultimately search for characters that are highly 
conserved over time. As Lynn (1976a, 1981) has 
argued, conservation of biological structure, espe-
cially in regard to the ciliate cortex, becomes more 
conserved as we investigate lower levels of biological 
organization (i.e., organellar complexes , organelles ), 
which we discuss in more detail below (see 3.2.1 
CORTEX). These highly conserved ‘characters’ may 
also be morphogenetic sequences or developmental 
patterns, which appear as structural similarities, 
especially in the division ontogeny of ciliates, unit-
ing different major taxa into higher assemblages 
the present day, the ultimate signals of common 
descent are the primary and secondary structures 
of gene and amino acid sequences (see 3.2.3 GENE 
 3.2.1 Ultrastructure, Especially 
of the Cortex 
 Since the late 1960s and early 1970s, electron 
microscopic investigations of ciliates have provided 
a substantial increase in the number of characters 
available to determine relationships. As argued 
in Chapter 1 and elsewhere (Lynn, 1976a, 1981), 
there are good reasons to believe that similarities 
at this level of biological organization reveal much 
more ancient common ancestry. The diversity 
of somatic and oral kinetids of ciliates has been 
described (Grain, 1969, 1984; Lynn, 1981, 1991; 
de Puytorac & Grain, 1976). Lynn (1976a, 1979a, 
1981) has argued that somatic kinetid features are 
more strongly conserved than oral features (Fig. 3.4).
Application of these criteria – lower levels of bio-
logical organization more conserved and “somatic 
over oral” – has enabled us to establish a number of 
the major classes of ciliates (Lynn & Small, 1997, 
2002; Small & Lynn, 1981, 1985). 
 While cortical characters have been of primary 
importance, the fine structure of other features has 
also been helpful: variations in the particle distribu-
tions on ciliary membranes (Bardele, 1981) and in 
the substructure of extrusomes , like toxicysts and tri-
chocysts (Hausmann, 1978; Rosati & Modeo, 2003). 
 The multitude of ultrastructural characters has 
meant that several studies have used both phenetic 
and cladistic approaches assisted by computer to 
assess relationships among ciliates. These stud-
ies have ranged from a broad assessment at the 
phylum level (Lynn, 1979a; de Puytorac, Grain, & 
Legendre, 1994; de Puytorac, Grain, Legendre, & 
Devaux, 1984) to focussed treatments of classes 
and orders (Lipscomb & Riordan, 1990, 1992). 
 Nevertheless, there are clear signs that mor-