Cap 3

structures, even at the ultrastructural 
level, have found their limits. Lynn (1991) noted 
that genera such as Transitella , Phacodinium , 
Plagiopyla , Lechriopyla , and Schizocaryum exhibit 
cortical features that cannot be used to confidently 
assign them to a major class. In fact, the latter four 
genera have now been assigned to a class based 
only on gene sequences! 
 3.2.2 Morphogenetic Patterns 
 The analysis of developmental patterns in revealing
phylogenetic relationships has its roots in the 
19th century in the work of Haeckel and von Baer 
(see Gould, 1977). While this approach must be 
applied with caution, Corliss (1968, 1979) noted 
that application of the Biogenetic Law to ciliate 
development – similarities in the ontogenies of 
different major groups of ciliates “recapitulating” 
their phylogeny – had provided important insights. 
Sewertzoff (1931) discussed a number of other 
principles, such as oligomerization and polymeri-
zation , which have been applied to the evolution of 
protozoan lineages (von Gelei; 1950; Poljansky & 
Raikov, 1976; Raabe, 1971a). Oligomerization and 
 polymerization , and the related principle of auxo-
morphy (Fauré-Fremiet, 1968), have been used to 
explain the origin of new types, primarily at the 
genus and species levels, but have not provided 
insights relating major groups of ciliates. 
 Ontogenetic patterns that have been the most 
illuminating in relating higher taxa are those 
exhibited by ciliates at asexual reproduction 
Fig. 3.4. A demonstration of the structural diversity of the oral region among ciliate genera from the class 
COLPODEA. When examined, all of these genera have the same basic somatic kinetid pattern (bottom right). 
However, prior to the Age of Ultrastructure, they were placed in different higher taxa: Colpoda and Bryophrya were 
trichostomes; Cyrtolophosis was a hymenostome; Platyophrya was a gymnostome; Bryometopus and Bursaria were 
heterotrichs (see Corliss, 1961). Sorogena and Grossglockneria were described during the Age of Ultrastructure. 
(Modified from Foissner, 1993a.)
3.2 Above the Genus-Species Level 83
84 3. Characters and the Rationale Behind the New Classification
during which new mouthparts are formed and the 
somatic region of the parent is partitioned for the 
progeny. These two related processes are termed 
cortical stomatogenesis and cortical somatogen-
esis , respectively (Lynn & Corliss, 1991). As 
noted in Chapter 1, similarities in oral structures 
and division morphogenesis of hymenostomes , 
 thigmotrichs , and peritrichs lead Fauré-Fremiet 
(1950a) to conclude these groups shared a common 
ancestry, while Guilcher (1951) used developmental 
patterns to infer the common ancestry of cyrto-
phorians , suctorians , and chonotrichs (Fig. 1.1). In 
addition to uniting major groups, stomatogenetic 
patterns can be used to separate major groups. 
For example, Small (1967) recognized a pattern 
of stomatogenesis among the hymenostomes in 
which the scutica or scutico-hook was formed, 
now called scuticobuccokinetal stomatogenesis , 
and this formed the basis for his distinguishing 
the Order Scuticociliatida within the oligohy-
menophorean clade. 
 Bardele (1989) has described a research program 
devoted to the careful analysis of morphogenesis 
using electron microscopy , arguing that this will 
enable us to identify with certainty the true devel-
opmental origin of the microtubular associates of 
kinetosomes and so determine homologies. In fact, 
Huttenlauch and Bardele (1987) proved the impor-
tance of this approach when they demonstrated that 
the microtubular ribbons supporting the cytophar-
ynx of the prostome Coleps were in fact postciliary 
microtubular ribbons . These postciliary ribbons 
change their orientation during stomatogenesis to 
appear like transverse microtubular ribbons , an 
interpretation previously given to them based on 
morphostatic ultrastructure (e.g., see Lynn, 1985; 
de Puytorac & Grain, 1972). Furness and Butler 
(1986) examined somatic kinetosomal replication 
in entodiniomorphids and revealed the transient 
appearance of a second transverse microtubular 
ribbon microtubule, providing support for align-
ment of entodiniomorphids to the litostome clade 
(Lynn, 1991; Lynn & Nicholls, 1985). Patterns of 
 oral kinetid assembly can involve the joining and 
rotation of kinetosomes and the appearance and 
disappearance of fibrillar structures in predictable 
sequences (Eisler, 1989; Jerka-Dziadosz, 1980, 
1981a, 1981b, 1982), and these features may 
ultimately prove useful to systematists when the 
database becomes sufficiently large. 
 Finally, brief mention should be made of the 
ultrastructure of the nuclear apparatus. Nuclear 
dimorphism – the micronucleus and macronucleus 
– is a synapomorphy for the Phylum Ciliophora . 
The inability of the macronucleus to divide has long 
been considered a “ karyological relict ” character 
(Corliss, 1979; Raikov, 1969, 1982, 1996). Related to 
this, Orias (1991a) has suggested that differences in the 
use of extra-macronuclear and intra-macronuclear 
microtubules during macronuclear division argue 
that macronuclear division evolved twice in the 
phylum. Lynn (1996a) used this feature to estab-
lish the Subphylum Intramacronucleata , uniting all 
ciliates that primarily use intra-macronuclear 
microtubules during macronuclear division. 
 Thus, morphogenetic patterns at a variety of 
 levels of biological organization and of a variety 
of structures have proved useful in revealing com-
mon descent among major groups of ciliates. These 
will continue to be useful at these higher levels, in 
addition to providing subtle differences that may 
distinguish species and genera. 
 3.2.3 Gene and Protein Sequences 
 The distinctive nature of the major groups of 
ciliates revealed both by light and electron micro-
scopy means that relatively few characters can 
be used to assemble them into larger groups. As 
noted above and in Chapter 1, features of the 
 somatic kinetid , similar patterns of division mor-
phogenesis , and nuclear features have been most 
useful. Sequences of genes and proteins provide a 
large number of characters, either as nucleotides 
or amino acids, and many of these may evolve 
independently of each other. This structural con-
servation with variation, at yet a lower level of 
biological organization , is presumed to signal 
deep common ancestry , and therefore permits us 
to test relationships established using morpho-
logical criteria, such as the ultrastructure of the 
 somatic kinetid . 
 The earliest studies used sequences of the 5S 
and 5.8S rRNAs, but their shorter lengths and 
conserved nature were not helpful in resolving 
deep relationships (Van Bell, 1985). Initial studies 
to sequence cloned small subunit ribosomal RNA 
(SSrRNA) genes (Elwood, Olsen, & Sogin, 1985; 
Sogin, Swanton, Gunderson, & Elwood, 1986b) 
and reverse transcripts of both SSrRNA and large 
subunit rRNA (LSUrRNA) (Baroin et al., 1988; 
Lynn & Sogin, 1988; Nanney et al., 1989; Preparata 
et al., 1989) provided clear evidence that these data 
would prove useful in elucidating deep phylogeny. 
Analyses were enabled by powerful sets of phy-
logenetic inference packages. Recent updates are 
found in Felsenstein (2004) and Swofford (2002). 
 The application of PCR using universal eukary-
ote primers provided both a rapid alternative 
to cloning genes and the potential to obtain 
sequence information from small numbers of 
cells, even a single cell (Medlin, Elwood, Stickel, 
& Sogin, 1988). The PCR sequencing approach 
has been extended to other genes, including 
 histones (Bernhard & Schlegel, 1998), tubulins 
(Baroin-Tourancheau, Villalobo, Tsao, Torres, 
& Pearlman, 1998; Israel, Pond, Muse, & Katz, 
2002), actins (Hogan, Hewitt, Orr, Prescott, & 
Müller, 2001), and translation factors (Moreira, 
Kervestin, Jean-Jean, & Philippe,