Cap 1

& Seravin, 1976; Seravin & Gerassimova, 1978); 
and for the oral cortex – the presence of transverse 
microtubular ribbons supporting the cytopharynx 
in the Subphylum Rhabdophora and the presence 
of postciliary microtubular ribbons supporting the 
cytopharynx in the Subphylum Cyrtophora (Small, 
1976) (Table 1.3). However, Huttenlauch and 
Bardele (1987) demonstrated in an ultrastructural 
study of oral development that the supposed oral 
transverse ribbons of the prostomate rhabdophoran 
Coleps were in fact postciliary microtubules that 
Table 1.3. Classifications systems proposed by Small and Lynn (1981, 1985).a
Small & Lynn (1981) Small & Lynn (1985)
Phylum Ciliophora Phylum Ciliophora
Postciliodesmatophora Postciliodesmatophora
KARYORELICTEA KARYORELICTEA
SPIROTRICHEA SPIROTRICHEA
Rhabdophora Heterotrichia
PROSTOMEA Stichotrichia
LITOSTOMEA Choreotrichia
Haptoria Rhabdophora
Vestibuliferia PROSTOMATEA
Cyrtophora LITOSTOMATEA
PHYLLOPHARYNGEA Haptoria
Phyllopharyngia Trichostomatia
Chonotrichia Cyrtophora
Suctoria PHYLLOPHARYNGEA
NASSOPHOREA Phyllopharyngia
Hypostomia Chonotrichia
Polyhymenophoria Suctoria
COLPODEA NASSOPHOREA
 OLIGOHYMENOPHOREA Nassophoria
Hymenostomia Hypotrichia
Peritrichia COLPODEA
Astomia OLIGOHYMENOPHOREA
Apostomia Hymenostomatia
 Peritrichia
 Astomatia
 Apostomatia
 Plagiopylia
a
 Classes are indicated in bold capital letters; subclasses, in italics.
became twisted during division morphogenesis, 
making them appear to be transverse microtubules. 
So, this rhabdophoran was really a cyrtophoran ! 
This undercut our confidence that these characters
had deep phylogenetic significance, and led Lynn 
and Corliss (1991) to abandon the subphyla, 
retaining only the eight classes of Small and 
Lynn. Later, de Puytorac et al. (1993) suggested 
three different subphyla, also based on signifi-
cant cortical ultrastructural features proposed by 
Fleury, Delgado, Iftode, and Adoutte (1992): the 
Subphylum Tubulicorticata – a microtubular cor-
tex; the Subphylum Filicorticata – a micro fibrillar 
cortex; and the Subphylum Epiplasmata – an epi-
plasmic cortex (Table 1.4). Fleury et al. (1992) 
had used molecular phylogenies derived from large 
subunit rRNA gene sequences to support these 
morphology-based subdivisions. Nevertheless, 
Lynn and Small (1997) argued that given the 
variability of cortical ultrastructures in ciliates 
it was extremely difficult to circumscribe the 
 limits of these subphyla. For example, virtually 
Fig. 1.4. Colpodeans and their somatic kinetids as a demonstration of the more conservative nature of the somatic 
kinetid and its “deeper” phylogenetic signal over the oral structures and general morphology of a group of ciliates. 
Sorogena was a gymnostome; Colpoda was a vestibuliferan; Cyrtolophosis was a hymenostome; and Bursaria was 
a spirotrich
1.3 The Age of Ultrastructure (1970–1990) 9
10 1. Introduction and Progress in the Last Half Century
all ciliates could be described as having a “corti-
cal cytoskeleton of superficial microtubules associ 
ated, or not, with cortical kinetosomes” – the major 
feature distinguishing ciliates in the Subphylum 
 Tubulicorticata (de Puytorac et al., 1993). 
 This reduced emphasis on oral structures as being 
of great phylogenetic significance extended to the 
homology of “ membranelles ” or oral polykinetids , 
used to establish the Classes Kinetofragminophora , 
 Oligohymenophora , and Polyhymenophora . De 
Puytorac and Grain (1976) and Grain (1984) had 
demonstrated the variety of “membranelles” or 
oral polykinetids in their reviews of the diversity 
of cortical ultrastructures of ciliates. This variety 
Table 1.4. A comparison of the macrosystems of the Phylum Ciliophora of de Puytorac (1994a) 
and the system proposed herein. Authorships for names will be found in Chapter 17.a
de Puytorac (1994a) Proposed system
Phylum Ciliophora Phylum Ciliophora
 Tubulicorticata Postciliodesmatophora
 POSTCILIODESMATOPHORA KARYORELICTEA
KARYORELICTEA HETEROTRICHEA
Trachelocercia Intramacronucleata
Loxodia SPIROTRICHEA
Protocruziidia Protocruziidia
Protoheterotrichia Phacodiniidia
HETEROTRICHEA Hypotrichia
Heterotrichia Oligotrichia
Clevelandellidia Choreotrichia
 SPIROTRICHA Stichotrichia
HYPOTRICHEA Licnophoria
Euplotia ARMOPHOREA
Oxytrichia LITOSTOMATEA
OLIGOTRICHEA Haptoria
Oligotrichia Trichostomatia
Strobilia PHYLLOPHARYNGEA
 TRANSVERSALA Cyrtophoria
COLPODEA Rhynchodia
Colpodia Chonotrichia
Bryometopia Suctoria
PLAGIOPYLEA NASSOPHOREA
 Filicorticata COLPODEA
LITOSTOMATEA PROSTOMATEA
VESTIBULIFEREA PLAGIOPYLEA
 Epiplasmata OLIGOHYMENOPHOREA
 CILIOSTOMATOPHORA Peniculia
PHYLLOPHARYNGEA Scuticociliatia
Cyrtophoria Hymenostomatia
Chonotrichia Apostomatia
Rhynchodia Peritrichia
Suctoria Astomatia
 MEMBRANELLOPHORA
NASSOPHOREA
Prostomatia
Nassulia
OLIGOHYMENOPHOREA
 Peniculia
 Scuticociliatia
 Peritrichia
 Hysterocinetia
 Astomatia
 Hymenostomatia
 Apostomatia
*Superclasses are indicated in capital letters; classes, in bold capital letters; subclasses, in italics.
lead to a proliferation of names to capture some 
of these differences. Oral polykinetids in kinetof-
ragminophorans could be pseudomembranelles , 
in oligohymenophorans could be membranoids or 
 membranelles , and in polyhymenophorans could 
be paramembranelles or heteromembranelles (see 
definitions in Chapter 2 ). This diversity suggested 
that these different complex oral structures were 
probably not homologues. In fact, what they 
undoubtedly illustrate are diverse solutions to the 
“problem” of filter feeding that had arisen through 
convergent evolution in a much larger number than 
three independent lineages or classes. Small and 
Lynn (1981, 1985) recognized these lineages as 
eight classes, established primarily on the basis of 
the ultrastructure of the somatic cortex, applying 
the principles of “structural conservatism” and 
“somatic over oral” (Fig. 1.4). 
 1.4 The Age of Refinement 
(1990–Present)
 Greenwood et al. (1991a) suggested that 1990 
might be designated as the beginning of the next 
age in ciliate systematics , the Age of Refinement , 
for it is in this period that tremendous advances 
have been made in confirming our basic notions 
derived from research on ciliate ultrastructure. As 
with the other ages, the technological roots of this 
age precede its formal beginning, and are based in 
the molecular phylogenetic work of Sogin’s lab 
on small subunit rRNA gene sequences (Elwood, 
Olsen, & Sogin, 1985; Lynn & Sogin, 1988) 
and Adoutte’s lab on large subunit rRNA gene 
sequences (Adoutte, Baroin, & Perasso, 1989; 
Baroin, Perasso, Qu, Brugerolle, Bachellerie, & 
Adoutte, 1988). Thus, it might also be called the 
 Age of Genetic Diversity , since the sequences of 
these highly conserved genes (see Chapter 16 ),
enabled us to test the structural conservatism of the 
ciliate somatic cortex , using the “molecular skel-
etons” of the ribosomal subunits – the small and 
large subunit rRNAs. 
 These early papers demonstrated tremendous 
genetic diversity within the phylum, a level 
of genetic diversity similar to differences among 
the “kingdoms” of multicellular organisms, like 
the plants , animals , and fungi . Further, the major 
clades established on the basis of ultrastructural 
research were generally confirmed, indicating that 
the somatic kinetid was a generally reliable feature 
to establish common descent (Lynn, 1991, 1996a; 
Lynn & Small, 1997). However, the molecular 
data suggested the need for further separation of 
clades, both at the “class” level and higher (Lynn, 
1996b; Lynn & Small). De Puytorac (1994a) 
had presaged this by elevating to class rank two 
groups that molecular genetic data confirmed to 
be distinct – the Class PLAGIOPYLEA and the 
Class HETEROTRICHEA