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, removing heterotrichs 
from the spirotrich assemblage (cf. Table 1.3, 
1.4). However, de Puytorac (1994a) elevated sev-
eral groups to class rank (e.g., HYPOTRICHEA , 
there is as yet no strong molecular genetic evidence 
(see Chapter 16 ). Two new clades differentiated by 
 small subunit rRNA gene sequences and now rec-
ognized as classes are the Class ARMOPHOREA 
(see Affa’a, Hickey, Strüder-Kypke, & Lynn, 2004; 
van Hoek, Akhmanova, Huynen, & Hackstein, 
2000a) and the Class PLAGIOPYLEA (see Embley 
& Finlay, 1994; Lynn & Strüder-Kypke, 2002) (Fig. 
1.5, Table 1.4). Lynn (2004) highlighted a diffi-
culty with each of these so-called “ riboclasses ”: the 
Class ARMOPHOREA associated genera, such as 
Metopus and Nyctotherus , whose somatic kinetids 
were dissimilar, while the Class PLAGIOPYLEA 
separated some genera, such as Plagiopyla and 
Trimyema , whose kinetids were quite similar to 
those of the Class OLIGOHYMENOPHOREA to 
which the plagiopyleans had been transferred as 
a subclass by Small and Lynn (1985) (Table 1.3). 
Thus, somatic kinetid structure seems not to be highly 
conserved in armophoreans and to be more highly 
conserved in some plagiopyleans! We have appar-
ently reached the limits of structural conservatism 
of the somatic cortex as a principle, and we can 
only say that these are the exceptions that prove 
the rule! 
 By the mid-1990s there was ample evidence 
from a variety of independent phylogenetic analy-
ses of both small subunit and large subunit rRNA 
gene sequences to demonstrate a fundamental 
bifurcation in the phylum (Baroin-Tourancheau, 
Tsao, Klobutcher, Pearlman, & Adoutte, 1995; 
Hammerschmidt, Schlegel, Lynn, Leipe, Sogin, 
& Raikov, 1996; Hirt et al., 1995) (Fig. 1.5). 
One branch, which separates the ciliates with 
 postciliodesmata sensu stricto , corresponds to 
1.4 The Age of Refinement (1990–Present) 11
Fig. 1.5. A molecular phylogeny of the Phylum Ciliophora based on small subunit rRNA gene sequences. Several 
representatives of each class have been chosen to demonstrate the genetic diversity within the phylum and the dis-
tinctness of the different clades that are considered to be of class rank in the classification proposed herein (see Table 
1.4) (see Chapter 16 for further discussion of molecular phylogenetics)
a concept proposed by Gerassimova and Seravin 
(1976). This subphylum now includes only the Classes 
excludes the spirotrich clade, which was included by 
Small and Lynn (1985) (cf. Tables 1.3, 1.4). While 
 karyorelicteans do not have dividing macronuclei, 
the heterotrichs do, apparently relying primarily 
on extramacronuclear microtubules for this proc-
ess (Diener, Burchill, & Burton, 1983; Jenkins, 
1973). Lynn (1996a) named the other branch, the 
Subphylum INTRAMACRONUCLEATA , because 
all ciliates in this clade have a dividing macronu-
cleus that relies predominantly on intramacronu-
clear microtubules for completion of division. The 
suggestion that macronuclear division has arisen 
separately twice during the evolution of ciliates is 
not unreasonable, considering that at least two kinds 
of nuclear division, using both extranuclear and 
intranuclear microtubules also occur in the dinoflag-
ellates (Perret, Albert, Bordes, & Soyer-Gobillard, 
1991), the sister clade to the ciliates (Leander & 
Keeling, 2003; Van de Peer, Van der Auwera, & De 
Wachter, 1996). 
 1.5 Major Differences in the New 
 Corliss (1979) noted in his discussion of the major 
differences of schemes that an obvious trend has 
been the inflation of taxa as our discovery and 
understanding of diversity have changed from 
the 1880s until the present. As discussed above, 
approaches have been influenced both by techno-
logical advances – light microscopy , cytological 
staining, electron microscopy , molecular biology 
– and by new conceptual views. With respect to 
the latter, the emphasis on the somatic cortex by 
Small and Lynn (1981) caused a major revision 
in our understanding of relationships between the 
mid-1970s and the mid-1980s. Currently, there are 
two recent classification systems of ciliates seeking 
adherents; one proposed by de Puytorac (1994a) and 
his colleagues in the second volume of the Traité 
de Zoologie and the other proposed most recently 
by Lynn (2004) and presented in a slightly revised 
version herein (Table 1.4). Since various differences 
between these views have been discussed above, this 
section will serve to summarize these. 
 1. The subphyletic divisions in the two systems 
are different: three by de Puytorac (1994a) and 
two here (Table 1.4). Data on genetic diversity 
support a major division into two subphyla, the 
 2. De Puytorac (1994a) recognizes five super-
classes, one essentially equivalent to our 
while we provide no such subdivisions (Table 
1.4). It is the case in molecular phylogenies 
that there is substructure within the Subphylum 
six classes (i.e., PHYLLOPHARYNGEA , 
ENOPHOREA ) are often consistently supported 
as a clade (Fig. 1.5). This grouping may repre-
sent a natural assemblage, and therefore repre-
sent a superclass assemblage. However, there 
is no obvious shared derived morphological 
feature uniting these taxa, and at this time we 
do not recognize it as a taxonomic category. 
 3. De Puytorac (1994a) recognizes 11 classes 
as does the system proposed here (Table 
1.4). However, the classes are different. De 
Puytorac (1994a) includes the prostomates 
in the Class NASSOPHOREA . Differences 
in the somatic kinetid (Eisler, 1989; Lynn, 
1991), stomatogenesis (Eisler; Huttenlauch & 
Bardele, 1987), and small subunit rRNA gene 
sequences (Stechmann, Schlegel, & Lynn, 
1998) between nassophoreans and prostomate-
ans argue against uniting them in the same class 
(Fig. 1.5). While both systems recognize the 
 spirotrichs as a larger assemblage, the eleva-
tion of the oligotrichs to class rank, equivalent 
to hypotrichs , is not justified by the molecular 
data, which suggest at least seven separate 
lineages in the Class SPIROTRICHEA , here 
recognized as subclasses (Strüder-Kypke & 
Lynn, 2003). 
 Finally, we cannot agree with de Puytorac 
(1994a) that elevation of the vestibuliferians to 
class rank is warranted. We prefer to refer to this 
clade by the Bütschlian moniker, Trichostomatia 
(Table 1.4). The trichostomatians in this sense and 
the haptorians share virtually identical somatic 
kinetid patterns (Lynn, 1981, 1991). This varies only
in the entodiniomorphids where Lynn (1991) has 
1.5 Major Differences in the New Scheme 13
14 1. Introduction and Progress in the Last Half Century
interpreted the appearance of a transient micro-
tubule during kinetid replication (see Furness 
& Butler, 1986) to be the homologue of the 
T2 transverse microtubular ribbon of litostomes . 
Moreover, extensive analyses of litostome small 
subunit rRNA gene sequences consistently group 
the haptorians and trichostomes (Wright & 
Lynn, 1997b; Strüder-Kypke, Wright, Foissner, 
Chatzinotas, & Lynn, 2006). 
 De Puytorac (1994a) elevated a considerable 
number of taxa to subclass and ordinal ranks, 
totalling 25 subclasses and 70 orders. Comparison 
with the scheme presented here will demonstrate 
considerable agreement in the basic groups or 
clades, despite possible differences in rank (Table 
1.4 and the original references). While Small and 
Lynn (1981, 1985) established 15 subclasses and 
48 orders, our revised scheme has 19 subclasses 
and 59 orders. Many of these changes have been 
influenced by genetic data obtained in the last 
few years, and these are discussed both by Lynn