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to refine its taxonomic position. 
 Corliss (1979) placed the dorsoventrally flat-
tened spirotrichs with prominent ventral cirri 
and less conspicuous dorsal bristle cilia in the 
Order Hypotrichida . Characters that support the 
monophyly of this group include the pattern of 
development of the ventral cirri and the overall 
organization of the body plan, which are claimed 
to be too similar to have evolved convergently 
(Fleury, 1988; Martin, 1982; Tuffrau, 1987). At the 
same time, there is a recognition of considerable 
diversity within the group, both in respect to mor-
phology, morphogenesis, and genetics. Fleury and 
coworkers (Fleury, 1988; Fleury, Iftode, Deroux, & 
Fryd-Versavel 1985a; Fleury, Iftode, Deroux, Fryd-
Versavel, & Génermont, 1985b; Fleury, Iftode, 
Deroux, & Fryd-Versavel, 1986) have used these 
morphological and morphogenetic differences to 
establish the suborder Euhypotrichina (Fleury et al., 
1985a) to include stichotrich-like forms and the 
suborder Pseudohypotrichina (Fleury et al., 1985b) 
to include euplotid-like forms. Euhypotrichs were 
so-named because they manifested truly derived 
\u201chypotrich\u201d characters: (1) the complete turn-over 
or replacement of the somatic ciliature, both ventral 
and dorsal, during all morphogenetic processes; (2) 
 cysts that typically resorb all infraciliary con-
stituents (i.e., kinetosome-resorbing cysts); and (3) 
 dorsal bristles that lose kinetodesmal fibrils at the 
completion of development. In contrast, pseudo-
hypotrichs were so-named because they appeared 
\u201chypotrich\u201d-like but lacked the derived characters 
noted above. Instead, they exhibit: (1) turn-over or 
replacement of only the ventral somatic infracili-
ature during morphogenetic processes; (2) encyst-
ment typically not accompanied by resorption of 
all kinetosomes; and (3) mature dorsal bristles that 
retain kinetodesmal fibrils . Small and Lynn (1981, 
1985) had used these kinetid differences, along 
with differences in the organization of the somatic 
cortex, to separate the hypotrichs into two clades: 
the Subclass Stichotrichia Small and Lynn, 1985, 
which is equivalent to the euhypotrichs (Fleury 
et al., 1985b) and the Oxytrichia (Tuffrau & Fleury, 
1994) of others; and the Subclass Hypotrichia 
Stein, 1859, which is equivalent to the pseudo-
hypotrichs (Fleury et al., 1985b) and the Euplotia 
(Tuffrau & Fleury, 1994). Small and Lynn (1985) 
7.1 Taxonomic Structure 145
146 7. Subphylum 2. INTRAMACRONUCLEATA: Class 1. SPIROTRICHEA
placed the Subclass Hypotrichia within the Class 
 NASSOPHOREA , based on similarities in the diki-
netid of members of these two groups. However, 
molecular evidence (Lynn & Sogin, 1988) clearly 
refuted this relationship, demonstrating instead 
that stichotrichs and hypotrichs belong to the same 
major clade, a fact that has led Lynn and Corliss 
(1991) and Lynn and Small (1997) to place both 
groups in the Class SPIROTRICHEA . 
 The stichotrichs and hypotrichs are separated 
deeply on small subunit ribosomal RNA (SSrRNA) 
gene trees with oligotrich and choreotrich genera 
diverging after the separation of the hypotrich lin-
eage (Bernhard et al., 2001; Chen & Song, 2001; 
Petroni, Dini, Verni, & Rosati, 2002; Snoeyenbos-
West, Salcedo, McManus, & Katz, 2002; Strüder-
Kypke et al., 2003). Moreover, there are substantial 
and deep differences in the allele frequencies of the 
 isoenzymes of hypotrichs and stichotrichs (Schlegel 
& Steinbrück, 1986). We have favored retaining 
separate subclasses for these four groups notwith-
standing the fact that the apparently fast molecular 
clock of the hypotrich ribosomal RNA genes may 
be creating a \u201ctreeing artifact\u201d for these molecular 
sequences due to the long branch attraction artifact 
(Felsenstein, 1978; Morin, 2000; Philippe, Chenuil, 
& Adoutte, 1994). 
 Molecular phylogenetic studies on a number of 
 hypotrich genera, such as Euplotes and Diophrys , 
consistently demonstrate them as basal lineages in 
the spirotrich radiation (Fig. 7.2). Depending upon 
taxon sampling and variations in sequence align-
ment, the hypotrichs appear to be monophyletic (Li 
& Song, 2006; Petroni et al., 2002) or paraphyletic 
(Chen & Song, 2001, 2002; Song, Wilbert, Chen, 
& Shi, 2004). Subdivision of the genus Euplotes is 
supported by some molecular analyses (Bernhard 
et al., 2001; Borror & Hill, 1995). We now rec-
ognize two orders in the Subclass Hypotrichia : 
(1) Order Kiitrichida to include spirotrichs with 
uniformly small and multiple cirri arranged in 
curving files; and (2) Order Euplotida to include 
those with well-developed and sparse ventral cirri 
arranged in frontal, ventral, and transverse groups 
(see Chapter 17 ). 
 Features of division morphogenesis have also 
been used to reevaluate systematic relation-
ships among oligotrich ciliates and these have 
now been tested by sequences of the small 
subunit ribosomal RNA genes . Oligotrich and 
 choreotrich SSUrRNA gene sequences support 
retention and separation of genera assigned to 
these two subclasses (Snoeyenbos-West et al., 
2002; Strüder-Kypke et al., 2003). Corliss (1979) 
placed the Order Oligotrichida in the Class 
 POLYHYMENOPHOREA , noting that its two 
suborders, the Oligotrichina and Tintinnina , were 
united by a reduced somatic ciliature and an 
anterior adoral zone of membranelles, which are 
primarily used in locomotion and feeding. Fauré-
Fremiet (1970) had already drawn attention to the 
diversity in the oral structures of the oligotrichs , 
recognizing strombidiids , like Limnostrombidium
and Laboea (Fig. 7.3) and halteriids , like Halteria
(Fig. 7.4), to have an \u201copen\u201d adoral zone with what 
has been called a \u201ccollar\u201d and \u201clapel\u201d arrange-
ment of the oral polykinetids. In contrast, there 
were the strombidinopsids , like Strombidinopsis , 
 strobilidiids , like Strobilidium , and tintinnids , like 
Codonella and Tintinnopsis , with a \u201cclosed circle\u201d 
of oral polykinetids (Fig. 7.3). 
 Fauré-Fremiet (1970) retained the classical sepa-
ration of the tintinnids , based on their being loricate , 
even while noting the similarity in the \u201cclosed 
circle\u201d oral structures of strobilidiids and tintinnids . 
Small and Lynn (1985) established the Subclass 
 Choreotrichia Small and Lynn, 1985 to include 
these latter two groups, placing the aloricate chore-
otrichs in the Order Choreotrichida Small and Lynn, 
1985 and retaining the Order Tintinnida for loricate 
choreotrichs. Division morphogenesis of oligotrichs 
was initially described by Fauré-Fremiet (1953), 
who described their division as enantiotropic and 
noted that the oral primordium of Strombidium
developed in an invagination. Deroux (1974) con-
firmed that oral development occurred in a pocket 
in Strombidium sulcatum , provided a new descrip-
tion for stomatogenesis in Strobilidium gyrans
(= Strobilidium caudatum ?), and drew attention to 
the similarity with the early stages of division mor-
phogenesis in Euplotes , which also occurs in a cor-
tical invagination (Wise, 1965). Petz and Foissner 
(1992) confirmed this \u201cpocket\u201d oral development in 
S. caudatum and also observed it in a Tintinnidium
species while Dale and Lynn (1998) observed the 
same pattern of \u201cpocket\u201d oral development in the 
aloricate choreotrich Strombidinopsis . Petz and 
Foissner (1992) used this as an additional charac-
ter to support the monophyly of the choreotrichs . 
Strombidium -like species may begin development of 
Fig. 7.3. Stylized drawings of representative genera from subclasses in the Class SPIROTRICHEA . Subclass 
 Choreotrichia : the choreotrich Strombidinopsis ; the tintinnid Codonella ; the choreotrich Strobilidium ; the tintinnid 
Tintinnopsis ; the tintinnid Cymatocylis . Subclass Oligotrichia : Limnostrombidium ; Laboea
7.1 Taxonomic Structure 147
148 7. Subphylum 2. INTRAMACRONUCLEATA: Class 1. SPIROTRICHEA