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Gates, & Berger, 1975), but these techniques were 
unable to practically separate all species (Gates & 
Berger, 1976b). This morphological “similarity” 
in multivariate space has been confirmed for the 
aurelia species complex and also demonstrated 
for the woodruffi grouping of species (Fokin & 
Chivilev, 2000). Nevertheless, the only new species 
in the aurelia complex, Paramecium sonneborni , 
has been characterized as being distinct by using 
mating-type reactivity and isoenzyme patterns 
(Aufderheide, Daggett, & Nerad, 1983). 
 Biochemical differences and their genetic basis 
continue to be discovered for Paramecium species 
(Tait, 1978), and used to identify other sibling spe-
cies within the genus (Allen, Nerad, & Rushford, 
1983a; Allen, Rushford, Nerad, & Lau, 1983b; 
Usuki & Irie, 1983). While the SSUrRNA genes of 
aurelia complex species are very similar (Hoshino, 
Hayashi, & Imamura, 2006; Strüder-Kypke et al., 
2000a), significant inter- and intra-specific genetic 
variation in the internal transcribed spacer regions 
has been discovered in aurelia complex species 
(Hoshino et al., 2006; Tarcz, Przybos, Prajer, & 
Greczek-Stachura, 2006). By modeling the second-
ary structure of internal transcribed spacer region 2 
(ITS2), Coleman (2005) correlated the phylogeny 
of Paramecium species with their mating charac-
terization. Stoeck and Schmidt (1998) have used 
fingerprints derived from randomly amplified poly-
morphic DNA (RAPD) to distinguish nine of these 
species: these results confirmed genetic studies that 
demonstrated this complex to be widely distributed 
geographically (Przybos, 1993; Stoeck, Przybos, 
Kusch, & Schmidt, 2000a). RAPD-fingerprint-
ing is fast and accurate. Furthermore, it does not 
require the careful axenic cultivation of the cili-
ates, which is necessary for the proper isoenzyme 
characterization of the strains, nor does one need 
to maintain genetic stocks to do proper mating 
tests . It has been used to reject sibling species for 
Paramecium caudatum (Hori, Tomikawa, Przybos, 
& Fujishima, 2006; Stoeck, Welter, Seitz-Bender, 
Kusch, & Schmidt, 2000b) and support them 
for Paramecium jenningsi (Skotarczak, Przybos, 
Wodecka, & Maciejewska, 2004). Recently, Barth, 
Krenek, Fokin, and Berendonk (2006) showed sig-
nificant intrahaplogroup variation within P. cauda-
tum and Paramecium multimicronucleatum using 
the mitochondrial cytochrome c oxidase subunit 1 
(cox-1) gene , suggesting that these “species” may, 
in fact, be sibling species complexes, contrary to 
what RAPD fingerprinting suggests. 
 Small (1967) was the first to formally recognize 
a monophyletic assemblage that he designated 
as an order at that time, but which has now been 
elevated to the subclass rank (Lynn & Small, 1997, 
2002; de Puytorac, 1994a, 1994e). The Subclass 
 Scuticociliatia is characterized by a paroral that is 
divided into three segments – anterior a , middle 
b , and posterior c or scutica . The scutica , named 
for its hook-like or “whiplash” configuration taken 
during stomatogenesis in some forms, is the major 
synapomorphy for the group. Although only a 
handful of the thousands of species has been exam-
ined by molecular techniques, the subclass has so 
far had strong support from small subunit rRNA 
sequences (Lynn & Strüder-Kypke, 2005; Miao, 
Fen, Yu, Zhang, & Shen, 2004b; Shang, Song, & 
Warren, 2003). The now “modern classic” research 
on this group (e.g., Evans & Corliss, 1964; Evans & 
Thompson, 1964; Raabe, 1967, 1972; Small, 1967; 
Thompson, 1963, 1964, 1965, 1966a, 1966b, 1967, 
1968, 1969) is being revised with the use of pro-
targol silver-staining , careful re-examination of liv-
ing specimens, and biogeographic analyses. Global 
distributions of species have been confirmed using 
both morphological (e.g., Esteban & Olmo, 1997; 
Foissner & Wilbert, 1981) and molecular (Goggin 
& Murphy, 2000) criteria; new genera have been 
recognized (Olmo, Tellez, & Esteban, 1998; Song 
& Wilbert, 2002); and synonymies of species have 
been proposed (Esteban & Olmo, 1997; Song & 
Wilbert, 2000a). Furthermore, molecular genetic 
studies are now casting doubts on the assignment 
of genera to families, and even on the identity 
of genera (Lynn & Strüder-Kypke, 2005; Ma, 
Song, Gong, & Warren, 2004; Paramá, Arranz, 
Álvarez, Sanmartín, & Leiro, 2005; Shang et al., 
15.1 Taxonomic Structure 283
2003). Shang and Song (2005) have successfully 
used RAPD fingerprinting to identify and separate 
marine scuticociliate species. 
 We have maintained a conservative subdivision 
of the subclass, recognizing three included orders: 
Order Philasterida , Order Pleuronematida , and 
Order Thigmotrichida . The philasterids appear to 
be strongly supported as a group by molecular phy-
logenetics (Lynn & Strüder-Kypke, 2005; Shang 
et al., 2003). It is still too early to tell for the other 
two orders: there are gene sequences for only a few 
representative pleuronematids while no thigmot-
rich has yet been sequenced. In fact, thigmotrichs 
have received relatively little attention since the 
monographic works of Chatton and Lwoff (1949, 
1950), Fenchel (1965a), and Raabe (1967, 1970a, 
1970b, 1971b, 1972). 
 The Order Philasterida is characterized by having a 
paroral shorter than the other oral structures, typically 
by reduction of the paroral a and c segments and with 
the scutica separate and posterior to the paroral. We 
include 16 families in the order: the Cinetochilidae , the 
 Cohnilembidae , the Cryptochilidae , the Entodiscidae , 
the Entorhipidiidae , the Loxocephalidae , the 
 Orchitophryidae , the Paralembidae , the Paraurone-
matidae , the Philasteridae , the Pseudocohnilembidae , 
the Schizocaryidae , the Thigmophryidae , the 
 Thyrophylacidae , the Uronematidae , and the 
 Urozonidae . The Family Schizocaryidae has been 
assigned to this order only on the basis of its 
SSUrRNA gene sequence (Lynn & Strüder-Kypke, 
2005). The Order Pleuronematida is characterized 
by an expansive oral region along whose right bor-
der extend the prominent paroral cilia forming a 
curtain or velum as the organism filter feeds. The 
 scutica is a permanent component of the paroral 
c segment. We include nine families in the order: 
the Calyptotrichidae , the Conchophthiridae , the 
 Ctedoctematidae , the Cyclidiidae , the Dragescoidae , 
the Histiobalantidiidae , the Peniculistomatidae , the 
 Pleuronematidae , and the Thigmocomidae . 
 Ngassam, de Puytorac, and Grain (1994) pro-
posed the new Subclass Hysterocinetia to separate 
the hysterocinetid ciliates from the thigmotrichs . 
These ciliates, which are endosymbionts of oligo-
chaetes and molluscs , are substantially different 
from other thigmotrichs (Ngassam & Grain, 2002; 
Njiné & Ngassam, 1993; de Puytorac, 1994f). 
However, given what we are already discovering 
about the differing views of relationships provided 
by morphological and molecular approaches on 
other scuticociliates (Lynn & Strüder-Kypke, 
2005; Shang et al., 2003), we prefer to await 
molecular evidence of hysterocinetid distinctiveness 
before recognizing this group as a subclass within 
the Class OLIGOHYMENOPHOREA . Therefore, 
we characterize the Order Thigmotrichida to include 
 ciliates having obviously differentiated thigmotac-
tic somatic ciliature and a subequatorial oral region 
whose oral ciliature may spiral around the poste-
rior end of the cell and whose oral polykinetids 
may quite often be reduced or even absent. We 
include four families in the order: the Ancistridae , 
the Hemispeiridae , the Hysterocinetidae , and the 
 Paraptychostomidae . 
 The Subclass Hymenostomatia , which was 
much more broadly inclusive (see Corliss, 1979), 
includes only the two orders Tetrahymenida and 
 Ophryoglenida . These “membrane-mouthed” cili-

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