[ref. ID; 4926 (Denis H. Lynn, 2003)]

The Infusoria or Ciliophora, as they are now called have long been recognized as a monophyletic assemblages. The composition of the group has remained largely unchanged since Faure-Fremiet (1950) included among holotrich ciliates, the suctorians, which had often not been included with the other ciliates by the specialists of the day (Corliss 1979). The classification of the group remained largely unchanged in the 20th century after Corliss (1961) formalized Faure-Fremiet's conceptual vision, based primarily on the morphostatic morphology of the cells, derived from observation of the silver-stained ciliate cortex, and coupled with ontogenetic characters revealed through observation of division morphogenesis, and particularly stomatogenesis. Electron microscopy was just beginning as Corliss (1961) went to press. In the ensuing decades exploration of this new level of organization revealed a wealth of new characters for both cell biologists and systematists. These new data, accompanied by new observations at the light microscopic level, resulted in several new classifications weighted still on features of the oral apparatus of the ciliates. Jankowski (1975) had proposed three classes and three infraclasses, resurrecting the suctorians as an independent class, while de Puytorac et al. (1974) and Corliss (1979) proposed three classes and six or more subclasses. The class names reflected the focus on oral features: Class Kinetofragminophora with simple oral kinetid fragments; Class Oligohymenophora with few oral membranelles; and Class Polyhymenophora with many oral membranelles. The primacy of oral structures as significant indicators of common ancestry was challenged by Lynn (1976, 1981) in his presentation of the structure conservatism hypothesis; that the conservation of structure through time is inversely related to the level of biological organization. Further, Lynn (1979, 1981) argued that oral structures themselves would be more quickly influenced by selective forces than somatic ones, and therefore less reliable indicators of common ancestry. Lynn (1981) identified kinetid patterns with major grouping of ciliates, groupings that undermined the system of relationships premised on oral features. These kinetid patterns or ultrastructural identities (Patterson 1999) were used by Small and Lynn (1981, 1985) to propose a radical revision of the ciliates, establishing several new classes to increase the number to eight with 15 subclasses. Small and Lynn (1985) pushed the somatic kinetid patterns to their "ideological" limits, placing peniculine ciliates with nassulid ciliates and adding the euplotid hypotrichs to this class, the Nassophorea, and placing the plagiopylid ciliates within the class Oligohymenophorea. The opportunity to test this appearance came with the discovery that ribosomal RNA gene sequences, a lower level of organization in the biological hierarchy, and therefore theoretically more conserved, were indeed able to reconstruct bacterial evolution (Woese 1987). In the mid-1980s, the first partial sequences of large subunit rRNA (LSrRNA) (Baroin et al. 1988; Adoutte, Baroin and Perasso 1989) and small subunit rRNA (SSrRNA) (Lynn and Sogin 1988) of protists, including ciliates, demonstrated extremely deep divergences among the lineages, and some initial support for the ultrastructural approach and its major conclusions.
The impact of continuing investigations at the ultrastructural level and increased analyses of gene sequences has resulted in considerable convergence in the revised classifications to the phylum. De Puytorac et al. (1993) proposed 11 classes while Lynn and Small (1997, 2002) proposed 10 classes: nine of these are essentially equivalent between the two systems, which conceive of different subphyletic divisions. The classification briefly described here adds an eleventh class, the Armophorea, to the Lynn and Small schemes cited above.
The classification divides the phylum into two subphyla, which are strongly supported by SSrRNA gene sequence data. The subphylum Postciliodesmatophora includes the classes Karyorelictea and Heterotrichea. Represented by Loxodes and Stentor respectively, these ciliates have kinetids with strongly developed postciliary microtubular ribbons, which extend to overlap in the so-called Km fibres. The karyorelicts have non-dividing macronuclei (Raikov 1982), while the heterotrichs have macronuclei that divide with the aid of extramacronuclear microtubules (Diener, Burchill and Burton 1983). The second subphylum, the Intramacronucleata includes the remaining nine classes of ciliates. This subphylum is strongly supported by SSrRNA gene sequences. Lynn (1996) has proposed that all these ciliates divide the macronucleus with intramacronuclear microtubules, a feature that may ultimately be associated with some fundamentally different way of processing the genomic DNA during macronuclear differentiation in this group (Katz 2001). Four of the classes assigned to this subphylum are strongly supported by both somatic kinetid patterns and/or features of division morphogenesis and SSrRNA gene sequences.

Phylum Ciliophora Doflein, 1901
Subphylum Postciliodesmatophora Gerassimova & Seravin, 1976
Class Karyorelictea Corliss, 1974 (Loxodes, Geleia, Tracheloraphis)
Class Heterotrichea Stein, 1859 (Stentor, Blepharisma, Climacostomum)

Subphylum Intramacronucleata Lynn, 1996
Class Spirotrichea Butschli, 1889
Subclass Protocruziidia de Puytorac et al., 1987 (Protocruzia)
Subclass Phacodiniidai Small & Lynn, 1985 (Phacodinium)
Subclass Hypotrichia Stein, 1859 (Euplotes, Aspidisca)
Subclass Oligotrichia Butschli, 1887 (Strombidium)
Subclass Choreotrichia Small & Lynn, 1985 (Strobilidium, Tintinnopsis, Favella)
Subclass Stichotrichia Small & Lynn, 1985 (Oxytricha, Sterkiella, Stylonychia)
Subclass Licnophoria Corliss, 1957 (Licnophora)

Class Armophorea Jankowski, 1964 (Metopus, Nyctotherus)

Class Litostomatea Small & Lynn, 1981
The class Litostomatea is strongly supported by SSrRNA gene sequences. It includes ciliates with a monokinetid that has two transverse ribbons, which may only appear transiently during kinetid replication. (Paul, Butler and Williams 1989; Lynn 1991)
Subclass Haptoria Corliss, 1974 (Didinium, Dileptus, Spathidium)
Subclass Trichostomatia Butschli, 1889 (Balantidium, Isotricha, Ophryoscolex)

Class Phyllopharyngea de Puytorac et al., 1974
The class Phyllopharyngea is strongly supported by SSrRNA gene sequences. It includes ciliates whose kinetid is a monokinetid with a laterally directed kinetodesmal fibril, a convergent (i.e. making a > 90 degrees angle with the kinety axis) postciliary ribbon, and a transverse spur associated with weakly developed transverse microtubules. A major feature of the oral apparatus of the included subclasses are radial ribbons of microtubules, the so-called phyllae which support the cytopharynx (Lynn and Small 1997)
Subclass Phyllopharyngia de Puytorac et al., 1974 (Chilodonella, Trithigmostoma)
Subclass Rhynchodia Chatton & Lwoff, 1939 (Ancistrocoma, Hypocoma)
Subclass Chonotrichia Wallengren, 1895 (Chilodochona, Spirochona)
Subclass Suctoria Claparede & Lachmann, 1858 (Ephelota, Tokophrya, Acineta)

Class Nassophorea Small & Lynn, 1981 (Pseudomicrothorax, Obertrumia)
The class Nassophorea is typically strongly supported by SSrRNA gene sequences. It includes ciliates whose monokinetid has a more anteriorly directed kinetodesmal fibril and whose kinetosomes in dikinetids are linked by filaments near the transverse ribbon (Eisler 1988; Lynn 1991). The strongest synapomorphies for this group are the complex features of the cytopharyngeal basket or nasse from which the class name is derived (Tucker 1968; Hausmann and Peck 1978)

Class Colpodea Small & Lynn, 1981 (Colpoda, Bursaria, Sorogena)
The class Colpodea is typically strongly supported by SSrRNA gene sequences. It includes ciliates which all share a somatic dikinetid composed of two kinetosomes, the posterior one of which ahs a well-developed transverse ribbon that extends posteriorly along the kinety forming the transversodesma or LKm fibre (Golder 1974; Lynn and Small 2002).

Class Prostomatea Schewiakoff, 1896 (Coleps, Urotricha, Cryoptocaryon)

Class Plagiopylea Small & Lynn, 1985 (Plagiopyla, Trimyema)

Class Oligohymenophorea de Puytorac et al., 1974
Subclass Peniculia Faure-Fremiet in Corliss, 1956 (Paramecium, Frontonia)
Subclass Scuticociliatia Small, 1967 (Cyclidium, Pleuronema, Dexiotricha)
Subclass Hymenostomatia Delage & Herouard, 1896 (Tetrahymena, Glaucoma, Ichthyophthirius)
Subclass Apostomatia Chatton & Lwoff, 1928 (Hyalophysa, Collinia)
Subclass Peritrichia Stein, 1859 (Vorticella, Epistylis, Zoothamnium)
Subclass Astomatia Schewiakoff, 1896 (Anoplophrya)