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and his group (Fauré-
Fremiet, 1948a, 1950a, 1950b). Corliss (1968) 
Fig. 16.7. Character evolution in the ciliates using 
a phylogenetic tree whose deep topology is based 
on the consensus of gene sequences, primarily from 
the small subunit rRNA and histone H4 genes (cf. 
Figs. 16.3, 16.5). A Presence of polytene chromo-
somes and chromosal fragmentation during macronu-
clear development . B Presence of replication bands 
during S phase of macronuclear DNA synthesis. Note 
that the genus Protocruzia does not have this feature 
although it clusters with the Class SPIROTRICHEA 
(cf. Figs. 16.3, 16.5). C Presence of somatic monoki-
netids . D Presence of buccokinetal (black), parakinetal 
(dark grey), telokinetal (grey), apokinetal (white), and 
mixokinetal (half black: half grey) modes of stoma-
togenesis . KA , Class KARYORELICTEA ; HE , Class 
PODEA ; NA , Class NASSOPHOREA ; PL , Class 
16.3 Character State Evolution 337
338 16. Deep Phylogeny, Gene Sequences, and Character State Evolution 
affirmed this view, and presented the basis of 
the current classification of stomatogenetic types 
(Corliss, 1979). Foissner (1996b) has updated and 
refined the classification of types, and provided a 
phylogenetic scenario for the evolution of these sto-
matogenetic types , assuming that the buccokinetal 
mode was ancestral or plesiomorphous. Foissner 
(1996b) noted that evidence for this assumption is 
weak, but he used as support the model proposed 
by Eisler (1992) for the evolution of the ciliate 
cortex. Distribution of all buccokinetal modes 
on the tree is not consistent with this view (Fig. 
16.7D). Instead, the most broadly distributed mode 
is the telokinetal mode (Fig. 16.7D). Thus, Eisler’s 
model (Eisler, 1992; Schlegel & Eisler, 1996) may 
be incorrect. Alternatively, soon after the ancestral 
cortex evolved by this “paroral model” of evolution 
(Eisler, 1992), a telokinetal mode of stomatogen-
esis may have evolved as the cell division process. 
As we have argued elsewhere, and is confirmed by 
this analysis, modes of stomatogenesis should be 
used only as descriptive features at this deep level. 
The usefulness of stomatogenetic characters is 
highest when characterizing and comparing genera 
and species. It is also useful in broadly associating 
ciliates into different clades based on the details of 
the stomatogenetic process rather than the mode 
itself (e.g. phyllopharyngean merotelokinetal vs. 
 colpodean merotelokinetal ; see Foissner, 1996b). 
 A final feature that we have not mapped on 
the tree, but which has been discussed by several 
research groups, is the evolution of hydrogeno-
somes from mitochondria (Embley et al., 1995; van 
Hoek et al., 2000b). Hydrogenosomes have been 
found in all species so far examined of the Classes 
not closely related (Figs. 16.6, 16.7), and in select 
members of the Classes LITOSTOMATEA and 
 OLIGOHYMENOPHOREA . The latter evidence 
– origin within a class – demonstrates unambigu-
ously the adaptive nature of the hydrogenosome 
(Fenchel & Finlay, 1990b, 1991a). 
 16.4 Summary 
 We have provided this discussion as an approach 
to demonstrating how to rationalize morphologi-
cal and molecular features of the ciliates. This 
approach can also serve as the basis for provid-
ing evidence of the robustness of a classification 
or suggesting deeper subdivisions, which may 
not be inspired immediately by morphology 
(e.g., Subphylum Intramacronucleata ; see Lynn, 
1996a). As the species sampling for our gene 
sequence database expands, this approach may 
be productively extended “higher” in the tree, 
testing relationships among subclasses within 
classes and orders within subclasses. For exam-
ple, the increased species sampling of SSUrRNA 
genes of suctorians provided very preliminary 
genetic evidence that the Orders Exogenida , 
 Endogenida , and Evaginogenida may capture 
the evolutionary diversification of the suctorians 
(Snoeyenbos et al., 2004). Extensive sampling 
within the Class OLIGOHYMEN-OPHOREA 
has confirmed the monophyly of the major sub-
classes classically based on morphology (Affa’a, 
Hickey, Strüder-Kypke, & Lynn, 2004; J.C. 
Clamp et al., 2008; Greenwood et al., 1991a; 
Lynn & Strüder-Kypke, 2005; Strüder-Kypke 
et al., 2000b). Yet, clearly, much work remains 
to be done!