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Katz et al., 2004). 
The unusual ciliate Protocruzia , which we place 
in the Class SPIROTRICHEA ( see Chapter 17 ), 
is associated with karyorelicteans (Bernhard & 
Schlegel, 1998) or the four-class assemblage (Katz 
et al., 2004), based on H4 nucleotide sequences. 
However, this genus is at the base of the intrama-
cronucleate clade (Bernhard & Schlegel, 1998) or 
associated with the spirotrichs (Katz et al., 2004), 
based on amino acid sequences (Fig. 16.5). 
Fig. 16.5. A phylogenetic tree derived from a neighbor-joining analysis of the amino acid sequences of the histone H4 
gene. The dots indicate bootstrap percentages >70%. Clades indicated by capital letters correspond to the respective 
classes. Note that only the Classes COLPODEA and PROSTOMATEA are supported >70%, but species sampling in 
these is very low. P1, P2, etc. indicate paralogs. (Redrawn from Katz et al., 2004.)
 Overall, the protein sequence database provides
us with little confidence in the deep phylogeny 
of the ciliates. Proteins refute or confirm the 
monophyly of the phylum. Since there is no 
doubt from a morphological perspective that the 
ciliates are monophyletic, reinforced strongly by 
the rRNA sequence databases, we must consider 
those protein molecules refuting this monophyly 
to be aberrant in some way, perhaps due to very 
high relative rates of evolution (Katz et al., 2004; 
Moreira et al., 2002; Zufall et al., 2006). The 
major assemblages suggested by the SSUrRNA 
database, including the Classes COLPODEA , 
 OLIGOHYMENOPHOREA , are supported at least
by H4 amino acid sequences (cf. Figs. 16.3, 16.5). 
 16.3 Character State Evolution 
 The review of gene sequence data for rRNA and 
protein genes, excluding those proteins with unu-
sually high relative rates of evolution (i.e., actins, 
elongation factors), leaves us to conclude that the 
Phylum Ciliophora is monophyletic, supporting the 
classical view based on morphology. The sampling 
16.3 Character State Evolution 335
336 16. Deep Phylogeny, Gene Sequences, and Character State Evolution 
density of sequence information across the phylum 
is really only significant for the SSUrRNA gene, 
for which we now have representatives sequenced 
for all major classes and most major subclasses or 
orders. Based on this gene, a simplified topology 
has been constructed to use in our evaluation of 
the evolution of character states within the phylum 
(Figs. 16.6, 16.7). This analysis will provide some 
of the evidential basis for the higher classification 
presented in Chapter 17 . 
 The ciliate tree is deeply divided into two 
major lineages. Mapping the presence of post-
ciliodesmata on the tree demonstrates that this 
character is restricted to one of these two major lin-
eages, which is now recognized as the Subphylum 
 Postciliodesmatophora (Fig. 16.6A) (Lynn, 1996a). 
 The next five characters are all related to nuclear 
features. The other major lineage of ciliates has the 
major unifying feature of dividing the macronucleus 
primarily by using intramacronuclear microtubules . 
Distribution of this character on the tree supports 
recognition of the Subphylum Intramacronucleata 
(Fig. 16.6B) (Lynn, 1996a). The other major lineage 
with dividing macronuclei uses extramacronuclear 
microtubules in the division process. Distribution 
of this character on the tree supports recognition of 
the Class HETEROTRICHEA , which is also char-
acterized by postciliodesmata whose ribbons are 
separated by a single microtubule (Fig. 16.6C) ( see
Chapter 6 ). The third nuclear character is the pres-
ence of non-dividing macronuclei. Distribution of 
this character on the tree supports recognition of the 
Class KARYORELICTEA , which is also character-
ized by postciliodesmata whose ribbons are sepa-
rated by the 2+ribbon+1 microtubular arrangement 
(Fig. 16.6D) ( see Chapter 5 ). As noted earlier, the 
topology of the tree does not permit us to unambigu-
ously conclude how dividing macronuclei evolved 
within the phylum. One view is that macronuclei 
gained the ability to divide using both intra- and 
extramacronuclear microtubules. This was followed 
by a loss of division in the karyorelicteans , an 
emphasis on extramacronuclear microtubules in 
 heterotrichs , and an emphasis on intramacronuclear 
microtubules in all other ciliates (Hammerschmidt 
et al., 1996). The other view is that dividing macro-
nuclei evolved twice independently from non-divid-
ing macronuclei (Katz, 2001; Orias, 1991a). 
 The next two nuclear characters are related to 
the molecular processing of macronuclear DNA. 
Following conjugation , the formation of poly-
tene chromosomes and extensive chromosomal
fragmentation can occur as the new macronu-
cleus differentiates (Jahn & Klobutcher, 2002; 
Prescott, 1994; Raikov, 1996). The distribution 
of this combined feature is restricted to three 
Fig. 16.6. 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 postciliodesmata . B Presence 
of intramacronuclear microtubules to divide macronu-
cleus. C Presence of extramacronuclear microtubules 
to divide macronucleus. D Presence of non-dividing 
macronuclei. KA , Class KARYORELICTEA ; HE , Class 
 PHYLLOPHARYNGEA (Fig. 16.7A). Riley and 
Katz (2001) argued that chromosomal fragmen-
tation may have had multiple origins. However, 
these three lineages often find their place at 
the “base” of the intramacronucleate radiation in 
gene sequence trees, sometimes separated by the 
Class LITOSTOMATEA (Fig. 16.7A). Thus, a 
common molecular mechanism of polytenization 
and genome fragmentation possibly underlies the 
explosive diversification of intramacronucleates . 
This mechanism has been refined or lost secondar-
ily, at least twice, as this radiation diverged: it may 
have been lost in the common ancestor to the Class 
 LITOSTOMATEA and in the common ancestor of 
clade (Fig. 16.7A). 
 The final nuclear feature is the presence of 
 replication bands , which pass through the macro-
nuclear karyoplasm during the S phase of DNA 
synthesis. Distribution of this character is restricted 
to lineages in the Class SPIROTRICHEA , and with 
the exception of Protocruzia , provides a rationale 
for the monophyly of this group (Fig. 16.7B) ( see
Chapter 7 ). 
 Finally, two features that have been considered 
important in systematic discussions are the pres-
ence of somatic monokinetids or somatic dikinetids 
and the kinds of stomatogenesis . Lynn and Small 
(1981) argued that the dikinetid state was likely 
the ancestral state for the ciliates, considering that 
the majority of flagellate taxa believed to be sister 
taxa to the ciliates had dikinetids. Distribution 
of the monokinetid character state on the ciliate 
tree is consistent with this view as four of the 
“early” emerging classes – KARYORELICTEA , 
MOPHOREA – are characterized by somatic diki-
netids (Fig. 16.7C). In fact, the character state 
distribution of monokinetids suggests a “gain” 
of this character as the common ancestor of 
the litostomes, phyllopharyngeans, and their 
sister taxa arose, with an independent second-
ary evolution of the somatic dikinetid character 
in the Class COLPODEA and within the Class 
 Ontogenetic features have assumed a cen-
tral place in ciliate systematics since the early 
researches of Fauré-Fremiet