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rolled up to ultimately form an ancestral prostomial 
form, while Small imagined that the ribbon-like 
form might have been very similar to the contem-
porary karyorelictean Kentrophoros , with an elon-
gate, flattened “ventral” surface, which it used for 
ingestion. Both these schema suggested that oral 
ciliature derived from somatic ciliature. 
 Eisler (1992) proposed a contrary model in which
the paroral dikinetids of ciliates represent the first 
ciliature of the ancestral ciliate and that the somatic 
kinetids derived from this. This model, most 
recently summarized by Schlegel and Eisler (1996), 
begins with a similar polyenergid stage as above. 
However, this “first” kinety is interpreted to be a 
 paroral , lying adjacent to a tube-like cytopharyngeal
apparatus supported by microtubules, as is found 
in some dinoflagellates (Fig. 4.2). At this stage, the 
paroral dikinetids are considered to lie orthogonal to 
the longitudinal axis of the cell and their postciliary 
microtubular ribbons extended to support the 
 cytopharynx . In the second stage, somatic Kinety 1 
(K1, Fig. 4.2) was derived from these paroral 
dikinetids by separation and rightward migration 
of the anterior or rightmost kinetosome of each 
paroral dikinetid (Step a, Fig. 4.2). Replication of 
these kinetosomes followed to reconstitute the 
ancestral dikinetid state (Lynn & Small, 1981). 
Eisler suggested that multiple repetitions of this 
process could give rise to multiple somatic kineties 
(Step b, Fig. 4.2). Alternatively, one could invoke the
processes of either torsion and fragmentation (see 
Small, 1984) or elineation to increase the number 
of somatic kineties . In a final stage, the adoral or 
“lefthand” oral structures are imagined to derive 
from the differentiation of somatic kinetids to the 
left of the oral region (Step c, Fig. 4.2). To support 
this, Schlegel and Eisler (1996) noted that the adoral 
ciliature is derived from a somatically-derived 
anlage in many contemporary ciliates. The paroral 
model has the advantage that, from the beginning, 
the ciliate ancestor, like many contemporary 
 dinoflagellates , has a cytopharynx supported by 
microtubules derived from the “paroral” dikinetids: 
there is no need to invoke an independent evolution 
Fig. 4.1. A phylogeny of the ciliates demonstrating the estimated time of divergence of some major lineages as 
 estimated by the divergence rate of small subunit rRNA gene sequences . The upper limit of 1% divergence per 80 
million years was used to determine the lengths of the branches on the tree. (from Wright & Lynn, 1997c.)
4. Phylum CILIOPHORA – Conjugating, Ciliated Protists with Nuclear Dualism 91
92 4. Phylum CILIOPHORA – Conjugating, Ciliated Protists with Nuclear Dualism
of the oral apparatus as in the competing models 
(see Orias, 1976; Small). Stomatogenesis and mor-
phogenesis of the progeny cell or opisthe would 
have been of a buccokinetal type. 
 Speculations on the evolution of another major 
feature distinguishing ciliates – nuclear dualism 
– are intriguing. Orias (1991b) used the life cycle 
of heterokaryotic foraminifera as an analogue to 
provide a rationale for how a heterophasic life cycle 
of a ciliate, ancestral to the karyorelicteans , might 
have evolved. This heterophasic life cycle had an 
alternation of haploid and diploid generations. 
From this, Orias developed the possible steps to the 
evolution of a karyorelictean cell cycle in which 
 nuclear dualism occurs but with divisionless macro-
nuclei differentiated at every cell cycle. While we 
now know that ciliates and foraminiferans are not 
closely related (Nikolaev et al., 2004), it is still 
possible that a heterophasic kind of life cycle might 
have been an intermediate stage in the evolution of 
ciliate nuclear dualism . 
 Orias (1991a) argued further that macronuclear 
division must have originated de novo within the 
ciliates. He noted that macronuclei in most cili-
ates fail to divide during the first postzygotic cell 
cycle following conjugation : more macronuclei are 
differentiated than is typical and these “excess” 
macronuclei are segregated without macronuclear 
division during postconjugation fissions , reminiscent
of the phenomenon that occurs at every cell cycle
in karyorelicteans . Macronuclear “dividers” may 
have had selective advantages: the division process 
is much faster than the nuclear differentiation proc-
ess and so “dividers” would outcompete “non-
dividers”; and dividing macronuclei may have 
increased the capability to assort intraclonally the 
genetic diversity of the parents and so increase the 
probability of generating more fit variants (Orias, 
1991a). Why do karyorelicteans still persist? Orias 
suggested that they may still be more fit in the 
“refugial” relict environments in which they are 
often found, and that many karyorelicteans may 
have compensated for macronuclear polyploidy by 
increasing the number of macronuclei, so support-
ing their increased cell size. 
 As additional evidence that macronuclear divi-
sion originated within the ciliates, Orias (1991a) 
noted that diversity in the modes of karyokinesis 
suggested at least two independent origins of 
 macronuclear division – heterotrichs use extrama-
cronuclear microtubules and other ciliates use 
intramacronuclear microtubules . Herrick (1994) 
argued that macronuclear division may have evolved 
independently perhaps three or more times, given 
the diversity of molecular mechanisms underlying 
 macronuclear differentiation . However, Katz (2001) 
has used current molecular phylogenies of ciliates 
to argue for a single origin of a differentiating 
Fig. 4.2. Scheme of evolution of the ancestral ciliate oral and somatic cortex as proposed by Eisler (1992). Step a
– an ancestral flagellate with a cytostome (c) and paroral of dikinetids separates the rightmost kinetosome of each 
dikinetid (arrowhead) to form somatic Kinety 1 (K1). Step b – this process is repeated (arrow) a number of times until 
the entire somatic cortex is covered by somatic kineties (Kn). Step c – adoral structures derive from the differentiation 
of somatic kinetids to the left of the cytostome. (Modified from Schlegel & Eisler, 1996.)
mechanism relying on trans -acting factors that 
emanate from the parental macronucleus to influ-
ence the differentiation of the developing macro-
nuclei. This epigenetic mechanism is conceived to 
be plastic enough to have generated the molecular 
genomic diversity that we see in contemporary 
 Nevertheless, the number of origins of macronu-
clear division is still unsettled. Two models have 
been proposed. For Model 1, the ancestral ciliate 
had a dividing macronucleus that lost its capacity 
to divide in the karyorelicteans . For Model 2, there 
were two independent origins of macronuclear 
division from a “non-dividing” ancestor – one 
with extramacronuclear microtubules in the het-
erotrich lineage and one with intramacronuclear
 microtubules in the intramacronucleate lineage 
(Hammerschmidt et al., 1996; Lynn, 1996a). We 
currently favor Model 2, which is consistent with 
the evidence presented by Orias (1991a, 1991b). 
For it, the macronucleus of intramacronucleate 
ciliates would “regain” the capacity to use intranu-
clear microtubules that continued to be used by the 
micronucleus during its mitoses while the hetero-
trich lineage would have “re-invented” the use of 
 extranuclear microtubules to divide their macronuclei,
an invention used also by some dinoflagellates 
(Perret, Albert, Bordes, & Soyer-Gobillard, 1991). 
 In summary, what would our ancestral ciliate 
look like? It would have had a pellicle with alveoli 
underlying the plasma membrane. If the paroral 
model is used for cortical evolution, the ances-
tral ciliate would have possessed a paroral , would 
have had a ventral oral region , would have had a