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Abstract The history of ciliate systematics has 
been divided into fi ve periods: (1) the Age of 
 Discovery; (2) the Age of Exploitation; (3) the 
Age of Infraciliature; (4) the Age of Ultrastructure; 
and (5) the Age of Refi nement. Progress in each 
of these periods arose through an interaction of 
technology and conceptual views. For example, 
refi ned silver staining techniques revealed the law 
of desmodexy of the ciliate cortex and enabled the 
development of comparative morphogenetics in 
the Age of Infraciliature. Electron microscopy was 
essential for the conceptual notion of levels of 
organization below the cell and provided the impetus 
for the structural conservatism hypothesis in the 
Age of Ultrastructure. In this latter age, the foundations
for the current classifi cation system have been laid. 
Gene sequencing has provided the next techno-
logical innovation, which has enabled testing and 
revising our views on relationships in the current 
Age of Refi nement. Major differences between the 
scheme presented herein with its two subphyla and 
11 classes and other competing schemes are briefl y 
Keywords Kinetid, cortex, rRNA gene, molecular
phylogeny, organic design 
 Systematics as a discipline was defined by Simpson 
(1961) as “the scientific study of the kinds and 
diversity of organisms and of any and all relation-
ships among them” (p. 7). One aim of modern 
systematics is to represent these relationships 
among organisms by natural classifications : these 
are hierarchical and reflect as closely as possible 
the true phylogeny of a group of organisms. The 
approach to establishing a hierarchical classifica-
tion is influenced by the conceptual views of how 
significant particular characters are in inferring 
relationships, and these conceptual views, in their 
turn, are influenced by the technical approaches in 
vogue. In this context, Corliss (1974a) discussed 
the historical development of ciliate systematics 
in four periods: (1) the Age of Discovery (1880–
1930), exemplified by Bütschli; (2) the Age of 
Exploitation (1930–1950), exemplified by Kahl; 
(3) the Age of the Infraciliature (1950–1970), 
exemplified by Chatton, Lwoff, and Fauré-Fremiet, 
and during which Corliss (1961) published the first 
edition of “The Ciliated Protozoa”; and (4) the Age 
of Ultrastructure , whose beginnings around 1970 
were summarized in the review chapter by Pitelka 
(1969). The zenith of the Age of Ultrastructure 
(1970–1990) was at the time of the second edition 
of “The Ciliated Protozoa” by Corliss (1979), and 
its ending might be established around 1990, at the 
appearance of the first reports on gene sequences 
of ciliates. Indeed, Greenwood, Sogin, and Lynn 
(1991a) suggested this criterion as the beginning of 
a fifth age – the Age of Refinement (1990–present), 
during which the major lines of evolution and our 
closest approach yet to a natural classification for 
the phylum might be possible. It is therefore useful 
to briefly review this history, especially empha-
sizing the last 50 years to understand how ciliate 
systematics has indeed progressed. 
 Chapter 1 
 Introduction and Progress 
in the Last Half Century 
2 1. Introduction and Progress in the Last Half Century
 1.1 The Ages of Discovery 
(1880–1930) and Exploitation 
 Bütschli (1887–1889) and Kahl (1930–1935), exem-
plifying the Ages of Discovery and Exploitation, 
respectively, primarily used light microscopic 
observations of living ciliates, without the use of 
sophisticated stains. From the Age of Discovery 
to the Age of Exploitation, the number of higher 
taxa doubled as our understanding of diversity 
exploded (Table 1.1). The conceptual approach 
focused on the character of the somatic and oral 
ciliature and on a consideration that evolution 
proceeded from simpler forms to more complex 
forms. This is reflected in the characterization of 
the higher taxa by Bütschli as Holotricha – evenly 
covered by somatic cilia – and Spirotricha – with a 
prominent spiralling adoral zone of membranelles 
(Table 1.1). The suctorians with their bizarre ten-
tacled appearance and absence of external ciliature 
were given equivalent stature to all other ciliates 
by both Bütschli and Kahl. Other specialized and 
“complex” sessile forms, like the chonotrichs and 
 peritrichs , were also segregated to a higher rank 
by Kahl, equivalent to Holotricha and Spirotricha 
(Table 1.1). Within these higher taxa, oral features, 
indicated by the suffix “-stomata”, were major 
characters to indicate common descent (Table 1.1). 
It is interesting to note that the opalinid “flagel-
lates” were considered “protociliates” during the 
Kahlian period based on the views of Metcalf 
(1923, 1940) among others (Table 1.1). 
 1.2 The Age of the Infraciliature 
 Five scientists – Chatton and Lwoff, Klein, von 
Gelei, and Fauré-Fremiet – stand out as the pioneers
of this period, which Corliss (1974a) suggested 
extended from about 1950 to 1970. Yet, the roots 
of this age originated earlier in the 20th century in 
descriptions of the different technical approaches 
to using silver to stain the cortex and other struc-
tures of ciliates – the dry silver method of Klein 
(1929) and the wet silver method of Chatton and 
Lwoff (1930). The observations made by these 
pioneers culminated in seminal conceptual papers 
attributing a variety of causal relationships to 
various infraciliary structures (Chatton & Lwoff, 
1935b; Klein, 1928, 1929; von Gelei, 1932, 1934b; 
von Gelei & Horváth, 1931). Chatton and Lwoff’s 
(1935b) law of desmodexy stands out as one of 
the “rules” emerging from this period that has 
stood the test of time: true kinetodesmata and/or 
kinetodesmal fibrils, when present, lie to or extend 
anteriad and/or to the organism’s right of the kinety 
with which they are associated (see Chapter 2 ).
With this rule, one can not only identify a ciliate, 
but also one can deduce the polarity of the cell. The 
developmental autonomy and “genetic” continuity 
Table 1.1. Major systems of ciliate classification popular 
prior to 1950.a
Bütschlian Erab Kahlian Era
(1880–1930)a (1930–1950)
INFUSORIA Subphylum Ciliophora
Holotricha Protociliata
 Gymnostomata Opalinata
 Trichostomata Euciliata
 Astomata Holotricha
Spirotricha Gymnostomata
 Heterotricha Prostomata
 Oligotricha Pleurostomata
 Hypotricha Hypostomata
 Peritricha Trichostomata
Suctoria Apostomea
 Classes are indicated in bold capital letters; subclasses, in ital-
ics; orders, in bold; suborders and “tribes”, further indented in 
Roman type.
 It should be noted that Bütschli (1887–1889) originally pro-
posed a scheme that differed slightly from that shown (see 
Corliss, 1962a; Jankowski, 1967a). Later workers in the period 
re-arranged it so that it came to resemble the form presented 
here. In all cases, the number of major groups remained essen-
tially the same.
of the infraciliature was summarized at the begin-
ning of this period by Lwoff (1950) in his book 
entitled “Problems of Morphogenesis in Ciliates”. 
 Fauré-Fremiet and his students applied these 
conceptual views of the developmental impor-
tance of infraciliary patterns to resolving phyloge-
netic problems within the phylum. Fauré-Fremiet’s 
(1950a) discussion of comparative morphogenesis 
of ciliates rested on the conceptual presumption 
that similarities in pattern of the ciliature during divi-
sion morphogenesis revealed the common ancestry 
of lineages (see Corliss, 1968). These similarities 
in division morphogenesis were particularly 
important in establishing the phylogenetic affinities 
of polymorphic