Cap 3

2002). Some 
of this research will be discussed in more detail 
in Chapter 16. Nevertheless, it appears for the 
moment, as judged by its agreement with mor-
phology, that the rRNA genes provide the most 
reliable signals for deep phylogenetic relation-
ships, in contrast to actins (Philippe, Chenuil, & 
Adoutte, 1994) and tubulins (Israel et al., 2002), 
which do not recover the same major clades as 
morphology, and may not even recover ciliates 
as a clade! 
 The SSUrRNA and LSUrRNA gene sequences 
have confirmed the major clades established 
using the somatic kinetid (Lynn, 1996b), and have 
enabled placement of enigmatic genera, such as 
Phacodinium (Shin et al., 2000) and Schizocaryum
and Licnophora (Lynn & Strüder-Kypke, 2002). 
On the other hand, there is strong indication of 
several lineages that can only be termed “ ribo-
classes ” (Lynn, 2004), since there are no obvious 
morphological synapomorphies for these groups. 
These include the genera Plagiopyla , Lechriopyla , 
and Trimyema now assigned to the “ribo”-Class 
 PLAGIOPYLEA , along with the odontostomatids , 
exemplified by Epalxella (see Chapter 14 ) and the 
genera Nyctotherus and Metopus now assigned to 
the “ribo”- Class ARMOPHOREA (see Chapter 
8 ). Perhaps we will discover morphological traits 
that will corroborate these gene sequence data or 
perhaps we will discover additional supporting 
molecular signals. 
 3.2.4 Summary 
 The three approaches discussed above outline 
the major avenues to determining relationships 
and providing criteria to establish groups above 
the genus-species level. Again, there are no easy 
directions that enable one to identify higher taxa. 
In general, somatic kinetids have proved very 
diagnostic as they exhibit universality, constancy, 
and consistency within clades. We have argued in 
Chapter 1 and elsewhere (Lynn, 1981) that simi-
larities in pattern at this level can be inferred to be 
 homologous and are therefore strong indicators of 
 common ancestry . 
 Gene and protein sequences continue to be 
the characters of choice in resolving the deeper 
relationships within the phylum. As discussed 
in Chapter 16, representatives of most of the 
major groups have now been sequenced. Thus, it 
is unlikely that our views on the major lines of 
diversification within the phylum will be radically 
changed in the immediate future. 
 3.3 Taxonomy and Nomenclature 
 We use scientific names to label taxa and pro-
vide a vocabulary for communicating about these 
organisms. Taxonomy is the discipline devoted 
to discovering, describing, and improving the 
characterization of taxa or groups of organisms. 
However, nomenclature is the discipline devoted to 
naming these taxa in ways that satisfy the criteria 
of availability, which are set out in the International 
Code of Zoological Nomenclature , herein called 
the Code. The most recent, 4th edition, of the Code 
was published by the International Commission on 
Zoological Nomenclature (1999a). Since the names 
of organisms are essential for scientific communi-
cation and are important as a key to the literature, 
taxonomy and nomenclature deserve a central 
place in biology. It is important to remember the 
difference between these two disciplines. An old 
example from the ciliate literature is illustrative. 
Hill (1752), as a taxonomic author, first described 
the genus Paramecium and provided a name. 
However, since “year zero” for the Code began on 
1 January 1758, O. F. Müller (1773) is credited as 
the nomenclatural author of the formal genus name 
– Paramecium O. F. Müller, 1773 – since he was 
3.3 Taxonomy and Nomenclature 85
86 3. Characters and the Rationale Behind the New Classification
the first to publish the name in a way that satis-
fied the criteria of availability of the Code. Names 
can change for a variety of reasons: for legalistic 
reasons related to the rules of nomenclature; for 
philosophical reasons related to whether a given 
taxonomist might be a “lumper” or “splitter”; or 
because novel characters have been discovered 
often after the application of new methods to the 
study of the taxa (Aescht, 2001). 
 In a number of papers, Corliss (1962a, 1962b, 
1972a, 1976, 1980, 1995) has dealt extensively 
with nomenclature and taxonomy as they relate to 
protozoa and protists. More recently, Aescht (2001) 
has provided a summary of important principles that
should be observed, especially noting matters raised 
in the new edition of the Code. Both authors direct 
readers to the original rules of the Code as the 
primary authority. Corliss (1962a) noted that errors 
or bad habits can arise from “ignorance of rules, 
carelessness in their application, lack of clarity in 
the rules themselves, and total lack of a pertinent 
directive anywhere in the rules” (p. 307). In this 
section, only brief mention will be made of some 
important issues in nomenclature. 
 The Code was established to provide rules to 
establish priority, to ensure consistency in naming 
of organisms, and to maintain stability or univer-
sality in names. As Corliss (1972a) emphasized, 
common sense and courtesy should be used and 
deference should be paid to the stability of the 
names while always being mindful of the provisions 
of the Code. While the Code does not apply to taxa 
above the family level, Corliss (1962a) argued that 
it is common sense to apply these principles at the 
suprafamilial level, and we have followed this 
recommendation. When a suprafamilial taxon has 
been simply transferred within a higher taxon or 
between higher taxa, even if it has changed its rank, 
we have retained the priority date from the original 
publication along with the original authorship. 
This promotes stability and recognizes priority. On 
the other hand, if in our view the proposed change 
involves a new taxonomic concept , then we have 
recognized a new authorship and date (see Corliss,
1972a). While not required by the Code, we have 
adopted a uniformity for the endings of the higher 
taxa of ciliates: for class – “-ea”; for subclass – “-ia”;
for order – “-ida”; and for suborder – “-ina”. The 
principle of typification is a primary principle in 
the Code. The fixation of the name-bearing type 
of a nominal taxon provides an objective standard 
of reference: the concept of species is linked to a 
concrete specimen, the holotype ; the concept of 
genus to a definite species, the type-species ; and 
the concept of family to a definite genus, the type-
genus . While this principle could be applied to the 
higher suprafamilial taxa of ciliates, we have not 
done so nor have we indicated the type genera of 
the families, a task that will need to be undetaken 
by a future revision. 
 While this monograph only treats ciliate taxa to 
the level of genus, nevertheless the principles and 
rules of the Code apply to the genus and family 
ranks treated herein. Aescht (2001) has served as 
our principle resource for the valid generic names 
of ciliates, and her excellent monograph should be 
the first source for all literature prior to about 13th 
March 2000 when her revisions on this monograph 
stopped. We have aimed to include all the literature 
subsequent to that date and up to 31st December 
2006. A brief review of some important nomen-
clatural matters follows. 
 3.3.1 The Matter of Types 
 Species names are linked to concrete specimens, 
ideally designated by the original author of the 
name as holotypes and lectotypes . Corliss (1962a) 
discussed the difficulty of preserving types, as indi-
vidual specimens, for the protozoa. However, much 
has changed since this time. With the development 
of more reliable mounting media and the refine-
ment of silver-staining techniques , type specimens 
of ciliates on type slides can be deposited in a 
variety of museum collections (see Corliss, 1972b). 
These type specimens must be recognized as “the 
property of science” and should be kept safely, 
labeled clearly and