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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 \u201c ribo- classes \u201d (Lynn, 2004), since there are no obvious morphological synapomorphies for these groups. These include the genera Plagiopyla , Lechriopyla , and Trimyema now assigned to the \u201cribo\u201d-Class PLAGIOPYLEA , along with the odontostomatids , exemplified by Epalxella (see Chapter 14 ) and the genera Nyctotherus and Metopus now assigned to the \u201cribo\u201d- 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 \u201cyear zero\u201d for the Code began on 1 January 1758, O. F. Müller (1773) is credited as the nomenclatural author of the formal genus name \u2013 Paramecium O. F. Müller, 1773 \u2013 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 \u201clumper\u201d or \u201csplitter\u201d; 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 \u201cignorance of rules, carelessness in their application, lack of clarity in the rules themselves, and total lack of a pertinent directive anywhere in the rules\u201d (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 \u2013 \u201c-ea\u201d; for subclass \u2013 \u201c-ia\u201d; for order \u2013 \u201c-ida\u201d; and for suborder \u2013 \u201c-ina\u201d. 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 \u201cthe property of science\u201d and should be kept safely, labeled clearly and