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Abstract Our understanding of the evolutionary 
diversifi cation of ciliates in the past two decades 
particularly has depended upon the interaction 
between conceptual views and technological advanc-
es. Transmission electron microscopy precipitated a 
revolution in our views of what characters might be 
signifi cant in inferring deep phylogenetic relation-
ships. The fi brillar patterns of somatic kinetids were 
considered crucial, based on the notion of the struc-
tural conservation of these cortical components. 
Molecular phylogenetic analyses have been used to 
test the conclusions based on electron microscopy. 
In the main, phylogenetic relationships inferred 
from sequences of the small subunit and large 
 subunit rRNA genes have confi rmed the major class-
es, and suggested several new ones (i.e., Classes 
tion, the rRNA genes demonstrated a fundamental 
subphyletic division – now named the Subphyla 
Postciliodesmatophora and Intramacronucleata. 
Protein gene sequences (e.g., elongation factor 1α,
α-tubulin, and histone H3 and H4) provide confi r-
mation for some clades. Using the rRNA phylogeny, 
the evolution of some major character states, 
particularly nuclear ones, can be assessed. 
Keywords Phosphoglycerate kinase, intramem-
branous particles, ciliary necklace 
 The progress in our understanding of the evolution-
ary diversification of ciliates has depended upon an 
interaction between conceptual views and techno-
logical advances . On the conceptual side, our views 
of which characters or features of ciliates were 
most important in revealing common ancestry have 
changed ( see Chapter 1 ). Briefly, in the 18th and 
19th centuries, overall ciliation patterns and the 
dominance of the “ spirotrich ” oral region divided 
the ciliates into “holotrichs” and “ spirotrichs ”. 
In the first half of the 20th century, ontogenetic 
patterns , particularly revealed by silver-staining 
organisms at cell division, received greater weight 
and aligned taxa that had previously been distantly 
separated (e.g., chonotrichs and suctoria were 
related to the cyrtophorines ). In the latter half of 
the 20th century, transmission electron microscopy 
revealed a whole new set of cytoskeletal charac-
ters, particularly the somatic kinetid patterns. The 
diversity of these somatic kinetid patterns initially 
suggested eight major clades or classes (Small & 
Lynn, 1981, 1985). 
 In the 1970s, microbiologists studying prokaryo-
tes had been successfully using small subunit 
(SSU) rRNA genes to resolve relationships among 
this group whose members were not rich in mor-
phological features (Stackebrandt & Woese, 1981). 
By the mid-1980s, several research groups began 
sequencing SSUrRNA genes of ciliates (Elwood, 
Olsen, & Sogin, 1985; Sogin & Elwood, 1986; 
Sogin, Swanton, Gunderson, & Elwood, 1986a), 
demonstrating that ciliates, even with this small 
sampling of species, appeared to be monophyletic 
and yet showed very deep divergences, equivalent 
to the genetic distances between the classical 
plant and animal “kingdoms”. The first denser 
samplings of species, using both the SSUrRNA 
(Lynn & Sogin, 1988; Sogin & Elwood) and the 
large subunit (LSU) rRNA (Baroin et al., 1988), 
provided enough taxon density to demonstrate 
 Chapter 16 
 Deep Phylogeny, Gene Sequences, 
and Character State Evolution – Mapping 
the Course of Ciliate Evolution 
328 16. Deep Phylogeny, Gene Sequences, and Character State Evolution 
 utility in testing the deeper relationships predicted 
by ultrastructural research. 
 The molecular phylogenetic approach is now 
a recognized method for testing and establishing 
phylogenetic relationships among organisms, and 
has been particularly fruitful in revealing the broad 
lines of evolutionary descent among eukaryotes. 
However, it rests on the basic assumption that 
phylogenetic trees based on genes truly represent 
the phylogeny of the organisms. Ultimately, our 
confidence in so-called “gene trees” increases 
when multiple and unlinked genes show patterns 
congruent with each other and with organismal 
phylogenies constructed on other features, such 
as morphology. It is the purpose of this chapter to 
briefly review the deep phylogeny of ciliates as 
inferred from features of cortical ultrastructure , 
primarily, and then to examine how this topology 
is congruent with gene tree topologies derived from 
rRNA genes and several protein coding genes. 
This will provide a consensus phylogenetic tree of 
the currently recognized classes of ciliates, which 
will provide the basis for a final discussion of the 
evolution of character states in the phylum. It is this 
distribution of character states that, in part, forms 
the rationale for the higher classification presented 
in Chapter 17 . 
 16.1 Deep Phylogeny 
and Ultrastructure 
 The transmission electron microscope provided 
a technical approach that opened up literally a 
vast array of detailed character information with 
which to investigate the cellular morphology of 
protists. Initially, there was a preoccupation with 
cortical fibrillar systems, an approach pioneered 
by Pitelka (1969). Later, comparative analyses 
of these cortical patterns, especially of somatic 
kinetids , suggested eight major clades or classes 
of ciliates: (1) Class KARYORELICTEA ; (2) 
(7) Class PROSTOMATEA ; and (8) Class 
 OLIGOHYMENOPHOREA (Lynn, 1981; Small 
& Lynn, 1981, 1985). As discussed in Chapter 1 , 
arrangement of these classes into subphyla based 
on morphology has not been supported by molec-
ular analyses (see below). While divided into 
subphyla by Small and Lynn (1985), the classes 
emerged “bush-like” from the common ancestor 
(Fig. 16.1). 
 Bardele (1981) analyzed the arrays of intramem-
branous particles of cilia in 68 genera, representing 
a broad diversity of ciliates. These particle array 
patterns were classified into a ciliary necklace that 
ringed the base of the cilium, ciliary plaques , ciliary 
rosettes , single- and double-stranded longitudinal 
rows, and orthogonal arrays covering most of the 
cilium. His analysis suggested six major assem-
blages: (1) SPIROTRICHA , corresponding to the 
which included representatives of the Classes 
 TRICHOSTOMATA , which included representatives 
from the Classes LITOSTOMATEA and COLPODEA ; 
(4) ENTO- DINIOMORPHA , which included repre-
sentatives from the Class LITOSTOMATEA ; (5) 
 HYPOSTOMATA + SUCTORIA , corresponding to 
sponding to the Class OLIGOHYMENOPHOREA . 
Bardele’s “ciliate bush” was anchored in a gymnos-
tome -like form and radiated out from there. While 
there was some broad agreement with the clades 
based on cortical ultrastructure, the particle array 
character set was not rich enough to tease out the 
details of this diversification (Fig. 16.2). 
 Bardele (1987, 1989) turned his “ciliate bush” 
upside down as he reviewed the data arising from 
his laboratory on the ultrastructure of ontogeny , 
and particularly stomatogenesis , in ciliates. These 
observations, coupled with the conception that 
the ciliate ciliature arose by proliferation from the 
 paroral (Eisler, 1989, 1992), suggested that gym-
nostomy – a simple, anterior oral region – may 
have arisen repeatedly as a derived and secondary 
feature of oral apparatus evolution and not as a pri-
mary feature. Bardele (1989) concluded by doubt-
ing that many of the major groups suggested by 
Small and Lynn (1981, 1985) would be confirmed 
to be monophyletic, and he strongly argued that a 
research program in ontogeny would reveal this 
view to be true. 
 By the early 1990s, there was general agree-
ment among morphologists