Cap 16
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Cap 16


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in our macrosystem. 
 The deeper relationships among these clades 
have not been strongly resolved. Cameron et al. 
(2001) performed statistical analyses and concluded
that there was good statistical support for the 
Classes KARYORELICTEA , HETEROTRICHEA , 
 SPIROTRICHEA , LITOSTOMATEA , PHYLL- 
OPHARYNGEA , PROSTOMATEA , and PLAGI 
OPYLEA . The Classes COLPODEA and NAS- 
SOPHOREA were often associated in their analyses,
while the Class OLIGOHYMENOPHOREA often 
did not form a well supported clade. 
 Review of the deeper topology demonstrated 
in the studies cited above provides no doubt of a 
deep bifurcation in the phylum, providing confir-
mation for the Subphylum Postciliodesmatophora 
to include the Classes KARYORELICTEA and 
 HETEROTRICHEA , and providing support for 
the Subphylum Intramacronucleata (Lynn, 
1996a, 2004). There is no consistent deep topol-
ogy within the intramacronucleates, although the 
following assemblages receive some support: 
 SPIROTRICHEA + ARMOPHOREA ; NASSO-
PHOREA + COLPODEA ; PROSTOMA-TEA + 
PLAGIOPYLEA ; and PHYLLOPHARNYGEA + 
( NASSOPHOREA + COLPODEA ) + ( PROSTOMA-
TEA + PLAGIOPYLEA ) + OLIGOHYMENOPHO-
REA . Based on an analysis of our SSU rRNA 
database, a summary tree provides support for some 
of these groupings (Fig. 16.3). 
 16.2.2 Protein Gene Sequences 
 There is a handful of studies that examine protein 
sequences, both as nucleotides and as amino acids, 
to provide further tests of the robustness of our 
understanding of relationships among ciliates. An 
underlying problem with using protein genes to 
16.2 Deep Phylogeny and Gene Sequences 331
Fig. 16.3. A phylogenetic tree based on sequences of the small subunit rRNA gene and using the profile-
neighbor-joining method implemented in Profdist ver. 0.9.6.1 (Friedrich et al., 2005). Note that the two subphyla \u2013 
 Postciliodesmatophora and Intramacronucleata - are strongly supported at >90%. Some classes are strongly supported 
(e.g., KARYORELICTEA , HETEROTRICHEA , ARMOPHOREA , LITOSTOMATEA , PHYLLOPHARYNGEA ,
 PLAGIOPYLEA ). Six \u201cterminal\u201d clades consistently cluster: the Classes PHYLLOPHARYNGEA , COLPODEA , 
 NASSOPHOREA , PLAGIOPYLEA , PROSTOMATEA , and OLIGOHYMENOPHOREA ) (cf. Fig. 16.5). We still 
have no rationalization outside of sequence data for this grouping. *Indicates support <20%
reconstruct the phylogeny of ciliates is the relatively 
high rate of protein diversification in the phylum, 
and especially in ciliate clades whose macronu-
clear genomes are extensively fragmented (Zufall, 
McGrath, Muse, & Katz, 2006). Nevertheless, 
 protein phylogenetic studies can be divided into 
two groups \u2013 those that have sequenced a small 
number of representative genera from across the 
phylum and those that have provided a larger sam-
pling of species. 
 Initial studies of the actin genes of ciliates 
indicated that the phylum was not recovered 
as a monophyletic group due to the high rela-
tive evolutionary rate of this gene in ciliates 
(Philippe & Adoutte, 1998). Kim, Yura, Go, and 
Harumoto (2004) have extended the sampling 
to about 20 genera of ciliates from five classes. 
Again, the ciliates are not recovered as a mono-
phyletic group, although several classes appear 
to be: the Class LITOSTOMATEA and Class 
 OLIGOHYMENOPHOREA . 
 Elongation factor 1\u3b1 (EF-1\u3b1) is a protein that, 
in addition to its role in protein synthesis, probably 
interacts with actin in the cytoskeleton of ciliates. 
It also shows unusually high rates of evolution, and 
again ciliates are not recovered as a monophyletic 
assemblage (Moreira, Le Guyader, & Philippe, 
1999). In an update of this research, Moreira, 
Kervestin, Jean-Jean, and Philippe (2002) provided 
sequences of eukaryotic release factor 1 (eRF1) 
and factor 3 (eRF3) in addition to sequences 
of EF-1\u3b1 and elongation factor 2 (EF-2). The 
genus sampling of eRF3 was too low to draw any 
definitive conclusions, but ciliates again were not 
recovered as monophyletic using either EF-1\u3b1 or 
eRF1. With seven genera representing five classes, 
the ciliates were recovered as monophyletic with 
EF-2 (Moreira et al., 2002). Moreira et al. specu-
lated that these accelerated rates of evolution in 
the ciliates may be due to loss of interaction of 
these proteins with cytoskeletal elements or may 
be a co-evolutionary phenomenon linked with 
the extremely fast-evolving actins of ciliates. The 
70 kDa heat shock proteins (Hsp70) comprise a 
multigene family that has been divided into three 
major subfamilies: (1) prokaryotic, mitochondrial, 
and chloroplast proteins; (2) eukaryotic cytosolic 
and nuclear proteins; and (3) eukaryotic proteins 
localized in the endoplasmic reticulum (Budin & 
Philippe, 1998). Budin and Philippe (1998) dem-
onstrated that Hsp70 subfamily sequences from 
Euplotes and Paramecium confirmed the ciliates as a 
monophyletic group. 
 Baroin et al. (1998) provided sequences 
of phosphoglycerate kinase (PGK) for seven 
species representing three classes \u2013 Classes 
 HETEROTRICHEA , SPIROTRICHEA , and 
 OLIGOHYMENOPHOREA \u2013 and showed that 
the phylum was monophyletic, although these 
data could be compared to only a limited sam-
pling of other eukaryotes. Thus far, only three 
protein genes \u2013 EF-2, Hsp70, and PGK \u2013 have 
confirmed the monophyly of the ciliates. The 
last two proteins that have been studied \u2013 the 
 tubulins and histones \u2013 also comprise multigene 
families, but they have been much more exten-
sively sampled across the phylum. 
 Baroin et al. (1998) provided nucleotide and amino 
acid sequences for \u3b1-tubulins from representatives 
of seven classes \u2013 Classes KARYORELICTEA , 
 HETEROTRICHEA , SPIROTRICHEA , LITOST- 
OMATEA , COLPODEA , NASSOPHOREA , 
and OLIGOHYMENOPHOREA . Israel, Pond, 
Muse, and Katz (2002) have added sequence 
data for the Classes ARMOPHOREA and
 PHYLLOPHARYNGEA . Although both studies 
only compared the ciliate sequences to alveolate 
sister taxa, the ciliates were monophyletic. Overall, 
although taxon sampling was low, most classes 
appeared to be monophyletic, excepting the Classes 
 HETEROTRICHEA and SPIROTRICHEA . While 
the classes were generally supported, there was no 
consistently recoverable deep topology (Fig. 16.4) 
(Israel et al., 2002). The ciliates were also recov-
ered as a monophyletic group based on \u3b2-tubulin 
sequences (Philippe & Adoutte, 1998). 
 Bernhard and Schlegel (1998) provided the first 
analyses of variation among the histone genes 
 H3 and H4 in six classes \u2013 Classes HETERO- TRICHEA , 
 SPIROTRICHEA , COLPODEA , NASSOPHOREA , 
 PROSTOMATEA , and OLI-GOHYMENOPHOREA . 
Katz, Bornstein, Lasek-Nesselquist, and Muse (2004) 
have expanded the database, adding sequences from 
representatives of the Classes ARMOPHOREA , 
 COLPODEA , PHYLLOPHARYNGEA , and 
 OLIGOHYMENOPHOREA . Thus, only repre-
sentatives of the Class PLAGIOPYLEA are mis-
sing. In unconstrained analyses of H4 nucleotides, 
the ciliates were not monophyletic, but they were 
monophyletic based on amino acid sequences 
(Katz et al., 2004). Based on amino acids, classes 
were generally monophyletic (Fig. 16.5). The deep 
16.2 Deep Phylogeny and Gene Sequences 333
334 16. Deep Phylogeny, Gene Sequences, and Character State Evolution 
Fig. 16.4. A phylogenetic tree derived from a neighbor-joining analysis of the amino acid sequences of the \u3b1-tubulin 
gene. The numbers on the branches represent bootstrap percentages for neighbor-joining (NJ) and maximum parsi-
mony (MP) while support estimates are provided for puzzle quartet analysis (PZ). The dots indicate branches with 
very low support values or inconsistent topology; P1 and P2 refer to paralogs of the \u3b1-tubulin gene. (Redrawn from 
Israel et al., 2002.)
 topology was generally unresolved, although four 
classes were often associated \u2013 Classes COLPO-
DEA , NASSOPHOREA , PROSTOMATEA , and 
 OLIGOHYMENOPHOREA (CONP, Fig. 16.5) 
(Bernhard & Schlegel, 1998;