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Katz et al., 2004). The unusual ciliate Protocruzia , which we place in the Class SPIROTRICHEA ( see Chapter 17 ), is associated with karyorelicteans (Bernhard & Schlegel, 1998) or the four-class assemblage (Katz et al., 2004), based on H4 nucleotide sequences. However, this genus is at the base of the intrama- cronucleate clade (Bernhard & Schlegel, 1998) or associated with the spirotrichs (Katz et al., 2004), based on amino acid sequences (Fig. 16.5). Fig. 16.5. A phylogenetic tree derived from a neighbor-joining analysis of the amino acid sequences of the histone H4 gene. The dots indicate bootstrap percentages >70%. Clades indicated by capital letters correspond to the respective classes. Note that only the Classes COLPODEA and PROSTOMATEA are supported >70%, but species sampling in these is very low. P1, P2, etc. indicate paralogs. (Redrawn from Katz et al., 2004.) Overall, the protein sequence database provides us with little confidence in the deep phylogeny of the ciliates. Proteins refute or confirm the monophyly of the phylum. Since there is no doubt from a morphological perspective that the ciliates are monophyletic, reinforced strongly by the rRNA sequence databases, we must consider those protein molecules refuting this monophyly to be aberrant in some way, perhaps due to very high relative rates of evolution (Katz et al., 2004; Moreira et al., 2002; Zufall et al., 2006). The major assemblages suggested by the SSUrRNA database, including the Classes COLPODEA , NASSOPHOREA , PROSTOMATEA , and OLIGOHYMENOPHOREA , are supported at least by H4 amino acid sequences (cf. Figs. 16.3, 16.5). 16.3 Character State Evolution The review of gene sequence data for rRNA and protein genes, excluding those proteins with unu- sually high relative rates of evolution (i.e., actins, elongation factors), leaves us to conclude that the Phylum Ciliophora is monophyletic, supporting the classical view based on morphology. The sampling 16.3 Character State Evolution 335 336 16. Deep Phylogeny, Gene Sequences, and Character State Evolution density of sequence information across the phylum is really only significant for the SSUrRNA gene, for which we now have representatives sequenced for all major classes and most major subclasses or orders. Based on this gene, a simplified topology has been constructed to use in our evaluation of the evolution of character states within the phylum (Figs. 16.6, 16.7). This analysis will provide some of the evidential basis for the higher classification presented in Chapter 17 . The ciliate tree is deeply divided into two major lineages. Mapping the presence of post- ciliodesmata on the tree demonstrates that this character is restricted to one of these two major lin- eages, which is now recognized as the Subphylum Postciliodesmatophora (Fig. 16.6A) (Lynn, 1996a). The next five characters are all related to nuclear features. The other major lineage of ciliates has the major unifying feature of dividing the macronucleus primarily by using intramacronuclear microtubules . Distribution of this character on the tree supports recognition of the Subphylum Intramacronucleata (Fig. 16.6B) (Lynn, 1996a). The other major lineage with dividing macronuclei uses extramacronuclear microtubules in the division process. Distribution of this character on the tree supports recognition of the Class HETEROTRICHEA , which is also char- acterized by postciliodesmata whose ribbons are separated by a single microtubule (Fig. 16.6C) ( see Chapter 6 ). The third nuclear character is the pres- ence of non-dividing macronuclei. Distribution of this character on the tree supports recognition of the Class KARYORELICTEA , which is also character- ized by postciliodesmata whose ribbons are sepa- rated by the 2+ribbon+1 microtubular arrangement (Fig. 16.6D) ( see Chapter 5 ). As noted earlier, the topology of the tree does not permit us to unambigu- ously conclude how dividing macronuclei evolved within the phylum. One view is that macronuclei gained the ability to divide using both intra- and extramacronuclear microtubules. This was followed by a loss of division in the karyorelicteans , an emphasis on extramacronuclear microtubules in heterotrichs , and an emphasis on intramacronuclear microtubules in all other ciliates (Hammerschmidt et al., 1996). The other view is that dividing macro- nuclei evolved twice independently from non-divid- ing macronuclei (Katz, 2001; Orias, 1991a). The next two nuclear characters are related to the molecular processing of macronuclear DNA. Following conjugation , the formation of poly- tene chromosomes and extensive chromosomal fragmentation can occur as the new macronu- cleus differentiates (Jahn & Klobutcher, 2002; Prescott, 1994; Raikov, 1996). The distribution of this combined feature is restricted to three classes \u2013 SPIROTRICHEA , ARMOPHOREA , and Fig. 16.6. Character evolution in the ciliates using a phylogenetic tree whose deep topology is based on the consensus of gene sequences, primarily from the small subunit rRNA and histone H4 genes (cf. Figs. 16.3, 16.5). A Presence of postciliodesmata . B Presence of intramacronuclear microtubules to divide macronu- cleus. C Presence of extramacronuclear microtubules to divide macronucleus. D Presence of non-dividing macronuclei. KA , Class KARYORELICTEA ; HE , Class HETEROTRICHEA ; SP , Class SPIROTRICHEA ; AR , Class ARMOPHOREA ; LI , Class LITOSTOMATEA ; PH , Class PHYLLOPHARYNGEA ; CO , Class COLPODEA ; NA , Class NASSOPHOREA ; PL , Class PLAGIOPYLEA ; PR , Class PROSTOMATEA ; OL , Class OLIGOHYMENOPHOREA PHYLLOPHARYNGEA (Fig. 16.7A). Riley and Katz (2001) argued that chromosomal fragmen- tation may have had multiple origins. However, these three lineages often find their place at the \u201cbase\u201d of the intramacronucleate radiation in gene sequence trees, sometimes separated by the Class LITOSTOMATEA (Fig. 16.7A). Thus, a common molecular mechanism of polytenization and genome fragmentation possibly underlies the explosive diversification of intramacronucleates . This mechanism has been refined or lost secondar- ily, at least twice, as this radiation diverged: it may have been lost in the common ancestor to the Class LITOSTOMATEA and in the common ancestor of the NASSOPHOREA - OLIGOHYMENOPHOREA clade (Fig. 16.7A). The final nuclear feature is the presence of replication bands , which pass through the macro- nuclear karyoplasm during the S phase of DNA synthesis. Distribution of this character is restricted to lineages in the Class SPIROTRICHEA , and with the exception of Protocruzia , provides a rationale for the monophyly of this group (Fig. 16.7B) ( see Chapter 7 ). Finally, two features that have been considered important in systematic discussions are the pres- ence of somatic monokinetids or somatic dikinetids and the kinds of stomatogenesis . Lynn and Small (1981) argued that the dikinetid state was likely the ancestral state for the ciliates, considering that the majority of flagellate taxa believed to be sister taxa to the ciliates had dikinetids. Distribution of the monokinetid character state on the ciliate tree is consistent with this view as four of the \u201cearly\u201d emerging classes \u2013 KARYORELICTEA , HETEROTRICHEA , SPIROTRICHEA , and AR- MOPHOREA \u2013 are characterized by somatic diki- netids (Fig. 16.7C). In fact, the character state distribution of monokinetids suggests a \u201cgain\u201d of this character as the common ancestor of the litostomes, phyllopharyngeans, and their sister taxa arose, with an independent second- ary evolution of the somatic dikinetid character in the Class COLPODEA and within the Class OLIGOHYMENOPHOREA (Fig. 16.7C). Ontogenetic features have assumed a cen- tral place in ciliate systematics since the early researches of Fauré-Fremiet