Phylogenetic Relationships of Orders Within the Class Colpodea (Phylum Ciliophora) Inferred from Small Subunit rRNA Gene Sequences

Abstract

Molecular analyses have been used recently to refine our knowledge of phylogenetic relationships within the ciliated protozoa (phylum Ciliophora). A current Hennigian phylogeny of the orders in the class Colpodea, based on light and electron microscopic analyses, makes three important assumptions with regard to apomorphic character states, namely, (1) that the kreyellid silver line evolved early in colpodean phylogeny, separating bryometopids, such as Bryometopus, from all other colpodeans; (2) that the macro-micronuclear complex is an autapomorphy of the cyrtolophosidids, such as Platyophrya; and (3) that merotelokinetal stomatogenesis is an apomorphic character of colpodids, such as Colpoda, Bresslaua, and Pseudoplatyophrya. These predictions of relationships within the class Colpodea were investigated by determining the complete small subunit rRNA gene sequences for the colpodid Bresslaua vorax, the grossglockneriid Pseudoplatyophrya nana, and the cyrtolophosidid Platyophrya vorax and a partial sequence for the bryometopid Bryometopus sphagni. These sequences were combined with the previously published complete SSrRNA sequences for the colpodid Colpoda inflata and the bursariomorphid Bursaria truncatella. The affiliations were assessed using both distance matrix and maximum-parsimony analyses. The tree topologies for the class Colpodea were identical in all analyses, with bootstrap support for bifurcations always exceeding 60%. The results suggest the following. (1) Since the clade including Bryometopus and its sister taxon, Bursaria, is never basal, the kreyellid silver-line system evolved later in colpodean phylogeny and does not separate bryometopids from all other colpodeans. (2) Since Platyophrya is always the sister taxon to the other five genera, there is a fundamental phylogenetic significance for its macro-micronuclear complex. (3) Since the colpodids, Colpoda, Bresslaua, and Pseudoplatyophrya, always group in one clade, merotelokinetal stomatogenesis appears to be a derived character state.

Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)

“…The GC contents are also in the same range as those of other ciliates (Lynn et al, 1999;Li et al, 2008a;Sun et al, 2012a, b;Gao et al, 2013;Li et al, 2013). Thus, this aspect of the genetic regions should not bias our phylogenetic analyses.…”

“…As with some other groups of ciliates, however, one should take into account the following considerations when assessing evolutionary relationships among peritrichous ciliates: (1) the low number of samples used in previous molecular phylogenetic analyses may have led to erroneous conclusions, as outlined previously (Dunthorn et al, 2008;Foissner et al, 2010); (2) the morphological and morphogenetic characters do not necessarily refl ect the evolutionary relationships between taxa because some morphological similarities might be due to phenotypic adaptation (Li et al, 2008a); (3) relationships inferred from molecular data do not always accurately refl ect the true phylogeny (Lynn et al, 1999;Strüder-Kypke et al, 2000;Li et al, 2008a); (4) the evolutionary rates of genes and morphological divergence might be different (Li et al, 2008a); (5) the status of the same morphological character may be different in assessments of deep phylogenetic relationships in some major groups of ciliates because of different rates of evolution (e.g., the silverline system as a taxonomic character is of limited value in relation to the family Zoothamniidae but is very important for the Vorticellidae) (Li et al, 2008a;Lynn, 2008;Foissner et al, 2010;Sun et al, 2012a, b); and (6) the difference in habitats (i.e. marine vs. freshwater) may lead to a fundamentally different evolutionary lineage.…”

A Molecular Approach to the Tangled Intrageneric Relationships Underlying Phylogeny in Euplotes (Ciliophora, Spirotrichea)

“…Molecular characters, in particular the sequences of the small (SSrRNA) and large (LSrRNA) subunits of rRNA genes and some protein-coding genes, are providing a new database with which to test phylogenetic hypotheses that have been primarily based on morphological observations (Greenwood et al, 1991;Schlegel et al, 1991;Baroin-Tourancheau et al, 1992Hirt et al, 1995;Hammerschmidt et al, 1996;Wright and Lynn, 1997;Stechmann et al, 1998;Lynn et al, 1999;Strü der-Kypke et al, 2000a,b;Bernard and Schlegel, 1998). Although these techniques may provide clear relationships between related taxa, only in a few cases have they been applied to distinguish species within a genus; e.g., Tetrahymena (Nanney et al, 1998;Strü der-Kypke et al, 2001) and Paramecium (Strü der- Kypke et al, 2000b).…”

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

“…Beyond this deep division, it is generally agreed that there are 11 major ciliate lineages or classes and a twelfth single species clade of Cariacotrichea (Adl et al, 2012;Lynn, 2008;Orsi et al, 2012;Stoeck et al, 2003). Most of these classes are strongly supported by morphology, with the exception of the ''riboclasses'' -the Armophorea and Plagiopylea, which are identified only by sequences of the 18S rRNA genes, as included taxa lack any morphological synapomorphies (Bernhard et al, 1995(Bernhard et al, , 2001Cameron et al, 2001;Embley et al, 1995;Greenwood et al, 1991;Leipe et al, 1994;Lynn, 2008;Lynn et al, 1999;Lynn and Strüder-Kypke, 2002;Snoeyenbos-West et al, 2004;Stechmann et al, 1998). Nevertheless, the monophyly of the class Spirotrichea has been challenged in several studies, notably those that include Protocruzia spp.…”