Sequence analyses of the small subunit rRNA gene confirm the paraphyly of oligotrich ciliates sensu lato and support the monophyly of the subclasses Oligotrichia and Choreotrichia (Ciliophora, Spirotrichea)

Abstract

Oligotrich ciliates are an abundant and important component of planktonic food webs. Classified together, based on morphology and the arrangement of the oral ciliature, they include sensu lato halteriids, strombidiids, strobilidiids, and tintinnids. The oral ciliature of tintinnids and strobilidiids, the subclass Choreotrichia, is composed of a closed circle of external polykinetids with internal polykinetids, leading to the cytostome. Strombidiid and halteriid species, the subclass Oligotrichia, have an open circle of adoral polykinetids and separate ventral polykinetids. Previous molecular phylogenetic analyses of spirotrichs have placed Halteria grandinella among the stichotrichs. Apart from H. grandinella, only one other small subunit ribosomal RNA (SSrRNA) gene sequence of an oligotrich ciliate (Strombidium purpureum) has been published. Fourteen additional species representative of the major oligotrich orders were collected to determine their phylogenetic relationships. These SSrRNA gene sequences include two strombidiids (Strombidium spp.), one strobilidiid (Strobilidium caudatum), and 11 tintinnid species (i.e. Codonellopsis americana, Eutintinnus pectinis, Eutintinnus sp., Favella panamensis, Metacylis angulata, Metacylis sp., Rhabdonella hebe, Tintinnidium mucicola, Tintinnopsis dadayi, Tintinnopsis fimbriata and Tintinnopsis tocatinensis). The subclasses Oligotrichia (excluding Halteria) and Choreotrichia form a monophyletic group and are sister group to the subclass Stichotrichia with high nodal support. The choreotrichs are confirmed as a monophyletic subclass whereas the halteriids do not cluster with the strombidiids, but within the subclass Stichotrichia. Therefore, the family Halteriidae is transferred to the order Sporadotrichida in the subclass Stichotrichia. The strombidiids form a sister clade to the subclass Choreotrichia. Since there are no clear morphological or genetical synapomorphies for these two groups combined, the separate subclasses Choreotrichia and Oligotrichia are retained. The genetic relationships among tintinnid genera do not correspond to relationships based on lorica morphology: species with agglomerated and hyaline loricae do not form separate branches but are interrelated.

Molecular Phylogeny of Litostome Ciliates (Ciliophora, Litostomatea) with Emphasis on Free-Living Haptorian Genera

“…Additionally, the molecular tree topologies are not congruent with morphological classifications. Similar discrepancies between morphological and molecular data have been shown before (Foissner et al 2004;Struder-Kypke and Lynn 2003). The diversity within haptorid litostomes is very large, and the comparison and analysis of sequence data of even this many representative genera may not be sufficient to infer their phylogeny unambiguously.…”

Morphologic and molecular description of Metopus fuscus Kahl from North America and new rDNA sequences from seven metopids (Armophorea, Metopidae)

“…DNA was extracted from each of four cells using a modified Chelex method (Strüder-Kypke and Lynn 2003) and the 18S rDNA was amplified and sequenced as previously described (Bourland et al 2012). Chromatograms were manually edited using 4-Peaks (Griekspoor and Groothuis 2006) and assembled into contiguous sequences using CAP3 (Huang and Madan 1999).…”

Discrepancy between conventional morphological systematics and nuclear phylogeny of tintinnids (Ciliophora: Choreotrichia)

“…Previous studies on the phylogeny of the Choreotrichia (including the order Tintinnida) were unable to clearly elucidate the phylogeny within the Tintinnida based on nuclear SSrRNA gene fragments (Snoeyenbos-West et al 2002, Strüder-Kypke & Lynn 2003, Gao et al 2009, Li et al 2009), because they analyzed a limited number of tintinnid species. Here we newly analyzed 55 sequences of the SSrRNA gene fragments of tintinnid species (23 morphospecies, 11 genera and 6 families) collected in Sendai Bay in Japan and its vicinity.…”

“…With sequence data from previous studies (Agatha & Strüder-Kypke 2007, Duff et al 2008, Gao et al 2009, Li et al 2009, Snoeyenbos-West et al 2002, Strüder-Kypke & Lynn 2003, we reconstructed SSrRNA phylogeny using a total of 44 tintinnid morphospecies (84 sequences). We aligned the sequences with the CLUSTAL W algorithm (Thompson et al 1994) and manually adjusted the alignment using BioEdit (Hall 1999) and MEGA 4 (Tamura et al 2007).…”

“…DNA sequences of nuclear small subunit rRNA (SSrRNA) gene fragments have been used to construct phylogenetic trees of ciliates, including tintinnids (Snoeyenbos-West et al 2002, Strüder-Kypke & Lynn 2003, Gao et al 2009). Strüder- Kypke & Lynn (2008) and Li et al (2009) reconstructed phylogenies based on the SSrRNA gene sequences of several tintinnid species.…”