Reconciling classical and molecular phylogenies in the stichotrichines (Ciliophora, Spirotrichea), including new sequences from some rare species

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.…”

“…However, it may also be due to the choice of molecule. Recently, Foissner et al (2004) concluded that the SSrRNA gene might not be providing a signal that reflects the true phylogeny of stichotrich genera. The same might be the case for the haptorian genera.…”

Comparative phylogenetic study of Stichotrichia (Alveolata: Ciliophora: Spirotrichea) based on 18S-rDNA sequences

“…This group is often recovered in molecular phylogenies (e.g., Bernhard et al, 2001;Hewitt et al, 2003;Foissner et al, 2004;Schmidt et al, 2007;Shao et al, 2007;Yi et al, 2008a,b) and so they were in both our trees, however, with discrepant placement of Steinia sphagnicola and Sterkiella histriomuscorum. Nevertheless, stylonychine external affinities did not follow the same pattern in both trees.…”

“…During the last years, attempts to hypothesize the evolutionary relationships among the Stichotrichia (= Hypotricha in Berger, 2006) and closely related groups based on molecular data (e.g., Bernhard et al, 2001;Hewitt et al, 2003;Strüder-Kypke and Lynn, 2003;Foissner et al, 2004;Foissner and Stoeck, 2006) have given results that generally contradict other hypotheses and classification systems based on morphological data (e.g., de Puytorac et al, 1994;Berger and Foissner, 1997;Eigner, 1997Eigner, , 1999Eigner, , 2001Lynn and Small, 2002;Lynn, 2003;Agatha, 2004;Foissner et al, 2007).…”

“…The most remarkable are: i) the placement of Halteria grandinella among the flexible-body oxytrichids (Bernhard et al, 2001;Strüder-Kypke and Lynn, 2003), referred to as the "Halteria paradox" (see Foissner et al, 2007); ii) the separation of Uroleptus from the urostylids (Croft et al, 2003;Hewitt et al, 2003;Foissner et al, 2004;Stoeck, 2006, 2008), which led to the "Convergent Evolution of Urostylids and Uroleptids" (CEUU) hypothesis, and the polyphyly of the non-uroleptid urostylids, suggested in subsequent studies (Schmidt et al, 2007;Yi et al, 2008a,b); iii) the polyphyly of Oxytricha (Schmidt et al, 2007), and iv) the splitting of the Stichotrichia, which were polyphyletic in Yi et al (2008b).…”