Phylogenetic position of the ciliates Phacodinium (Order Phacodiniida) and Protocruzia (Subclass Protocruziidia) and systematics of the spirotrich ciliates examined by small subunit ribosomal RNA gene sequences

Reframing the ‘Everything is everywhere’ debate: evidence for high gene flow and diversity in ciliate morphospecies

“…Genealogical analyses of the resulting sequences reveal 7 distinct clades of sequences (< 2% divergence within clades). We chose a 2% cutoff as a starting point, as some authors have suggested that 1 to 2% rDNA divergence is equivalent to morphospecies designations (Jerome et al 1996, Shin et al 2000. In fact, intraclade divergences based on this cutoff are all ≤ 0.5%, while interclade divergences are as high as 7.64% (Table 3).…”

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

“…In the first molecular study of its histone H4 and H3 genes, Bernhard and Schlegel (1998) showed that Protocruzia had an ambiguous position dependent upon whether nucleotide or protein sequences were used. Subsequent studies using 18S rRNA gene sequences showed the genus to be more closely related to Spirotrichea (in a basal position) than Postciliodesmatophora (Hammerschmidt et al, 1996;Shin et al, 2000).…”

“…Multiple analyses have since been employed using a limited number of genes but the exact phylogenetic position of Protocruzia remains unresolved; it has been considered a karyorelictid, heterotrich and spirotrich (Bernhard and Schlegel, 1998;De Puytorac, 1994;Grolière et al, 1980;Lynn, 1981Lynn, , 1991Lynn, 2008;Shin et al, 2000;Small and Lynn, 1981;Song and Wilbert, 1997). Some investigators have proposed that Protocruzia be given its own lineage status (Li et al, 2010).…”

“…Nevertheless, the monophyly of the class Spirotrichea has been challenged in several studies, notably those that include Protocruzia spp. While Protocruzia has been formally assigned to the Spirotrichea (Lynn, 2008), its phylogenetic position remains as one of the most ambiguous since it is rarely recovered with the Spirotrichea (Bernhard and Schlegel, 1998;Shin et al, 2000;Song and Wilbert, 1997). Some researchers have suggested that Protocruzia be assigned its own independent lineage status (Li et al, 2010).…”

Phylogenetic framework of the systematically confused Anteholosticha–Holosticha complex (Ciliophora, Hypotrichia) based on multigene analysis

“…Thus, it would be wiser to await a more comprehensive concatenated phylogeny before drawing any conclusions as to the correct position of A. monilata and other members of subgroup E. Anteholosticha multistilata, originally described under the name Holosticha multistilata (Kahl, 1928), was transferred to Anteholosticha by Berger (2003). Shin et al (2000) identified a population with four frontal cirri as ''Holosticha multistylata'' sensu Shin and Kim (1993) and sequenced the SSU-rRNA gene (GenBank Accession No. AJ277876).…”