Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data

Abstract

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.

Morphology of Nyctotheroides hubeiensis Li et al. 1998 from Frog Hosts with Molecular Phylogenetic Study of Clevelandellid Ciliates (Armophorea, Clevelandellida)

“…, ; Lynn and Wright ; Paiva et al. ) this supporting the prescient hypothesis of Jankowski (, ). However, the taxonomy within the Armophorida is controversial as the phylogenetic data based on the analysis of the SSU‐rDNA sequences do not correspond with the morphological classification.…”

Redescription of Atopospira galeata (Kahl, 1927) nov. comb. and A. violacea (Kahl, 1926) nov. comb. with redefinition of Atopospira Jankowski, 1964 nov. stat. and Brachonella Jankowski, 1964 (Ciliophora, Armophorida)

“…The distances between these Metopus species and B. spiralis range from 9.9-10.9%. Phylogenetic studies at the suprageneric level support a sister group relationship to the Litostomatea (Paiva et al 2013;Vd'ačný et al 2010). …”

“…Study of the Armophorida (i.e. caenomorphids and metopids) and its relationship to other orders is further hampered by the lack of corresponding morphologic data for most of the taxa with available gene sequences (Paiva et al 2013). Consequently, the taxonomy and the phylogeny of the metopids remains unresolved and in need of much broader taxon sampling.…”

A Huge Diversity of Metopids (Ciliophora, Armophorea) in Soil from the Murray River Floodplain, Australia. II. Morphology and Morphogenesis of Lepidometopus platycephalus nov. gen., nov. spec.

“…The armophorid family Metopidae Kahl, 1927 is consistently depicted as paraphyletic since it includes the monophyletic order Clevelandellida. The "Metopidae + Clevelandellida" assemblage is very likely related to the class Litostomatea (Vďačný et al 2010;Lynn and Wright 2013;Paiva et al 2013;Bourland et al , 2017da Silva-Neto et al 2015;Li et al 2016Li et al , 2017. On the other hand, the armophorid family Caenomorphidae Poche, 1913 could be a sister group of the "Metopidae + Clevelandellida" cluster or, more likely, could have diverged at the base of the Spirotrichea or the Intramacronucleata (Paiva et al 2013).…”

“…The "Metopidae + Clevelandellida" assemblage is very likely related to the class Litostomatea (Vďačný et al 2010;Lynn and Wright 2013;Paiva et al 2013;Bourland et al , 2017da Silva-Neto et al 2015;Li et al 2016Li et al , 2017. On the other hand, the armophorid family Caenomorphidae Poche, 1913 could be a sister group of the "Metopidae + Clevelandellida" cluster or, more likely, could have diverged at the base of the Spirotrichea or the Intramacronucleata (Paiva et al 2013). Thus, the class Armophorea is very likely non-monophyletic with caenomorphids not being closely related to metopids + clevelandellids within the "SAL" (Spirotrichea + Armophorea + Litostomatea) supercluster recognized from extensive molecular datasets (Gentekaki et al 2014(Gentekaki et al , 2017Gao et al 2016).…”