Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium

Abstract

Little is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees were reconstructed with SSU rRNA gene sequences by using four different methods (Bayesian analysis, maximum-likelihood, neighbour-joining and maximum-parsimony) and had a consistent branching pattern. Members of the genera Vorticella (except V. microstoma) and Carchesium formed a clearly defined, well supported clade that was divergent from the clade comprising members of the genera Pseudovorticella and Epicarchesium, suggesting that the differences in the silverline system (transverse vs reticulate) among vorticellids may be the result of genuine evolutionary divergence. Members of the newly established genus Apocarchesium clustered within the family Vorticellidae basal to the clade containing members of the genera Pseudovorticella and Epicarchesium and were distinct from members of the genus Carchesium, supporting the validity of Apocarchesium as a novel genus. Additional phylogenetic analyses of 21 strains representing seven genera from the families Vorticellidae and Zoothamniidae were performed with single datasets (ITS1–5.8S–ITS2, ITS2 alone) and combined datasets (SSU rRNA+ITS1–5.8S–ITS2, SSU rRNA+ITS2) to explore further the phylogenetic relationship between the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium, using characteristics not included in previous analyses. The phylogenetic trees reconstructed with combined datasets were more robust and therefore more reliable than those based on single datasets and supported the results of trees based on SSU rRNA sequences.

Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic

“…Further analyses including more members of Peniculia will likely resolve the position of this taxon. Another very frequent relationship is that of the Hymenostomatia as sister taxon to the Sessilida (Li et al, 2008;Sun et al, 2011;Utz et al, 2010;Zhan et al, 2009). In contrast, our analyses show that Hymenostomatia is sister to Scuticociliatia, confirming the phylogenomic analyses of Feng et al (2015).…”

“…Sequences of the 18S rRNA have confirmed the monophyly of each of the two orders. However, the monophyly of the subclass has been rigorously debated: numerous molecular studies throughout the years have failed to recover monophyly (Gong et al, 2006;Li et al, 2008;Miao et al, 2001Miao et al, , 2004Sun et al, 2011;Williams and Clamp, 2007;Utz and Eizirik, 2007;Zhan et al, 2009). Zhan et al (2012) critically evaluated various methods of alignment and removal of ambiguous positions.…”

An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group

“…Morphological variation within species can overlap with variation among species [9], thus, identification using molecular characters is an important alternative for this genus. Information from the ITS1-5.8S-ITS2 region, especially ITS2, has proved to be a source of strong molecular markers for resolving phylogenetic relationships among sessile peritrichs at different taxonomic levels [13,15]. In this work, therefore, we provide a new evaluation of the phylogenetic relationship of Vorticella species using both ITS1-5.8S-ITS2 and ITS2 sequences.…”

“…Moreover, genetic distances between SSU rRNA sequences of morphospecies were small [12], and this high degree of conservation makes it difficult to resolve phylogenetic relationships within the genus and make a clear discrimination between morphospecies. Furthermore, the long-standing assumption that the family Vorticellidae was a distinct, stable taxon and that Vorticella was equally distinct and stable at the generic level was upset by convincing molecular evidence [12][13][14][15]. Given these important systematic uncertainties and the low resolution at the infrageneric level of phylogenies based on SSU rRNA sequences, molecular phylogenies of Vorticella that include a broader sample of taxa and additional genes are desirable.…”

Two Newly Recorded Vorticellid Species (Ciliophora, Oligohymenophorea, Peritrichia) from Jindo Island with Other Populations in Korea

“…The family Vorticellidae Ehrenberg, 1838 is one of highly diverse taxa within the group Peritrichia and is characterized by zooid, contractible, and helically twisted spasmoneme (Ehrenberg, 1838;Corliss, 1979;Warren, 1986;Lynn, 2008;Sun et al, 2011). Carchesium Ehrenberg, 1831 andVorticella Linnaeus, 1767 are members of Vorticellidae and commonly found in eutrophic freshwater environments.…”