Molecular phylogeny ofPseudokeronopsis(Protozoa, Ciliophora, Urostylida), with reconsideration of three closely related species at inter- and intra-specific levels inferred from the small subunit ribosomal RNA gene and the ITS1-5.8S-ITS2 region sequences

Genetic Diversity and Phylogeny of the Genus Euplotes (Protozoa, Ciliophora) Revealed by the Mitochondrial CO1 and Nuclear Ribosomal Genes

Nuclear ribosomal and mitochondrial genes have been utilized individually or in combination to identify known species and discriminate closely related species. However, compared with metazoans, genetic diversity within the ciliate order Euplotida is poorly known. The aim of this study is to investigate how much nucleotide sequence divergence occurs within Euplotes. A total of 14 new gene sequences, comprising four SSU rDNA and 10 CO1 (including three species for the first time) were obtained. Phylogenetic analyses were carried out based on sequences of two DNA fragments from the same 27 isolates. We found that CO1 revealed a larger interspecific divergence than the SSU rRNA gene, thus demonstrating a higher resolution for separating congeners. Genetic distances differ significantly at the species level. Euplotes balteatus was revealed to have a large intraspecific variation at two loci, while E. vannus showed different levels of haplotype variability, which appeared as a polyphyletic cluster on the CO1 tree. These high genetic divergences suggest the presence of more cryptic species. By contrast, the CO1 gene showed low variability within E. raikovi, appearing as monophyletic clusters, which indicates that this species could be identified based on this gene. Conclusively, CO1 is a suitable marker for the study of genetic diversity within Euplotes, and increased taxon sampling gives an opportunity to screen relationships among members of this genus. Additionally, current data present no clear biogeographical pattern for Euplotes.

DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Phylogenetically distinct lineages may be hidden behind identical or highly similar morphologies. The phenomenon of morphological crypticity has been recently detected in symbiotic ciliates of the family Clevelandellidae, as multivariate and Fourier shape analyses failed to distinguish genetically distinct taxa. To address the question of species boundaries, the phylogenetic information contained in the rDNA cistron of clevelandellid ciliates, which had been isolated from the digestive tract of blaberid cockroaches, was studied using a multifaceted statistical approach. Multigene phylogenies revealed that the genus Clevelandella is paraphyletic containing members of the genus Paraclevelandia. To resolve the paraphyly of Clevelandella, two new genera, Anteclevelandella gen. nov. and Rhynchoclevelandella gen. nov., are proposed based on morphological synapomorphies and shared molecular characters. Multigene analyses and Bayesian species delimitation supported the existence of 13 distinct species within the family Clevelandellidae, eight of which represent new taxa. Moreover, two new Nyctotherus species were recognized within the clade that is sister to the Clevelandellidae. According to the present distance and network analyses, the first two domains of the 28S rRNA gene showed much higher power for species discrimination than the 18S rRNA gene and ITS region. Therefore, the former molecular marker was proposed to be a suitable group-specific barcode for the family Clevelandellidae.

Systematic Redefinition of the Hypotricha (Alveolata, Ciliophora) Based on Combined Analyses of Morphological and Molecular Characters

The systematics of Hypotricha is one of the most puzzling problems in ciliate biology, having spanned numerous conflicting hypotheses with unstable relationships at various levels in molecular trees, for which the constant addition of newly discovered species has only increased the confusion. The hypotrichs comprise a remarkable morphologically diversified group of ciliates, and the phylogenetic potential of morphological traits is generally recognized. However, such characters were rarely used in phylogenetic reconstructions, and congruence with molecular data never assessed from simultaneous analyses. To properly reconciliate morphological and molecular information, maximum-likelihood and parsimony analyses of 79 morphological characters and 18S rDNA sequences were performed for 130 ingroup terminals, broadly sampled to represent the known hypotrich diversity. As result, well-supported and relatively stable clades were recovered, based on which the redefined Hypotricha comprises at least six higher taxa: The "arcuseriids", Holostichida, Parabirojimida, and the "amphisiellids", plus the two large clades Kentrurostylida nov. tax. (Hispidotergida nov. tax. and Simplicitergida nov. tax.) and Diatirostomata nov. tax. ("bistichellids", "kahliellids", Gonostomatida and Dorsomarginalia [Postoralida nov. tax. and Uroleptida]). Each taxon was circumscribed by synapomorphies, of which most were homoplastic, as the natural history of hypotrichs is portrayed by an outstanding quantity of convergences and reversions.

Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene

Background

Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms.

Results

Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms.

Conclusions

The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.

Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea)

The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.

Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)

Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.

Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora)

Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

Evolution of the germline actin gene in hypotrichous ciliates: multiple nonscrambled IESs at extremely conserved locations in two urostylids

In hypotrichous ciliates, macronuclear chromosomes are gene-sized, and micronuclear genes contain short, noncoding internal eliminated segments (IESs) as well as macronuclear-destined segments (MDSs). In the present study, we characterized the complete macronuclear gene and two to three types of micronuclear actin genes of two urostylid species, i.e. Pseudokeronopsis rubra and Uroleptopsis citrina. Our results show that (1) the gain/loss of IES happens frequently in the subclass Hypotrichia (formerly Stichotrichia), and high fragmentation of germline genes does not imply for gene scrambling; and (2) the micronuclear actin gene is scrambled in the order Sporadotrichida but nonscrambled in the orders Urostylida and Stichotrichida, indicating the independent evolution of MIC-actin gene patterns in different orders of hypotrichs; (3) locations of MDS-IES junctions of micronuclear actin gene in coding regions are conserved among closely related species.

Three-gene based phylogeny of the Urostyloidea (Protista, Ciliophora, Hypotricha), with notes on classification of some core taxa

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36 new sequences for three genes are characterized from 20 species (12 genera) in the core group of Urostyloidea.

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More well-supported and reliable nodes are detected in the concatenated topologies.

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Multi-gene phylogenies and morphological features are discussed to improve the understanding of the evolution of urostyloids.

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A new genus Arcuseries (type A. petzi) is established to contain three distinctly deviating Anteholosticha species.

Classifications of the Urostyloidea were mainly based on morphology and morphogenesis. Since molecular phylogeny largely focused on limited sampling using mostly the one-gene information, the incongruence between morphological data and gene sequences have risen. In this work, the three-gene data (SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA) comprising 12 genera in the “core urostyloids” are sequenced, and the phylogenies based on these different markers are compared using maximum-likelihood and Bayesian algorithms and tested by unconstrained and constrained analyses. The molecular phylogeny supports the following conclusions: (1) the monophyly of the core group of Urostyloidea is well supported while the whole Urostyloidea is not monophyletic; (2) Thigmokeronopsis and Apokeronopsis are clearly separated from the pseudokeronopsids in analyses of all three gene markers, supporting their exclusion from the Pseudokeronopsidae and the inclusion in the Urostylidae; (3) Diaxonella and Apobakuella should be assigned to the Urostylidae; (4) Bergeriella, Monocoronella and Neourostylopsis flavicana share a most recent common ancestor; (5) all molecular trees support the transfer of Metaurostylopsis flavicana to the recently proposed genus Neourostylopsis; (6) all molecular phylogenies fail to separate the morphologically well-defined genera Uroleptopsis and Pseudokeronopsis; and (7) Arcuseries gen. nov. containing three distinctly deviating Anteholosticha species is established.

Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)

The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria+Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.

Evolution of the order Urostylida (Protozoa, Ciliophora): new hypotheses based on multi-gene information and identification of localized incongruence

Previous systematic arrangement on the ciliate order Urostylida was mainly based on morphological data and only about 20% taxa were analyzed using molecular phylogenetic analyses. In the present investigation, 22 newly sequenced species for which alpha-tubulin, SSU rRNA genes or ITS1-5.8S-ITS2 region were sampled, refer to all families within the order. Following conclusions could be drawn: (1) the order Urostylida is not monophyletic, but a core group is always present; (2) among the family Urostylidae, six of 10 sequenced genera are rejected belonging to this family; (3) the genus Epiclintes is confirmed belonging to its own taxon; (4) the family Pseudokeronopsidae undoubtedly belongs to the core portion of urostylids; however, some or most of its members should be transferred to the family Urostylidae; (5) Bergeriellidae is confirmed to be a valid family; (6) the distinction of the taxon Acaudalia is not supported; (7) the morphology-based genus Anteholosticha is extremely polyphyletic; (8) ITS2 secondary structures of Pseudoamphisiella and Psammomitra are rather different from other urostylids; (9) partition addition bootstrap alteration (PABA) result shows that bootstrap values usually tend to increase as more gene partitions are included.