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Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea).

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Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea).

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Discrimination of closely related species in tintinnid ciliates: new insights on crypticity and polymorphism in the genus Helicostomella.

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EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so, and develops reliable reference databases across the diversity of microbial eukaryotes.
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Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods.

The findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of py rosequencing processing for using this method to address ecological questions.
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Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria.

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EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

The approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date, which is superior to the current SILVA database in classifying HTS reads from a global marine survey.
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Phylogeny of the Order Tintinnida (Ciliophora, Spirotrichea) Inferred from Small‐ and Large‐Subunit rRNA Genes

This study contributes to tintinnid phylogenetic reconstruction by increasing both the number of species and the range of genetic markers analyzed.
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Diversity and Biogeography as Revealed by Morphologies and DNA Sequences

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Unexpected biodiversity of ciliates in marine samples from below the photic zone

High‐throughput sequencing is used to analyse the spatial distribution of planktonic ciliate diversity from shallow waters to beyond the continental shelf along a 163 km transect off the coast of New England, USA, and it is observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors.
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