Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea)
[Display omitted] •New sequencing of 27 species and curation of all GenBank sequences for three rDNA loci.•Concatenated phylogeny with 18 families and updated classification with 23 families.•Favella forms a distinct family and Tintinnopsis is spread among 11 lineages.•A previously-unknown environme...
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| Published in: | Molecular phylogenetics and evolution Vol. 112; pp. 12 - 22 |
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| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
United States
Elsevier Inc
01-07-2017
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| Subjects: | |
| Online Access: | Get full text |
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| Summary: | [Display omitted]
•New sequencing of 27 species and curation of all GenBank sequences for three rDNA loci.•Concatenated phylogeny with 18 families and updated classification with 23 families.•Favella forms a distinct family and Tintinnopsis is spread among 11 lineages.•A previously-unknown environmental clade matches Leegaardiellidae.•Prevalence of uncharacterized and cryptic diversity in aloricates.
Ciliated protists in the subclasses Choreotrichia and Oligotrichia are major components of marine plankton. Despite their ecological relevance, there are uncertainties in their systematics and diversity. We retrieved and curated all the GenBank ribosomal DNA (rDNA) sequences from these groups, which were analyzed in two ways. The first approach was based on morphologically-identified sequences (including those of two families and six genera newly studied here by single-cell sequencing), and aimed at improving phylogenetic inferences using concatenated sequences of three rDNA loci. Based on phylogenetic and morphological support, we update the taxonomic classification of these subclasses into 23 families, including the re-established Favellidae. We also propose an informal naming system for incertae sedis taxa, namely Tintinnopsis and five related genera that are spread among eleven lineages. The second approach included unidentified environmental sequences, and was used to explore potentially novel diversity in these subclasses. Our results support high proportions of both synonyms in tintinnids and uncharacterized taxa in choreotrichids and oligotrichs. One previously unidentified, environmental clade is here linked to our new Leegaardiellidae sequences. Our curation of almost 4000 rDNA sequences exemplifies known issues of public repositories, and suggests caution in both the use and contribution to these unique resources for evolutionary and diversity studies. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1055-7903 1095-9513 |
| DOI: | 10.1016/j.ympev.2017.03.010 |