scholarly journals Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

2021 ◽  
Vol 5 ◽  
Author(s):  
Ľubomír Rajter ◽  
Micah Dunthorn
Keyword(s):  
Species Richness ◽  
Ssu Rdna ◽  
Phylogenetic Position ◽  
Phylogenetic Placement ◽  
Rdna Sequences ◽  
Ecological Parameters ◽  
Taxonomic Assignments

Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

scholarly journals Erratum to: Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences

2013 ◽  
Vol 12 (3) ◽  
pp. 615-615
Author(s):  
Daria A. Erastova ◽  
Mikhail V. Okun ◽  
Yuri K. Novozhilov ◽  
Martin Schnittler
Keyword(s):  
Ssu Rdna ◽  
Phylogenetic Position ◽  
Rdna Sequences

Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences

2013 ◽  
Vol 12 (3) ◽  
pp. 599-608 ◽  
Author(s):  
Daria A. Erastova ◽  
Mikhail V. Okun ◽  
Anna Maria Fiore-Donno ◽  
Yuri K. Novozhilov ◽  
Martin Schnittler
Keyword(s):  
Ssu Rdna ◽  
Phylogenetic Position ◽  
Rdna Sequences

Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 680-688 ◽  
Author(s):  
Xinpeng Fan ◽  
Saleh A. Al-Farraj ◽  
Feng Gao ◽  
Fukang Gu
Keyword(s):  
Phylogenetic Analyses ◽  
Eastern China ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Contractile Vacuole ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
North West ◽  
Rdna Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

scholarly journals Gastronautidae Deroux, 1994 and Trithigmostoma Jankowski, 1967: Evolutionary Links Among Cyrtophorian Ciliates (Protista, Ciliophora, and Phyllopharyngea)

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhishuai Qu ◽  
Hongbo Pan ◽  
Congcong Wang ◽  
Honggang Ma ◽  
Thorsten Stoeck ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Ssu Rdna ◽  
Phylogenetic Position ◽  
Special Position ◽  
Morphological Taxonomy ◽  
Rdna Sequences ◽  
Closed Circle ◽  
The Family ◽  
Morphological Research

Studies on cyrtophorian ciliates (Cyrtophoria) have accumulated much knowledge on morphological taxonomy and molecular phylogeny, and the general classification and phylogenetic relationships of most families have thereby been revealed. However, the phylogenetic position of the family Gastronautidae Deroux, 1994 remains uncertain. This is due to the presence of specialized characteristics (in particular a circumoral kinety in a closed circle), and most importantly, the lack of molecular data of this family. In addition, TrithigmostomaJankowski, 1967 holds a special position among genera in Chilodonellidae Deroux, 1976 due to its divergent characteristics. In the present work, we studied a new gastronautid, Gastronauta paraloisi sp. n., and three populations of Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967, using integrative methods. Species identifications were confirmed by morphological research. We also obtained SSU rDNA sequences, which included the first available sequence of Gastronautidae. The following SSU rDNA-inferred phylogenetic analyses showed that the establishment of the family Gastronautidae is necessary, and Gastronautidae and Trithigmostoma may represent intermediate evolutionary links in the order Chlamydodontida.

Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species

Zootaxa ◽  
2010 ◽  
Vol 2427 (1) ◽  
pp. 55 ◽  
Author(s):  
DOROTA L. PORAZINSKA ◽  
ROBIN M. GIBLIN-DAVIS ◽  
WAY SUNG ◽  
W. KELLEY THOMAS
Keyword(s):  
Species Richness ◽  
Relative Abundance ◽  
Environmental Samples ◽  
Tropical Rainforest ◽  
Species Recognition ◽  
Nematode Species ◽  
Ssu Rdna ◽  
Actual Number ◽  
Rdna Sequences ◽  
Specific Species

DNA-sequence-based approaches such as single nematode PCR and sequencing have been successfully used in nematode species diagnostics. Here, we use SSU rDNA sequences generated from an artificially-assembled community of nematodes of known identity and relative abundance to assess a relationship between nematode species and operationally clustered taxonomic units (OCTUs). OCTUs that formed at 95% similarity underestimated species richness by ca 30%, and all expected species were recovered only at 99% OCTU similarity. Although the number of OCTUs formed at 99% similarity was considerably higher than the actual number of nematode species, a pattern of the distribution of OCTUs within each species allowed an assignment of OCTUs to specific species. The pattern was highly predictable and helped to discern rather than obscure species recognition. The patterns and parameters that emerged from the control nematode dataset were then used to test our approach on environmental samples of nematodes obtained from a tropical rainforest in Costa Rica.

Paepalanthus fabianeae (Eriocaulaceae): A New Microendemic Species from a Morphologically Coherent Clade

2020 ◽  
Vol 45 (4) ◽  
pp. 794-801
Author(s):  
Caroline Oliveira Andrino ◽  
Marcelo Fragomeni Simon ◽  
Jair Eustáquio Quintino Faria ◽  
André Luiz da Costa Moreira ◽  
Paulo Takeo Sano
Keyword(s):  
New Species ◽  
Iucn Red List ◽  
Phylogenetic Position ◽  
Similar Species ◽  
Infrageneric Classification ◽  
Espinhaço Range ◽  
Nuclear Its ◽  
Two Populations

Abstract—We describe and illustrate Paepalanthus fabianeae, a new species of Eriocaulaceae from the central portion of the Espinhaço Range in Minas Gerais, Brazil. Previous phylogenetic evidence based on analyses of nuclear (ITS and ETS) and plastid (trnL-trnF and psba-trnH) sequences revealed P. fabianeae as belonging to a strongly supported and morphologically coherent clade containing five other species, all of them microendemic, restricted to the Espinhaço range. Due to the infrageneric classification of Paepalanthus being highly artificial, we preferred not assigning P. fabianeae to any infrageneric group. Paepalanthus fabianeae is known from two populations growing in campos rupestres (highland rocky fields) in the meridional Espinhaço Range. The species is characterized by pseudodichotomously branched stems, small, linear, recurved, and reflexed leaves, urceolate capitula, and bifid stigmas. Illustrations, photos, the phylogenetic position, and a detailed description, as well as comments on habitat, morphology, and affinities with similar species are provided. The restricted area of occurrence allied with threats to the quality of the habitat, mainly due to quartzite mining, justifies the preliminary classification of the new species in the Critically Endangered (CR) category using the guidelines and criteria of the IUCN Red List.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

Panagrellus levitatus sp. n. (Rhabditida: Panagrolaimidae), a nematode suppressing Drosophila melanogaster in laboratory cultures

Nematology ◽  
2018 ◽  
Vol 20 (3) ◽  
pp. 285-297 ◽  
Author(s):  
Elena Ivanova ◽  
Ksenia Perfilieva ◽  
Sergei Spiridonov
Keyword(s):  
Drosophila Melanogaster ◽  
New Species ◽  
Nematode Species ◽  
Laboratory Culture ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Red Palm Weevil ◽  
Rdna Sequences ◽  
Mass Reproduction ◽  
First Time

A new nematode species recovered from the laboratory culture ofDrosophila melanogasteris described and illustrated. The mass reproduction ofPanagrellus levitatussp. n. in the fly culture occurred several times and resulted in a significant reduction of the fly population. Nematode outbreaks happened after the introduction ofD. melanogasterto the culture from natural sources. The new species is morphologically similar toP. ulmi. Partial LSU rDNA and SSU rDNA sequences were obtained and subjected to phylogenetic analysis that demonstrated the affinity of the new species withPanagrellussp. ‘MC2014’ from a red palm weevil. For the first time, the dauer juveniles ofPanagrelluswere described.

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