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FIGURE 10. Rhabdopleura decipula n in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 10. Rhabdopleura decipula n. sp., A, C, D, holotype 162592; B, E, paratype 3 NIWA 162591; F, paratype 4 NIWA 158517; G‒K, paratype 2 NIWA 161213. A, broken-tipped erect tube. B, distal end of young erect tube. C, D, subdistal and middle parts of same fully formed erect tube. E, F, parts of creeping tubes with some point-to-point suture zigzags highlighted. G, a prosicula (ps) and metasicula (ms); H‒K, reflected-light (H, I) and SEM (J, K) images of new colonies, with numbers indicating the inferred budding sequence (subsequent development seems to vary) of creeping tubes; the metasicula produces one or two metasiculae while one side of the prosicula is internally partitioned off to produce both a backwards-directed tube and an opposing creeping tube. Black stolons occur in H and a zooid in I. Scale bars: A, E‒H, 200 μm; B, 100 μm; C, D, K, 50 μm; I, J, 400 μm.

FIGURE 7. Rhabdopleura chathamica n in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 7. Rhabdopleura chathamica n. sp., A‒C, F, paratype 90265; D, E, holotype 161214: A, part of colony showing three blind side branches, the proximal part of which is adherent; only one ringed erect tube (et) remains. B, close-up of middle side branch in A; note part of the pectocaulus/black stolon (bs) seen through a tear in the cuticle. C, the longest zooid seen, somewhat fouled and partly twisted in profile. D, non-fouled part of another erect tube showing well-developed fusellar collars. E, fusellar sutures on surface of creeping tube, with some point-to-point suture zigzags highlighted. F, close-up of fusellar sutures seen on adherent tube in B. Scale bars: A, 1 mm; B, 300 μm; C, F, 100 μm; D, 50 μm; E, 200 μm.

FIGURE 5 in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 5. Original illustrations of three described species of Rhabdopleura characterized by direct-frontal inception of ringed erect tubes (A‒C). Erect-tube inception in R. compacta (D‒F) appears to be a form of indirect erect-tube inception. Note that the direction of zooid budding is the same in A to C. A, Rhabdopleura mirabilis (from Sars 1872, pl. 1, fig. 5). B, Rhabdopleura annulata (from Norman 1921, fig. 4). C, Rhabdopleura recondita (after Beli et al. 2018, fig. 2C). D‒F, Rhabdopleura compacta (respectively after Hincks 1880, pl. 72, fig. 8; Stebbing 1970b, fig. 1; Stebbing 1970a, fig. 3).

FIGURE 6. Rhabdopleura grimaldii Jullien, 1890 in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 6. Rhabdopleura grimaldii Jullien, 1890 (A‒D, syntype MNHN-IB-2014-386) and R. manubialis Jullien & Calvet, 1903 (E, syntype MNHN-IB-2014-387). A, B, oblique views of two erect ringed tubes. C, adherent proximal part of a side branch (apsb), with a tapering pectocaulus (tp) (its side walls appearing as converging brown lines) and the broken base of an erect tube (bbet). D, similar to C, but also showing the creeping tube (ct) from which the broader side branch originated; note the faint outlines of oblique sutures on the creeping tube and side branch. E, erect ringed tube. Scale bars: A, B, 100 μm; C‒E, 200 μm. Images cropped from photos supplied by Pierre Lozuet, MNHN, Paris.

FIGURE 2. Interpretative images illustrating morphological terms and measured characters. A in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 2. Interpretative images illustrating morphological terms and measured characters. A, part of creeping tube (ct) of an unidentified Rhabdopleura (NIWA 158518) from Kermadec Ridge, with flat lateral margin (flm), faint oblique fusellar sutures and two ringed erect tubes (et) produced directly from the frontal surface of a creeping tube. B, distal end of an erect tube of Rhabdopleura francesca n. sp. (NIWA 158157), showing a vertical series of ring-like fuselli (f), the rim of each comprising a curled fusellar collar (fc). Tube diameter (td) is measured between fusellar collars; fusellus height (fh) is the distance between the bases of a pair of fusellar collars. C, transmitted-light image of part of a principal ('creeping') tube of R. emancipata n. sp. (NIWA 161211) showing a young zooid with contracted arm tentacles (at), stomach (st), rectum (r) and cephalic shield (cs), part of which is concealed by the reddish-brown stolon (black stolon or pectocaulus). D, aperture of an erect tube of R. francesca n. sp.; note the smooth-surfaced interior devoid of vertical fusellar fibrils. E, part of a creeping tube of an unidentified Rhabdopleura (NIWA 90267) from Cavalli Seamount with frontal fusellar sutures (fs, two arrowed). The white lines show the zigzag (zz) portion of the sutures (note the proximalwards shift to the left), with zigzags rendered as straight lines between points of intersection, regardless of suture curvature, to obtain measured angles (one example shown). F, close-up of part of R. francesca n. sp. (NIWA 158157) showing chains of dark 'dormant buds' (db) lying upon short stretches of the black stolon (bs); walls of enveloping creeping tubes almost invisible in image.

FIGURE 1 in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 1. Map showing the localities of four new Rhabdopleura taxa from New Zealand. From north to south these are R. emancipata n. sp., R. francesca n. sp., R. chathamica n. sp. and R. decipula n. sp. The boundary of the Extended Continental Shelf is shown surrounding New Zealand. The grey contour lines show the 1000 m depth interval. The map was generated using ArcGIS Pro.

FIGURE 8. Rhabdopleura francesca n in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 8. Rhabdopleura francesca n. sp., A‒E, holotype NIWA 158157; F‒H, paratype NIWA 162577: A, complete erect tube 2.5 mm long. B, holotype, possibly comprising more than one colony, on broken scallop shell. C, close-up of B showing that the black tubarium tracery in A is accentuated by continuous series of what look like dormant buds lying along black stolons. D, section of tube bracketed in A. E, apertural end of another erect tube. F, black stolon emergent from a 'dormant body' in part of a creeping tube. G, H, variations in creeping-tube width and fusellar patterning, the latter typically weak and thinly developed throughout colony; some point-to-point suture zigzags highlighted. Scale bars: A, 1 mm; B, 2 cm; C, 3 mm; D‒F, 100 μm; g, h, 200 μm.

FIGURE 13 in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 13. Epibionts of Rhabdopleura emancipata n. sp.: A, at top, an ancestrula of Chaperia sp. (Bryozoa) and, at bottom, a juvenile of the homotrematid foraminiferan Sporadotrema cylindricum. B, Chaperiopsis n. sp. (Bryozoa). C, Celleporina n. sp. (Bryozoa). D, annelid tube (at) draped along a principal tube. E, Galeopsis brevissimus (Bryozoa). F, units of a chain-like unidentified epibiont on a principal tube. G, Strongylopora gracilis (Bryozoa). H, Microtylostylifer n. sp. (Porifera) at left and Tubulipora sp. (Bryozoa) at right. R = Rhabdopleura host. Scale bars: A, D‒G, 500 μm; B, C, H, 1 mm.

FIGURE 3 in Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa

FIGURE 3. Maximum likelihood phylogeny for Rhabdopleura reconstructed on: A, concatenated 16S+18S rRNA genes; B, 13 mitochondrial protein-coding genes. Numbers adjacent to nodes represent bootstrap support (≥ 50) /posterior probability (≥0.8) values.

opencc-by-4.0Mar 2024View details →

Supplementary material of article "Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control"

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opencc-by-4.0Mar 2024View details →

Supplementary Information: Multimodal binding and inhibition of bacterial ribosomes by the 2 antimicrobial peptides Api137 and Api88

<div> <div>This dataset contains important data files for the MD simulation that are part of this publication.</div> <div> </div> <div>The "simulations" directory contains Gromacs parameter files (.mdp) and the run input files (.tpr) as well as the final coordinate files (.gro) of each individual production simulation.</div> <div> </div> <div>The directory "figure3" contains the raw data used to create Figure 3 in the manuscript.</div> <div> </div> <div>The subdirectory "a" contains the data for the PCA projection plot in subfigure 3a. It includes projections of the simulation ensembles of Api88 conformation I-III on to the two dominant conformational modes (.xvg) and the respective extreme conformations (.pdb). The projections of the three initial models and the optimized structure set are also included.</div> <div> </div> <div>Subdirectory "b" contains a numpy array (.npy) with the data for the correlation heatmap in subfigure 3b.</div> <div> </div> <div>Subdirectory "c" contains the results of several correlation-optimization searches. Each directory "N#_maps", where # is to be replaced by the number of structures in the set, contains the search results for N correlation-optimized structures in the Api88 trajectories in the form of a pickled python dictionary (state.pkl). The dictionary has the following keys:</div> <ul> <li>used: Already used sets of MD structures (frozenset)</li> <li>selection: Structure set selected in the last iteration (set)</li> <li>weights: weights of each structure in the selected structure set (numpy array)</li> <li>iteration: Counter of the last iteration (int)</li> </ul> <div> </div> <div>The directory "supplentary_figure_correlation_time" contains the data for a plot of the optimized correlation coefficient as a function of simulation time. The results of the optimization algorithms (as pickled python objects) are included in the subdirectories with the associated trajectory length as a name.</div> </div> <p> </p>

dryad32/100

Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

<p><span>This study aimed to reveal the evolutionary timescale and processes underlying the diversity of <em>Rubus</em> in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, <em>R. chamaemorus</em>, <em>R. pedatus</em>, <em>R. vernus</em>, <em>R. pseudojaponicus</em>, and <em>R. ikenoensis</em>, were found to belong to anciently diverged lineages; in particular, <em>R. ikenoensis</em> formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. <em>Malachobatus</em>, <em>Chamaebatus</em>, and sects. <em>Pungentes</em>, <em>Idaeanthi</em>, and <em>Parvifolii</em> (subg. <em>Idaeobatus</em>), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, <em>R. sieboldii</em> has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. <em>Microphylli</em>, <em>Corchorifolii</em>, <em>Peltati</em>, and <em>Rosifolii</em> (subg. <em>Idaeobatus</em>), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, <em>R. sumatranus</em>, <em>R. peltatus</em>, <em>R. corchorifolius</em>, and <em>R. chingii</em>, was incongruent among gene trees. At the lower taxonomic levels, <em>R. illecebrosus</em>, <em>R. grayanus</em>, and the thornless species of sect. <em>Microphylli</em> showed earlier divergence.</span></p>

opencc-zeroAug 2022View details →

Supplementary material 4 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579

SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment with the SRP RNA sequences of Dumesic et al. (2015; Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum) aligned to our newly generated ITS sequences of Russula and Lactarius.

Supplementary material 3 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579

ITS/SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment comprising the 63 public ITS1 sequences with SRP RNA found in them, the three newly generated sequences, and the SRP RNA sequences from Dumesic et al. (2015) (Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum).

Supplementary material 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140

Full information and metadata about the genomic and metagenomic samples : Explanation note: Detailed information about metadata, DNA quality and genomic/metagenomic results of fruit-body and EcM root tip samples.

Supplementary material 2 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579

ITS multiple sequence alignment : Explanation note: A multiple sequence alignment in the NEXUS format (Maddison et al. 1997) comprising all 63 matching ITS sequences, plus the three newly generated ones (KU356730, KU356731, and KU356732). The alignment was produced in MAFFT without manual adjustment (Katoh and Standley 2013). The alignment is composed of partial nSSU (bases 1-34 in the alignment), the full ITS1 (bases 35-678), the full 5.8S (bases 679-838), the full ITS2 (bases 839-1395), and partial nLSU (bases 1396-end). The SRP RNA occupies position 203-474 in the alignment. The alignment is provided for overview purposes only; the two-order nature of the taxa (Boletales and Russulales) coupled with the high variability of the ITS region jointly mean that the alignment will not be suited for phylogenetic inference.

Supplementary material 1 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579

Output from cmsearch and primers used : Explanation note: A) The output from cmsearch showing all 63 relevant matches to the three ectomycorrhizal lineages. B) Detail of the primers used to re-amplify the specimens.

opennotspecifiedFeb 2015View details →

Fig. 3 in A phylogeny of Sericini with particular reference to Chinese species using mitochondrial and ribosomal DNA (Coleoptera: Scarabaeidae)

Fig. 3 Projections of phylogenetic relationships of selected Sericina clades into geographical space, illustrating the spatial within clade divergence between Himalayan and Chinese lowland species. a Sericina subclade 2 (Fig. 2), the North American clade is not shown, b detail of

opennotspecifiedNov 2023View details →

Figure 5 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 5. Phylogenetic relations of the ITS1–5.8S rDNA–ITS2–LSU rDNA sequences of Opalinida by the maximum likelihood (ML) method. The numbers at the nodes represent* respectively* the bootstrap support as computed from 1000 replicates for ML and maximum parsimony methods* and the posterior probability values of the Bayesian analysis. The tree is rooted considering the Protoopalina sequences at the basal position according to the results obtained in the phylogenetic analysis of the SSU rDNA sequences. New sequences are noted in bold.