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Figure 3 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 3. Maximum-likelihood tree under an HKY85+I+G model (–logL = 25513.945, s/v ratio = 1382, pinvar = 0.189, gamma = 0.463).
Figure 2 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 2. Strict consensus tree of 22 most parsimonious trees using all alignment positions of the 18S rRNA data set. Bootstrap values (above branches) refer to 1000 replications, maximum-likelihood puzzling values (below branches; values lower than 30 not given) refer to 100 000 puzzling steps. A, subtree showing the position of Anomalodesmata among the Heterodonta. B, subtree of the Anomalodesmata. Pha., Pharidae; Ven., Veneridae. Asterisks mark species of the polyphyletic Myoida. Arrowheads indicate the anomalodesmatan nodes collapsing when 506 positions of uncertain alignment in the
Figure 1 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 1. Single most parsimonious tree resulting from the analysis of the entire morphological data set of Harper et al. (2000). Asterisks mark taxa not available for the present study. The Euciroidae as recognized by Poutiers & Bernard (1995) was not separated from the Verticordiidae.
Figure 1 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 1. Phylogenetic trees derived from the DNA/DNA hybridization analysis. A and B: Consensus trees resulting from the bootstrap analysis of delta-Tm (A) and delta-mode (B) 12*12 matrices. BP values are indicated when different from 100%. The lengths of the branches correspond to one tree arbitrarily selected among those of the consensus. C and D: Average consensus trees resulting from the weighted jacknife procedure for delta-Tm (C) and delta-mode (D) 13*13 matrices. The thin lines represent nodes that were not present in maximum and minimum consensus trees or that are not supported for all combinations of single deletion analysis. uUnlabelled taxa. The names in bold indicate the differences that can be observed between the two distance estimators (Tm, Mode).
Figure 4 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 4. Fifty per cent majority rule consensus of 52 trees derived from the morphological analysis. Each mostparsimonious tree is 54 steps long, and has a Consistency Index of 0.52, a Retention Index of 0.72, and a Rescaled Consistency Index of 0.37. Values given below the branches represent the percentage of trees containing the specified clades.
Figure 3. Synthetic tree derived from the 12S in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 3. Synthetic tree derived from the 12S rRNA datasets with the inclusion of all substitutions (TV + TI). The thin lines indicate nodes that are not robustly supported by all kinds of analysis. The robustness of the different nodes are indicated as follows: [BP(BPweighted analysis)/BSI (Parsimony)]/[BP(NJ)/Reliability Percentage (ML)].
Microbial 16S rRNA gene (DNA) and transcripts (cDNA) along a boreal soil-freshwater-estuary continuum
<p>This repository stores the processed files of the 16S rRNA sequencing reads (DNA and cDNA) of the La Romaine project, which were processed through the DADA2 pipeline. Files are '.rds' files and/or '.csv' files readable by the open statistical software R. The project is part of the Industrial Research Chair in Carbon Biogeochemistry in Boreal Aquatic systems (CarBBAS Chair) led by Paul A. del Giorgio.</p> <p>Samples were pooled by plate ID and season to be processed by DADA2. The number before each '*_seqtab.rds' file corresponds to a pool. ID details are in "splitdf_new.rds".</p> <p>Raw sequences can be found on SRA under the Bioproject number: PRJNA693020. Intermediate processing files are stored here. And scripts are available on <a href="https://github.com/CarBBAS/Paper_Stadler-delGiorgio_ISMEJ_2021">Github</a>.</p> <p>Files are being uploaded as manuscripts are published.</p> <p>Currently available files:</p> <ul> <li>2015-2017: 16S rRNA gene and transcripts (DNA and cDNA) in spring, summer, autumn (shallow sequencing) <ul> <li>Part of the manuscript: "Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network". The ISME Journal. 2021.</li> </ul> </li> </ul>
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S in New record and new species of Laubierpholoe Pettibone, 1992 (Annelida, Sigalionidae) from the soft bottom of submarine caves near Marseille (Mediterranean Sea) with discussion on phylogeny and ecology of the genus
Fig. 6. Bayesian phylogenetic tree obtained with the 18S rRNA and 28S rRNA concatenated dataset showing position of Laubierpholoe massiliana Zhadan sp. nov. within Sigalionidae Kinberg, 1856. Posterior probabilities and bootstrap values are shown for each medium supported node.
Figure 2 in Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percicthyidae: Gadopsis) from south-eastern Australia
Figure 2. Phylogenetic trees, using the PAUP software package (Swofford, 1998). A, Maximum parsimony, using a full exhaustive search with 1000 bootstrap replicates. B, Distance analysis, using the neighbour-joining option, bootstrap replicates set at 1000. C, Maximum likelihood, using the Tamura-Nei model with 100 bootstrap replicates.
16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces
<p>This file is intended as supplementary information for a forthcoming publication: 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in <em>Streptomyces</em>. </p>
Comparing bacterial microbiome composition of Xylocopa species across populations using PacBio 16S rRNA gene sequencing
Open the record for dataset details and reuse information.
A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences
Open the record for dataset details and reuse information.
Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon" - PART I
<p>Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon". See Supplementary Table 2 for associating each sample to its barcode.</p> <p>- FC1_1 includes data for the HM mock community from BEI resources and skin microbiome of the chin in dogs.</p> <p>- FC1_2 includes data for the dorsal skin samples</p> <p>- FC2 includes data for the Zymobiomics mock community and Staphylococcus pseudintermedius isolate</p> <p> </p> <p> </p>
Supplementary data (simulated metagenome set 2) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
Supplementary data (simulated metagenome set 3) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of closely related Bacteorides strains.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
16S rRNA sequences from Mediterranean Sparidae gut microbiome
<p><span>Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity in microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse and ancient group of vertebrate, have received little attention from the microbiome perspective and our understanding of its determinants is currently limited. In this study, we assessed the gut microbiome of 12 co-occurring species of teleost representing a large breadth of ecological diversity and originating from a single family (<i>i.e.</i> the Sparidae). We tested how host evolutionary history, diet composition and morphological traits are related to fish gut microbiome. Despite fish species having different microbiomes, there is no phylosymbiosis signal in this fish family, but gut length and diet had a strong influence on the microbiome. We revealed that the only species with a specialized herbivorous diet, <i>Sarpa salpa</i> had a 3.3 times longer gut than carnivorous species and such a long gut favor the presence of anaerobic bacteria typical of herbivorous gut microbiomes. Hence, dietary uniqueness is paired with both unique gut anatomy and unique microbiome.</span></p>
16S rRNA Sequence Data, Brazilian Coffee Soils
<p>16S sequencing data for DNA extracted from soils from Brazillian coffee farms. Sequenced on Illumina MiSeq with primers from Caporaso (2011, 2012).</p>
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 4. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI and 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 3. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using 16S rRNA sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
16S rRNA sequences from Siganidae (S. rivulatus and S. luridus) gut microbiome in their native (Red Sea) and invaded (Mediterranean Sea) ranges
<p><span><span><span>T</span><span>he microbiome </span><span>of i</span><span>nvasive species </span><span>is increasing</span><span>ly</span><span> seen as</span><span> </span><span>a potential</span><span> </span><span>key factor of </span><span>their ecological</span><span> </span><span>success, </span><span>and t</span><span>his </span><span>appears</span><span> particularly true in herbivorous </span><span>invaders</span><span> whose digestive abilities rely on the microb</span><span>es</span><span> hosted in their </span><span>gut</span><span>. </span><span>We</span><span> characterize</span><span>d</span><span> the</span><span> gut microbiome of two invasive herbivorous fishes </span><span>(</span><span><em>S</em></span><span><em>iganus</em></span><span><em> rivulatus </em></span><span>and </span><span><em>S</em></span><span><em>iganus</em></span><span><em> luridus</em></span><span>) </span><span>in their </span><span>native (Red Sea) and invaded (Levantine Sea and Northern Crete) range</span><span>s. </span><span>We </span><span>found</span> <span>that </span><span>gut bacterial communities </span><span>contain a higher taxonomic and phylogenetic diversity </span><span>while</span> <span>bec</span><span>o</span><span>m</span><span>ing</span><span> increasingly different </span><span>from the native microbiome </span><span>as the fishes move away from the native zone. </span><span>This </span><span>shift </span><span>resulted in </span><span>the </span><span>homogenization of the microbiome</span><span>s</span><span> between </span><span>individuals from the same species </span><span>as well as between the two </span><span>species. Firmicutes and Tenericutes reduced drastically in abundance </span><span>while </span><span>Proteobacteria and Bacteroidetes </span><span>became more dominant in both species</span><span>. </span><span>This led to a modification of the functional potential of the gut microbiome associated with the metabolism of short-chanin fatty acids that also became more homogeneous in the invaded range. </span><span>Altogether, our results suggest that the plasticity of the gut microbiome in Siganidae could be a key factor underlying their ecological success </span><span>in </span><span>Mediterranean ecosystems</span><span>.</span></span></span></p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.