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42 results for “toadfish”
Supplemental Results for Assembly, Annotation, and Analysis from HiFi reads of Gulf Toadfish Genome and Transcriptome fOpsBet2.1
<p>This repository contains gzipped tarballs of the results of the various assembly, annotation, and analysis steps performed during the assembly of the fOpsBet2.1 genome assembly for Opsanus beta at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science for the McDonald Toadfish Lab. These results are too numerous to include as supplemental data for a journal publication and so are available here for review. In this repository you will find results for:</p><p>Scripts:</p><p>-all bash and LSF scheduler job scripts used as part of the analysis, both exploratory and final. </p><p>QC:</p><p>-GenomeScope2 estimation of genome metrics from HiFi Reads</p><p>-QUAST genome statistics for each assembly step</p><p>-BUSCO completeness assessments for each assembly step </p><p>-inspector logs for polishing of initial assembly</p><p>-logs from Kraken2 contaminant screen</p><p>Assembly and Scaffolding:</p><p>-ntLINKS logs and intermediates for initial scaffolding</p><p>-ragtag logs and metrics for super-scaffolding to the ThaAma1.1 T. amazonica reference assembly</p><p>-mitoHIFI results for mitogenome assembly from HiFi reads, primary assembly, and purged alternate assembly</p><p>Annotation:</p><p>-PASA directory with full input and output for SQLite PASA assembly of transcriptome for gene predictors</p><p>-Results folder for Funannotate::annotate for gene models, annotations, and CDS/mRNA/protein fastas</p><p>-InterProSCan5 results for protein annotation used as input into Funannotate</p><p>-ghostKOALA KEGG assignment results for predicted proteins from funannotate results</p><p>Repetitive Elements:</p><p>-tidk telomere repeat analysis results</p><p>-TRAH satellite DNA analysis with subsequent analysis with HiCAT and StainedGlass</p><p>-RepeatModeler results for de novo TE prediction</p><p>-repclassifier results for TE curation</p><p>Comparative Analysis:</p><p>-OrthoFinder ortholog search for O. beta to several other vertebrates</p><p>-CAFE5 gene family expansion and contraction of Orthogroups from OrthoFinder results</p><p> </p>
Figure 2 in Use of tide pools as a spawning site by the bocon toadfish Amphichthys cryptocentrus (Batrachoidiformes: Batrachoididae), state of Maranhão, Brazil
Figure 2. - Amphychthys cryptocentrus larva (1.1 cm TL) caught in a tide pool on Panaquatira Beach, São José de Ribamar, State of Maranhão, Brazil. Photo: N.M. Piorski
Figure 1 in Use of tide pools as a spawning site by the bocon toadfish Amphichthys cryptocentrus (Batrachoidiformes: Batrachoididae), state of Maranhão, Brazil
Figure 1. - Adult male Amphychthys cryptocentrus (12.3 cm TL) caught in a tide pool on Panaquatira Beach, São José de Ribamar, state of Maranhão, Brazil. Photo: N.M. Piorski.
Data for: ToadFishFinder classifier model v4: A catalog of oyster toadfish (Opsanus tau) calls for machine learning
<p>This data repository contains labeled passive underwater acoustic data used to train and test the machine-learning model of Bohnenstiehl (in prep – 2023), <span>Automated cataloging of oyster toadfish (<em>Opsanus</em> <em>tau</em>) calls using template matching and machine learning</span>. The software accompanying this paper is known as ToadFishFinder, and the classifier model presented in the paper is v4. It consists of more than 10000 labeled toadfish and 10000 labeled other signals. Labeled spectrogram images are provided, along with pressure-corrected waveforms (micro-Pascals) sampled at 24 kHz. Each waveform sample is 1350 ms long. The center 850 ms of these waveform segments represent the portion of the signal used in training and testing the classifier model. Waveform data are provided in multiple formats: 1) MATLAB (.mat) files containing the 'boatwhistle' and 'other' waveforms stored in column format, and 2) individual .wav files, each containing a labeled waveform example. Codes are provided to demonstrate how these .wav files can be read into MATLAB and PYTHON. These labeled data can be used to re-train the ToadFishFinder model or develop alternative classifiers. </p>
Data for: ToadFishFinder classifier model v4: A catalog of oyster toadfish (Opsanus tau) calls for machine learning
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Fig. 4 in Acoustic communication in the Lusitanian toadfish, Halobatrachus didactylus: evidence for an unusual large vocal repertoire
Fig. 4. Long grunt trains (LGT) were significantly longer (A), were made up of more grunts (B), but had similar grunt periods (C) than grunt trains (GT). Grunts in LGT had similar duration (D) and dominant frequency (F), but had a higher number of pulses (E) than grunts in GT. Medians and quartiles are depicted. Mann–Whitney tests,, P, 0.001;, P, 0.01.
Fig. 3 in Acoustic communication in the Lusitanian toadfish, Halobatrachus didactylus: evidence for an unusual large vocal repertoire
Fig. 3. During the present study, nesting Lusitanian toadfish males emitted sounds that have not previously been described such as triple croaks (A), long grunt trains (B) and combinations of long grunt trains with other sound types (C). In (C) a long grunt train (thin line) combines with a grunt train (double line) that ends in a croak (thick line), which blends into a boatwhistle (dashed line), which is then followed by another long grunt train (thin line). Note that in (C), the LGT is hardly visible in the oscillogram due its much lower amplitude than the other sounds. Sonograms used a 30 Hz filter bandwidth.
Fig. 2 in Acoustic communication in the Lusitanian toadfish, Halobatrachus didactylus: evidence for an unusual large vocal repertoire
Fig. 2. Mean percentage of the different sound types emitted per hour by 16 nesting males during one week in the peak of the breeding season.
Tactic-specific antimicrobial activity suggests a parental care function for accessory glands in a marine toadfish
<p>Males of some species possess extra reproductive organs called accessory glands which are outgrowths of the testes or sperm duct. These organs have a well-established role in reproduction; however, they also appear to have other important functions that are less understood. Here we investigate the function of the highly complex accessory glands of a marine toadfish, <em>Porichthys notatus, </em>a fish with two reproductive male types: large care-providing 'guarder' males and small non-caring 'sneaker' males. While both male types have accessory glands, guarder male accessory glands are much larger relative to their body size. We show that accessory gland fluids strongly inhibit the growth of bacterial genera associated with unhealthy eggs and have no effect on the growth of strains isolated from healthy eggs. This antibacterial effect was particularly pronounced for extracts from guarder males. Furthermore, we demonstrate that both healthy and unhealthy plainfin midshipman eggs have diverse but distinct microbial communities that differ in their composition and abundance. The highly specific inhibitory capacity of accessory gland fluid on bacteria from unhealthy eggs was robust across a wide range of ecologically relevant temperatures and salinities. Collectively, these ecological and molecular observations suggest a care function for the accessory gland, mediated by antimicrobial agents.</p>
Data from: Wall structure and material properties cause viscous damping of swimbladder sounds in the oyster toadfish Opsanus tau
Despite rapid damping, fish swimbladders have been modelled as underwater resonant bubbles. Recent data suggest that swimbladders of sound-producing fishes use a forced rather than a resonant response to produce sound. The reason for this discrepancy has not been formally addressed, and we demonstrate, for the first time, that the structure of the swimbladder wall will affect vibratory behaviour. Using the oyster toadfish Opsanus tau, we find regional differences in bladder thickness, directionality of collagen layers (anisotropic bladder wall structure), material properties that differ between circular and longitudinal directions (stress, strain and Young's modulus), high water content (80%) of the bladder wall and a 300-fold increase in the modulus of dried tissue. Therefore, the swimbladder wall is a viscoelastic structure that serves to damp vibrations and impart directionality, preventing the expression of resonance.
FIGURE 5 in Austrobatrachus iselesele, a new toadfish species from South Africa (Teleostei: Batrachoididae)
FIGURE 5. Second dorsal fin of freshly collected holotype of Austrobatrachus iselesele. Photograph by A. Connell.
FIGURE 6 in Austrobatrachus iselesele, a new toadfish species from South Africa (Teleostei: Batrachoididae)
FIGURE 6. Underwater photograph of Austrobatrachus foedus, Algoa Bay, South Africa. Photograph by J. Swanepoel.
FIGURE 2 in Austrobatrachus iselesele, a new toadfish species from South Africa (Teleostei: Batrachoididae)
FIGURE 2. Dorsal view of head of preserved holotype of Austrobatrachus iselesele showing ridges. Photograph by D.W. Greenfield.
FIGURE 4 in Austrobatrachus iselesele, a new toadfish species from South Africa (Teleostei: Batrachoididae)
FIGURE 4. Anal fin of freshly collected holotype of Austrobatrachus iselesele. Photograph by A. Connell.
FIGURE 3 in Austrobatrachus iselesele, a new toadfish species from South Africa (Teleostei: Batrachoididae)
FIGURE 3. Pectoral-fin axil of freshly collected holotype of Austrobatrachus iselesele showing axillary foramen. Photograph by A. Connell.
FIGURE 4 in Colletteichthys flavipinnis, a new toadfish species from Sri Lanka and India (Teleostei: Batrachoididae)
FIGURE 4. Eye of Colletteichthys dussumieri (CAS 233658) showing three tentacles above it (Fig. 5 from Greenfield, 2012).
FIGURE 8 in Colletteichthys flavipinnis, a new toadfish species from Sri Lanka and India (Teleostei: Batrachoididae)
FIGURE 8. Distribution of species of Colletteichthys. Circles = C. occidentalis, stars = C. dussumieri, squares = C. flavipinnis.
FIGURE 10 in Colletteichthys flavipinnis, a new toadfish species from Sri Lanka and India (Teleostei: Batrachoididae)
FIGURE 10. Neighbor Joining tree of Cytochrome oxidase I (COI) gene sequences derived from Colletteichthys species using K2P distances.
FIGURE 3 in Colletteichthys flavipinnis, a new toadfish species from Sri Lanka and India (Teleostei: Batrachoididae)
FIGURE 3. Eye of holotype of Colletteichthys flavipinnis showing single tentacle above it. Photograph by D.W. Greenfield.
FIGURE 6 in Colletteichthys flavipinnis, a new toadfish species from Sri Lanka and India (Teleostei: Batrachoididae)
FIGURE 6. Head coloration of freshly collected paratype of Colletteichthys flavipinnis. Photograph by K.K. Bineesh.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.