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6,234 results for “phenotypes”
Fig. 4 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula
Fig. 4. Phylogenetic tree based on the Maximum Likelihood (ML) analysis of the species of the Order Trypanorhyncha found in Octopus maya constructed on partial large subunit ribosomal gene (28S) (likelihood = – 15209.189111). Bootstrap support values for ML are provided at the nodes; ex = host; the stage of development of the cestode in parentheses.
Fig. 3 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula
Fig. 3. Scanning electron microscopy of whole specimens and the detail of scolecis of the cestodes found as parasites of Octopus maya. Trypanorhyncha (A–L): A-C Eutetrarhynchus sp.; D-F Kotorella pronosoma; G-I Nybelinia sp.; J-L Prochristianella sp. Onchoproteocephalidea (M–R): M-N Acanthobothrium sp. O–P Phoreiobothrium sp.; Q-R Prosobothrium sp.
Fig. 2 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula
Fig. 2. Schematic drawings and photographs of the stained specimens of cestode parasitizing Octopus maya. Trypanorhyncha (A–D): A- Eutetrarhynchus sp.; B. Kotorella pronosoma; C- Nybelinia sp.; D- Prochristianella sp. Onchoproteocephalidea (E–G): E- Acanthobothrium sp.; F- Phoreiobothrium sp.; G- Prosobothrium sp.- Abbreviations: as = apical sucker; bot = bothridia cc = calcareous corpuscles; lo = loculi; pb = pars bulbosa; pbo = pars bothrialis; ppb = pars postbulbosa; ps = pedunculus scolecis; pv = pars vaginalis; sc = scolex; sp = septa; st = strobilo; vel = velum.
Fig. 5 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula
Fig. 5. Phylogenetic tree based on the Maximum Likelihood analysis of the species of the Order Trypanorhyncha found in Octopus maya constructed on partial small subunit ribosomal gene (18S) (likelihood = – 7987.787948). Bootstrap support values for ML are provided at the nodes; ex = host; the stage of development of the cestode in parentheses.
Fig 2 in A new species of Macrocypraea (Gastropoda, Cypraeidae) from Trindade Island, Brazil, including phenotypic differentiation from remaining congeneric species
Fig 2. Macrocypraea mammoth shells of types. (A-F) Holotype MZSP 137544 (L 133.1 mm). (A) Dorsal view. (B) Apertural view. (C) Right view. (D) Left view. (E) Anterior view. (F) Posterior view. (G-I) paratype MZSP 137545 (L 100.0 mm). (G) Dorsal view. (H) Apertural view. (I) right view. (J-N) Paratype MZSP 137546 (now broken) (L 112.3 mm). (J) Apertural view. (K) Dorsal view. (L) Left view. (M) Right view. (N) Same, right portion of shell removed.
Fig 6 in A new species of Macrocypraea (Gastropoda, Cypraeidae) from Trindade Island, Brazil, including phenotypic differentiation from remaining congeneric species
Fig 6. Macrocypraea mammoth anatomy. (A) Head, ventral view, foot and columellar muscle removed, radular sac uncoiled downwards. (B) Buccal mass, left view. (C) Visceral mass and posterior part of pallial cavity, ventral view, midgut seen as in situ, kidney opened longitudinally, only topology of gill shown. (D) Odontophore, dorsal view, both cartilages (oc) deflected, left m4 and m5 (right in figure) partially sectioned. Scales = 5 mm.
Fig. 2 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 2 Collapsed chronogram for Basidiomycota and Entorrhizomycota evolution. The tree topology represents the consensus of trees inferred with BEAST from combined 18S + 28S + rpb1 domains B-C sequences from 83 Basidiomycota species, three Entorrhizomycota species and three Ascomycota species as outgroup. Alignment length = 3903. The age estimation mean is followed by the 95% highest density probability range in square brackets. Numbers on branches represent bootstrap values obtained from 1000 replicates (values ≥ 70), maximum support of 100 is encoded with bold lines. For full dataset, see Supplementary material (Fig. S1). Abbreviations: Ordo., Ordovician; Sil., Silurian; Carbon., Carboniferous; Paleo., Paleogene; N., Neogene
Black Soldier Fly detection, phenotyping and sex prediction dataset
<p>BSF_Larvae for training the detection and segmentation model consists of 321 images with over 5000 larvae instances. </p> <p>Single_Larvae_data consists of 1608 single larvae images for the measurement of body weight, length and width of the individual larva. </p> <p>The Larvae size excel sheet contains the size and sex data corresponding to the individual larva. </p> <p>The Larvae sex classification dataset includes images cropped from the Single_Larvae_data for sex classification.</p>
Data and Analysis Scripts for "Drift in Individual Behavioral Phenotype as a Strategy for Unpredictable Worlds"
<p>This document contains the raw data and analysis scripts for the paper "Drift in Individual Behavioral Phenotype as a Strategy for Unpredictable Worlds", including <em>Drosophila melanogaster</em> circling and handedness behavior at multiple timepoints and across genotypes and experimental conditions manipulating serotonin. It also contains code used to run ecological simulations in the paper and the results of those simulations, as well as code to generate figures for the paper.</p>
Supplement: Genomic and phenotypic imprints of microbial domestication on cheese starter cultures
<p>This data repository contains the latest version of the supplemental data, code and figures for the following manuscript:</p> <p>Vincent Somerville, Nadine Thierer, Remo S. Schmidt, Alexandra Roetschi, Laurianne Braillard, Monika Haueter, Hélène Berthoud, Noam Shani , Ueli von Ah, Florent Mazel & Philipp Engel 2024. “Genomic and phenotypic imprints of Neolithic domestication on Cheese Starter cultures” </p> <p>All additional genomic data is stored under the following Bioprojects on NCBI:</p> <p>PRJNA717134<br>PRJNA1048529<br>PRJNA1083966<br>PRJNA1157897</p> <p> </p> <p> </p> <p> </p>
Supporting data and code for: Myzus persicae resistance to neonicotinoids - unravelling the contribution of different mechanisms to phenotype
<p>This is the first release of the final data and code for the article accepted for publication in <em>Pest Management Science</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
MTClass: Identification and annotation of multi-phenotype cis-eQTLs using machine learning
<p>This dataset contains the aggregated results from three iterations of MTClass. Brief descriptions of the file names are below:</p> <ul> <li><strong>multi-tissue.zip</strong>: Multi-tissue study containing the 9-tissue, 13 brain tissue, and 48-tissue results from MTClass, MultiPhen, and MANOVA</li> <li><strong>multi-exon.zip</strong>: Multi-exon study containing the multi-exon results from the 13 individual brain tissues (MTClass, MultiPhen, and MANOVA for each tissue)</li> <li><strong>2D_exon_tissue.zip</strong>: Multi-tissue/multi-exon combined eQTL study, done in 9 tissues using multi-layer perceptron. MTClass was only run once on this dataset due to the relatively higher computational burden.</li> <li><strong>PsychENCODE_isoQTL.zip</strong>: Multi-isoform eQTL study, done in human prefrontal cortex using PsychENCODE data.</li> <li><strong>OneK1K_scRNAseq.zip</strong>: Multi-cell-type eQTL study, done using scRNA-seq data from the OneK1K cohort.</li> </ul>
Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system
<h3><span>Inbreeding depression, functional traits and phenotypic plasticity in an endangered tree species from Congo basin with a mixed mating system</span></h3> <h1><a name="_Hlk166486742"></a><strong><span>Abstract</span></strong></h1> <p><span><span>1. Most tree species can suffer from inbreeding depression (ID), which they escape by reproducing predominantly through outcrossing. A remarkable exception is <em>Pericopsis elata</em>, an African timber species naturally producing 54% of self-fertilized seeds in the eastern Congo Basin. This species is highly logged and suffers from a deficit of natural regeneration, so that silviculture is needed for its sustainable management. While selecting good genetic material can increase the value of plantations, we lack fundamental biological knowledge on the effect of inbreeding and competition on growth potential, variability in leaf traits and phenotypic plasticity. We hypothesize that ID in <em>P. elata</em> could result from the expression of deleterious mutations affecting functional traits, or from a reduction of adaptive phenotypic plasticity in inbred genotypes.</span></span></p> <p><span><span>2. To test our hypotheses, 540 <em>P. elata</em> seedlings were monitored for 4 years in a Nelder-type device located in the DRC, in which trees were planted along concentric circles to generate a density gradient. Nine leaf morphological traits (including specific leaf area, stomata density and size), eight leaf chemical traits, diameter, and total height were measured regularly, while paternity analyses allowed distinguishing inbred and outbred plants. To explain the observed ID on growth, we tested whether inbreeding affected leaf traits and/or their plasticity expressed across years, across the density gradient or across sunlight exposure. </span></span></p> <p><span><span>3. Outbred plants grew faster than inbred ones, demonstrating ID for each level of competition. Despite the significant correlation found between specific leaf area and growth, and the impact of planting density, plant age, and leaf exposure to sunlight on multiple traits, mean leaf trait values did not differ according to inbreeding. However, </span></span><span><span>a few leaf traits (chlorophyl content, </span></span><span><span>maximum stomatal water vapor conductance</span></span><span><span>, and leaf fresh mass) showed significantly higher plasticity in outbred than inbred plants. </span></span></p> <p><span><span>4. Synthesis: the observed ID on growth was not explained by a direct effect of inbreeding on the mean values of functional traits but possibly by a reduction of phenotypic plasticity with inbreeding. Additional studies on the interplay between ID, functional traits and plasticity should be conducted at the intra-specific level to identify general patterns<em>.</em></span></span></p> <p><span><strong><span>Key-words : </span></strong></span><span><span>Inbreeding depression, phenotypic plasticity, silviculture, functionals traits, <em>Pericopsis elata</em>, mating system, Nelder device.</span></span></p>
RNA phenotypes, xQTLs, xTWAS weights, and xTWAS results for Geuvadis and GTEx using Pantry
<div> <div> <p>This repository contains RNA phenotyping genetic analysis results for 55 human tissue datasets using Pantry. It includes RNA phenotypes, covariates, cis-QTL results from tensorQTL, and weights and associations for multimodal transcriptome-wide association study (xTWAS) results using FUSION, for six RNA modalities, for Geuvadis and 54 GTEx tissues. The xTWAS data covers 114 traits using GWAS data from <a href="https://doi.org/10.5281/zenodo.3629742" target="_blank" rel="noopener">Publicly available GWAS summary statistics, harmonized and imputed to GTEx v8' variant reference</a>. For more information, see the publication "Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics".</p> </div> </div>
UV mutagenesis conjugated to high throughput screening as a tool to generate new phenotypic diversity in wine yeast
<p><strong>The current global changes, societal and climatic, strongly challenge the wine industry. Multiple methods are applied in the development of new strains for the industry, but many are based on the existing phenotypic and genetic diversities. UV mutagenesis, as an untargeted strategy, has been successfully used for years, with significant examples on wine. Here we developed and validated a UV-mutant generation strategy coupled with a high throughput screening in wine-like conditions. This strategy led to the production of a 502 mutant’s library for which concentrations of eight primary metabolites after fermentation were assessed. This data paper presents the resulting data.</strong></p>
Merging metabolomics and genomics provides a catalog of genetic factors that infuence molecular phenotypes in pigs linking relevant metabolic pathways
<h3>Content</h3> <p>Metabolites included in the study. Summary statistics of metabolite levels for the Large White and Duroc pig populations are provided.</p>
Data and scripts used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p>Images, script and data used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
One for all and all for one: phenotype assortment and reproductive success in masculinized females
<p>Homophily by morphological and behavioral traits has been described in several species of vertebrates, but its functional consequences remain poorly studied. Homophily by plurally breeding females may improve direct fitness by enhancing reproductive success. Female mammals may exhibit phenotypical masculinization due to exposure to androgens during early development, a condition that is associated with maternal performance during subsequent breeding. Our goal was to assess whether female composition (in terms of masculinization) of plurally breeding groups influences female fitness in a natural population of degus <i>(Octodon degus).</i> We assessed if plurally breeding female degus assort themselves by anogenital distance (AGD), an accurate measure of masculinization level. We also quantified if homophily by AGD phenotype affects female reproductive success and the reproductive output of the group. Plurally breeding groups typically included similarly masculinized (i.e., long AGD) females or similarly feminized (short AGD) females, indicating a strong degree of homophily. Females weaned more offspring in plurally breeding groups with more masculinized females. Additionally, standardized variance in the number of offspring weaned decreased in plurally breeding groups with mostly masculinized females, indicating greater reproductive equality in these groups. We conclude that female degus organize into homophilic social groups of similar AGD, and that social groups of masculinized females exhibit higher reproductive success.</p>
Figures 9–17 in Geographical distribution and phenotypic variation of Anovia punica Gordon (Coleoptera: Coccinellidae: Noviini), a predatory ladybeetle of fluted scales (Hemiptera: Coccoidea: Monophlebidae)
Figures 9–17. Male genitalia of Anovia punica. Peru: 9–11) San Martin State. Colombia: 12–14) San Andres Island. 15–17) Magdalena State. 9), 12), 15) Tegmen in ventral view. 10), 13), 16) Tegmen in lateral view. 11), 14), 17) Sipho.
Figures 1–8 in Geographical distribution and phenotypic variation of Anovia punica Gordon (Coleoptera: Coccinellidae: Noviini), a predatory ladybeetle of fluted scales (Hemiptera: Coccoidea: Monophlebidae)
Figures 1–8. Morphological variation of Anovia punica. Peru. 1–2) San Martín State. Colombia: 3) San Andres Island. 4) Magdalena State. 5) Valle del Cauca State. 6–7) Antioquia State. 8) Atlantico State.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.