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187 results for “phenotypic traits”

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zenodo48/100

MSPB: a longitudinal multi-sensor dataset with phenotypic trait measurements from honey bees

<p>We present a one-year-long <strong>M</strong>ulti-<strong>S</strong>ensor dataset with <strong>P</strong>henotypic trait measurements from honey <strong>B</strong>ees (MSPB). Data were continuously collected between April-2020 and April-2021 from 53 hives located at two apiaries in Qu&eacute;bec, Canada. The sensor data included audio features, temperature, and relative humidity. The phenotypic measurements contained beehive population, number of brood cells (eggs, larva and pupa), <em>Varroa</em> destructor infestation levels, defensive and hygienic behaviors, honey yield, and winter mortality. Our study is amongst the first to provide a wide variety of phenotypic trait measurements annotated by apicultural science experts, which facilitate a broader scope of analysis on honey bees, such as bee acoustics analysis, multi-modal hive monitoring, queen presence detection, <em>Varroa </em>infection detection, hive population estimation, biological analysis of bees, etc.</p> <h3>Related Info</h3> <p>The data collection process, feature pre-processing, preliminary data analysis, and usage notes can be found in our paper <a href="https://arxiv.org/abs/2311.10876">https://arxiv.org/abs/2311.10876</a></p> <p>Check the project webpage (<a href="https://zhu00121.github.io/MSPB-webpage/">https://zhu00121.github.io/MSPB-webpage/</a>) and Github repo (<a href="https://github.com/MuSAELab/MSPB">https://github.com/MuSAELab/MSPB</a>) for more information.</p> <h3>Citation</h3> <p>Kindly cite the following paper:</p> <p>@misc{zhu2023mspb,</p> <p>&nbsp; &nbsp; &nbsp;title={MSPB: a longitudinal multi-sensor dataset with phenotypic trait measurements from honey bees}, &nbsp;</p> <p>&nbsp; &nbsp; &nbsp;author={Yi Zhu and Mahsa Abdollahi and S&eacute;gol&egrave;ne Maucourt and Nico Coallier and Heitor R. Guimar&atilde;es and Pierre Giovenazzo and Tiago H. Falk},</p> <p>&nbsp; &nbsp; &nbsp;year={2023},</p> <p>&nbsp; &nbsp; &nbsp;eprint={2311.10876},</p> <p>&nbsp; &nbsp; &nbsp;archivePrefix={arXiv},</p> <p>&nbsp; &nbsp; &nbsp;primaryClass={eess.AS}</p> <p>}</p> <h3>Contact</h3> <p>You can contact us at Yi.Zhu@inrs.ca, if you encounter any questions accessing the data.</p>

opencc-by-nc-4.0Oct 2023View details →
zenodo44/100

Supporting data for "The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor"

<p>Methylome of the fresh water snail <em>Biomphalaria glabrata</em>.&nbsp;DNA was extracted from the feet of 10 individuals of <em>B. glabrata</em> originally isolated from Brazil. These snails have been cultivated in the laboratory since 1960. Tissue were grinded at 4&deg;C and incubated in 1 ml volume of lysis buffer (20 mM TRIS pH 8; 1 mM EDTA; 100 mM NaCl; 0.5% SDS), with 0.3 mg of proteinase K at 55&deg;C for 1 night. Afterwards, lysate was purified with phenol-chloroform and DNA was isopropanol&nbsp;precipitated.&nbsp;The extracted DNA (around 138ng/&micro;L) was poled in equivalent amounts and Whole Genome Bisulfite Sequencing&nbsp;was done by GATC-biotech (www.gatc-biotech.com). The principle of this treatment is to convert non-methylated cytosines of gDNA into deoxy-uracil, whereas methylated cytosines remain intact.&nbsp;WGBS was done according to the Lister protocol &nbsp;(sequence 2 forward strands only).&nbsp;The reference genome (Biomphalaria-glabrata-BB02_SCAFFOLDS_BglaB1.fa) and annotation (Biomphalaria-glabrata-BB02_BASEFEATURES_BglaB1.3.gff3) used in this project are available on VectorBase (https://www.vectorbase.org/).&nbsp;To align our short reads, we chose to use two specific bisulfite mapping tools, BSMAP 1.0.0 (https://code.google.com/p/bsmap/) and Bismark 0.10.2 (www.bioinformatics.babraham.ac.uk /projects/bismark/), to compare their efficiency and convenience to finally work with the more suitable one on our datasets.&nbsp;IGV (Interactive Genomics Viewer, https://www.broadinstitute.org/igv/) was used to visualized final alignments.<br> BSMAP performed better than Bismark and was used for downstream analyses. Without default parameters alignement efficiency for BSMAP is&nbsp;47.1%, allowing for 2 mismatches increases it to 55.6%.&nbsp;Methylation occurs predominantly in CpGs. (C methylated in CpG context:&nbsp;12.4%,&nbsp;C methylated in CHG context: 0.5%,&nbsp;C methylated in CHH context: 0.5%)&nbsp;The major part of CpG sites, 95.7% were unmethylated, of the remaining 4.3% of CpG sites around 3.8% had low methylation, and 0.5% were completely methylated.&nbsp;Methylation is of the mosaic type. Methylation is relatively low with 1.2% of total cytosines. Our analyses suggested that conserved genes and genes with stable expression are localized in high methylated regions of the genome. Finally, we see that repetitive sequences were predominantly situated in low methylated regions of <em>B. glabrata</em>.&nbsp;</p> <p>Wiggle files were generated for CpG pairs only.</p> <p>Produced at IHPE (http://ihpe.univ-perp.fr/)</p>

opencc-by-4.0Nov 2020View details →
zenodo44/100

Predicting Phenotypic Traits Using a Massive RNA-seq Dataset

<h2><strong>Abstract</strong></h2><p>The included datasets are a conglomerate of all available <i>Arabidopsis thaliana</i> RNA-seq data available from NCBI as of November 2022 processed to count data. In addition, the associated annotation files from NCBI BioProject database and processed versions of this data is included. Data has been processed according to the "Data Description Methods" in the manuscript titled "Predicting Phenotypic Traits Using a Massive RNA-seq Dataset" (in publication). The associated Methods can be found at this repository:<a href="https://gitlab.com/ficklinlab-public/modeling-with-transcriptomics"> https://gitlab.com/ficklinlab-public/modeling-with-transcriptomics</a>. These datasets can be used for exploring machine learning methods for predicting both continuous (Age) and categorical (Tissue) phenotypic traits using gene expression. Additionally, the gene expression data can be used on its own for the investigation of gene expression in <i>Arabidopsis thaliana.</i></p><h3><strong>Note to Researchers</strong></h3><p>This repository contains all of the datasets and information necessary to recreate the experiments in our paper. However, if may be that you are interested in our dataset for testing your own hypotheses/programs. If this is the case, we predict that you are looking for one or more of the the following 5 datasets<br>&nbsp;</p><h3><strong>Note on File Compression</strong></h3><p>All files in this repository are compressed using bzip2 to conserve space and allow for easier file transfer. The unzip command on linux systems is `bzip2 -d FILE_NAME`. For other computer systems (Windows and Apple) please consult your user manual.</p><h3><strong>Description All Datasets:</strong></h3><p><strong>Title:</strong> Gene Expression Count Data of all <i>Arabidopsis thaliana</i> data available from NCBI SRA as of November 2022<br><strong>Abstract: </strong>Gene Expression Count data was created using the workflow GEMmaker. The resulting Gene Expression Matrix (GEM) was then normalized and thresholded. The following 4 files are normalizations of the same data for Trimmed Mean of M values (TMM), Median Ratios Normalization (MRN), Transcripts Per kilobase Million (TPM), and No Normalization (NoNo) respectively. Additionally, Each file is included as a tsv and a python pickle. The tsv file is human readable, whereas the pickle file can be read into memory substantially faster. Format for tsv is each row represents a sample and each column represents a gene. <strong>NCBI_Nov2022_SRR_runinfo.csv</strong> is the starting file from NCBI which reports SRR information for each sample. <strong>Note 1 to Researchers: </strong>MRN normalization performed the best in our experiments and is likely what you want to use if you are doing additional expermentation with this dataset. Otherwise start with NoNo and perform your own normalizations. <strong>Note 2 to Researchers:</strong> the 54547 dataset will need to be thresholded prior to use. We include it in addition to the 32432 datasets in case you wish to try a different thresholding to the one outlined in our manuscript.&nbsp;<br><strong>Author:</strong> John Anthony Hadish<br><strong>Data Type: </strong>Gene Expression Count Data<br><strong>Organism:</strong> <i>Arabidopsis thaliana</i><br><strong>Files:</strong></p><p><strong>NCBI_Nov2022_SRR_runinfo.csv - </strong>Arabidopsis RNA-seq SRA RunInfo Retrieved from NCBI November 2022. This is the unprocessed data.<br><strong>Dataset_54547_NoFilter_raw.pkl </strong>- Raw File Before thresholding (".pkl" format). Same as NoNo normalization without thresholding.<br><strong>Dataset_54547_NoFilter_raw.tsv </strong>- Raw File Before thresholding (".tsv" format). Same as NoNo normalization without thresholding.<br><strong>Dataset_32432_MRN.pkl</strong> - MRN normalized (".pkl" format)<br><strong>Dataset_32432_MRN.tsv - </strong>MRN normalized (".tsv" format)<br><strong>Dataset_32432_NoNo.pkl - </strong>NoNo normalized (".pkl" format)<br><strong>Dataset_32432_NoNo.tsv - </strong>NoNo normalized (".tsv" format)<br><strong>Dataset_32432_TMM.pkl - </strong>TMM normalized (".pkl" format)<br><strong>Dataset_32432_TMM.tsv - </strong>TMM normalized (".tsv" format)<br><strong>Dataset_32432_TPM.pkl - </strong>TPM normalized (".pkl" format)<br><strong>Dataset_32432_TPM.tsv - </strong>TPM normalized (".tsv" format)<br><br><br><strong>Title: </strong>Meta Data Arabidopsis Age and Tissue<br><strong>Abstract: </strong>Meta Data for Age and Tissue after processing. In our experiment this was used as response variable to gene expression. Shared columns are "bio_sample", "bioproject_name", "experiment". In addition to these processed datasets, <strong>NCBI_Nov2022_BioSample_data.tsv </strong>is the unprocessed starting material for these two data frames.<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>Metadata on phenotypes. ".tsv" format&nbsp;<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:&nbsp;</strong><br><strong>NCBI_Nov2022_BioSample_data.tsv - </strong>Arabidopsis BioSample data retrieved from NCBI November 2022. This is the unprocessed data.<br><strong>df_metadata_tissue.tsv</strong> - Tissue Annotations for 24876 samples<br><strong>df_metadata_age.tsv</strong><i><strong> - </strong></i>Age Annotations for 16078 samples. In addition to shared columns includes<i> "</i>days<i>_</i>age"(how many days old the sample is converted to days) and "annotation_age" (how the annotation was reported for this sample in the raw data file-- i.e. "days", "weeks" etc.)<br><br><br><strong>Title: </strong>Machine Learning Dataset for <i>Arabidopsis thaliana</i> <strong>Age</strong><br><strong>Abstract: </strong>The dataset used for Machine learning on the phenotype Age that is a combination of the Gene Expression Matrix and the Annotation Matrix. Consists of a list of 4 for the train and test splits.<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>Gene Expression Matrix and Annotations Combined, split into train and test&nbsp;<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:</strong><br><strong>Dataset_Age_TrainTestSplits_mrn.pkl</strong> - MRN normalized<br><strong>Dataset_Age_TrainTestSplits_NoNo.pkl </strong>- NoNo normalized<br><strong>Dataset_Age_TrainTestSplits_tmm.pkl </strong>- TMM normalized<br><strong>Dataset_Age_TrainTestSplits_tpm.pkl - </strong>TPM normalized<br><br><br><strong>Title: </strong>Machine Learning Dataset for <i>Arabidopsis thaliana</i> <strong>Tissue</strong><br><strong>Abstract: </strong>The dataset used for Machine learning on the phenotype Tissue that is a combination of the Gene Expression Matrix and the Annotation Matrix. Consists of a list of 4 for the train and test splits. Saved as python ".pkl" files.<br><strong>Author:</strong> John Anthony Hadish<br><strong>Data Type: </strong>Gene Expression Matrix and Annotations Combined, split into train and test. Saved as python ".pkl" files.<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:</strong><br><strong>Dataset_Tissue_TrainTestSplits_mrn.pkl </strong>- MRN normalized<br><strong>Dataset_Tissue_TrainTestSplits_NoNo.pkl </strong>- NoNo normalized<br><strong>Dataset_Tissue_TrainTestSplits_tmm.pkl </strong>- TMM normalized<br><strong>Dataset_Tissue_TrainTestSplits_tpm.pkl </strong>- TPM normalized<br><strong>Dataset_Tissue_TrainTestSplits_mrn_4category.pkl </strong>- MRN for the tissue-4 dataset<br><br><br><strong>Title: </strong>BioProject Names<br><strong>Abstract:</strong> Three Column File With BioProject Name, BioSample Name, and Experiment Name<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>".tsv"<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:</strong><br><strong>BioProject_Names_All.tsv</strong><br><br><br><strong>Title:</strong> Manuscript Supplemental Material<br><strong>Abstract:</strong> Supplemental tables and figures described in the manuscript (included with manuscript and here for convenience). Please see manuscript for additional information.<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>".tsv", ".png".pdf"<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:</strong><br><strong>Supplemental_Figures.zip </strong>- Supplemental figures from the manuscript. Includes description of each figure.<br><strong>Supplemental_Tables.zip </strong>- Supplemental tables from the manuscript. Includes description of each table.<br><br>&nbsp;</p><p><strong>Title:</strong> Splits of data for 3 experiments<br><strong>Abstract:</strong> 2 column tsv files. The first column is the experiment (sample) name, and the second column is if it is included in the train or test data. <strong>Included here to make sure pkl files are reproducible in case the pkl package breaks in the future.</strong> Not used by scripts, included to prevent future potential loss of data.<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>".tsv"<br><strong>Organism: </strong><i>Arabidopsis thaliana</i><br><strong>Files:</strong><br><strong>Dataset_Tissue_TrainTestSplits_4category_namesOnly.tsv</strong><br><strong>Dataset_Tissue_TrainTestSplits_namesOnly.tsv</strong><br><strong>Dataset_Age_TrainTestSplits_namesOnly.tsv</strong></p><p>&nbsp;</p><p><strong>Title:</strong> Git Code Repository<br><strong>Abstract:</strong> A tar bz2 compression of the git repository containing all of the code created for this manuscript. The same code found in this file is also avalible on GitLab at the link: https://gitlab.com/ficklinlab-public/modeling-with-transcriptomics<br><strong>Author: </strong>John Anthony Hadish<br><strong>Data Type: </strong>Git Repository, python code<br><strong>Files:</strong><br><strong>modeling-with-transcriptomics-main.tar.bz2</strong> - Compressed Git repository of all code used in paper.</p>

opencc-by-4.0Nov 2023View details →
zenodo44/100

Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

<p>Red clover (<em>Trifolium pratense</em> L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses.</p> <p>A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by <em>Colletotrichum trifolii</em>, and clover rot caused by <em>Sclerotinia trifoliorum, </em>was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide, once validated, a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.</p>

opencc-by-4.0May 2022View details →
zenodo44/100

Salmonella enterica serovar Derby isolated from eggs show genomic and phenotypic traits that may be linked to inability to produce human infection.

<p><em><span>Salmonella enterica</span></em><span> serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to <em>S</em>. Enteritidis from poultry, we conducted a large survey of commercially available eggs, where we isolated many <em>S.</em> Enteritidis strains but surprisingly also a much larger number (ratio 5:1) of <em>S</em>. Derby strains. No single case of <em>S</em>. Derby infection was detected in that period, suggesting that the <em>S</em>. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates, as well as fifteen isolates from pork or human infection that were isolated in Uruguay before and after that period, and all sequenced strains had the same sequence type <span>(ST40). Phylogenomic genomic analysis was conducted using more than 3500 genomes from the same sequence type (ST), revealing that Uruguayan isolates clustered into four distantly related lineages. Population structure analysis (BAPS) suggested the division of the analyzed genomes into nine different BAPS1 groups, with Uruguayan strains clustering within four of them. </span>All egg isolates clustered together as a monophyletic group and showed marked differences in gene content with the strains in the other clusters. <span>Differences included the absence of a C-terminal fragment of the <em>speF</em> gene, as well as variations in the composition of mobile genetic elements, such as plasmids, insertion sequences, transposons, and phages, between egg isolates and human/pork isolates.</span></span> <span>Egg isolates showed an acid susceptibility phenotype, reduced ability to reach the intestine after oral inoculation of mice, and reduced induction of SPI-2 <em>ssaG</em> gene, compared to human isolates from other monophyletic groups. Mice challenge experiments showed that mice infected intraperitoneally with human/pork isolates died between 1-7 days p.i., while all animals infected with the egg strain survived the challenge. Altogether, our results suggest that loss of gene functions and the absence of plasmids in egg isolates may explain why these <em>S</em>. Derby were not capable of producing human infection despite being at that time, the main serovar recovered from eggs countrywide.</span></p>

opencc-by-4.0Dec 2023View details →
zenodo44/100

Contemporary phenotypic change in plant quantitative traits

<p>This is a new version of the Gorn&eacute; &amp; D&iacute;az 2017 database (doi:10.5281/zenodo.580095). We cheked&nbsp;the categorization of each case, fixed&nbsp;of some mistakes. Also, we&nbsp;disambiguated&nbsp;the trait type moderator and add a&nbsp;new (mean based) measure of change.</p> <p>This database included studies that provide data of changes in quantitative traits of angiosperms within a known temporal framework (&lt;300 years). The search was performed by Scopus (www.scopus.com), up to 22 December 2015 (search strings in Gorn&eacute; and D&iacute;az 2017). The database includes studies that measured intraspecific change in a quantitative trait and which report the elapsed time when the phenotypic change occurred. The studies recorded a single population before and after a change in the environment or compared two (or more) populations by measuring a quantitative trait across two situations, where one of them was a new condition of known age. Both, by measuring change directly in the field or&nbsp;by performing common condition experiments (e.g. common garden experiments or&nbsp;reciprocal transplants). Studies reporting results from artificial selection or interspecific hybridization were excluded. The environmental changes included expansions of distributional range, soil or air pollution, exposure to herbicides, changes in salinity, pH, climate, disturbance or irrigation regime, and addition or loss of species in the local community. All data available in each study were recorded, including several observations of the same species. These procedures resulted in a database containing 1716 observations from 128 studies, with changes in populations of 152 species from 34 families, in elapsed times of &lt; 260 years, and covering a wide range of traits, lifespan, growth forms and environmental situations.</p> <p>All data points were categorized according to biological properties of the study system (lifespan, growth form, trait type) and methodological ones. The amount and rate of phenotypic change is expresed as&nbsp;the standardized mean difference Hedges <em>g</em> (Hedges 1981, 1982), a rate of change which is the Hedges <em>g</em> over the elapsed time in years, and the log-transformation of both of them.&nbsp;The standardized mean difference is equal to the <em>haldane</em> numerator, which is a standard rate of evolution (Haldane 1949; Gingerich 1993). In addition, we upgraded the D&iacute;az and Gorn&eacute; (2017) database, computing the response ratio effect size (<em>logRR</em>) (Hedges et al. 1999) whenever possible. The response ratio is a mean-scaled metric equal to the <em>darwins</em> numerator (Haldane 1949). So that we compute a rate of change similar to <em>darwins</em> (time expressed as years instead of million years).</p> <p>&nbsp;</p> <p>contact email address: gorneld@gmail.com</p>

opencc-by-4.0Jul 2019View details →
edi44/100

Phenotypic trait variation of Herminium monorchis in the Qinghai-Tibetan Plateau with grazing intensity and climatic conditions

This data set contains raw data supporting the research entitled “Livestock grazing outweighs climate in driving trait variation of a widespread alpine plant” (currently under peer review), which documents how phenotypic traits of a widespread herbaceous plant in the Qinghai-Tibetan Plateau, Herminium monorchis, vary with grazing intensity and environmental conditions.

openCC0Mar 2023View details →
zenodo40/100

Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits

<p>Dataset associated with the manuscript &quot;Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits&quot; (Arroyo-Correa et al. 2020), including&nbsp;plant-pollinator interactions, individual plant attributes and the plant polygon map created with drone flights.&nbsp;</p>

opencc-by-4.0Apr 2020View details →
zenodo40/100

Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

<p>Data and code from: &quot;Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana&quot; published at Annals of Botany PLANTS. This is a dataset on phenotypic traits of Arabidopsis in response to different abiotic stresses and a reproducible R script to generate all figures and tables in the publication.</p>

opencc-by-4.0Dec 2021View details →
zenodo40/100

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&nbsp;: </span></strong></span><span><span>Inbreeding depression, phenotypic plasticity, silviculture, functionals traits, <em>Pericopsis elata</em>, mating system, Nelder device.</span></span></p>

opencc-zeroOct 2024View details →
dryad40/100

Improving wheat yield prediction using secondary traits and high-density phenotyping under heat stressed environments

<p>A primary selection target for wheat (Triticum aestivum) improvement is grain yield. However, the selection for yield is limited by the extent of field trials, fluctuating environments, and the time needed to obtain multiyear assessments. Secondary traits such as spectral reflectance and canopy temperature (CT), which can be rapidly measured many times throughout the growing season, are frequently correlated with grain yield and could be used for indirect selection in large populations particularly in earlier generations in the breeding cycle prior to replicated yield testing. While proximal sensing data collection is increasingly implemented with high-throughput platforms that provide powerful and affordable information, efficient and effective use of these data is challenging. The objective of this study was to monitor wheat growth and predict grain yield in wheat breeding trials using high-density proximal sensing measurements under extreme terminal heat stress that is common in Bangladesh. Over five growing seasons, we analyzed normalized difference vegetation index (NDVI) and CT measurements collected in elite breeding lines from the International Maize and Wheat Improvement Center at the Regional Agricultural Research Station, Jamalpur, Bangladesh. We explored several variable reduction and regularization techniques followed by using the combined secondary traits to predict grain yield. Across years, grain yield heritability ranged from 0.30 to 0.72, with variable secondary trait heritability (0.0–0.6), while the correlation between grain yield and secondary traits ranged from−0.5 to 0.5. The prediction accuracy was calculated by a cross-fold validation approach as the correlation between observed and predicted grain yield using univariate and multivariate models. We found that the multivariate models resulted in higher prediction accuracies for grain yield than the univariate models. Stepwise regression performed equal to, or better than, other models in predicting grain yield. When incorporating all secondary traits into the models, we obtained high prediction accuracies (0.58–0.68) across the five growing seasons. Our results show that the optimized phenotypic prediction models can leverage secondary traits to deliver accurate predictions of wheat grain yield, allowing breeding programs to make more robust and rapid selections.</p>

opencc-zeroSep 2021View details →
dryad40/100

Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)

<p><span><strong>Premise</strong>:</span><span> Island systems have long served as a model for evolutionary processes due to their unique species interactions. Many studies of the evolution of species interactions on islands have focused on endemic taxa. Fewer studies have focused on how antagonistic and mutualistic interactions shape the phenotypic divergence of widespread non-endemic species living on island populations. </span></p> <p><span><strong>Methods</strong>:</span><span> We used the widespread plant <em>Tribulus</em> <em>cistoides</em> (Zygophyllaceae) to test phenotypic divergence in traits that mediate antagonistic interactions with vertebrate granivores (birds) and mutualistic interactions with pollinators and how this is explained by bioclimatic variables. We used both herbarium specimens and field-collected samples to compare phenotypic divergence between continental and island populations. </span></p> <p><span><strong>Results</strong>:</span><span> Fruits from island populations were larger than on continents, but the presence of lower spines on mericarps was lower on islands. The presence of spines was largely explained by environmental variation among islands. Petal length was on average 9% smaller on island than continental populations, an effect that was especially accentuated on the Galápagos Islands. </span></p> <p><span><strong>Conclusions</strong>:</span><span> <em>Tribulus</em> <em>cistoides</em> exhibits phenotypic divergence between island and continental habitats for antagonistic traits (seed defence) and mutualistic traits (floral traits). Further, the evolution of phenotypic traits that mediate antagonistic and mutualistic interactions depended on the abiotic characteristics of specific islands. This study shows the potential of using a combination of herbarium and field samples for comparative studies on a globally distributed species to test phenotypic divergence on island habitats.</span></p>

opencc-zeroJan 2023View details →
dryad40/100

Energy allocation explains how protozoan phenotypic traits change in response to temperature and resource supply

Open the record for dataset details and reuse information.

publicMar 2024View details →
dryad40/100

Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)

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publicJan 2023View details →
dryad40/100

Data from: Is phenotypic plasticity use-it-or-lose-it? Exploring genetic assimilation of salinity-plastic traits across threespine stickleback (<em>Gasterosteus aculeatus</em>) populations

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publicOct 2025View details →
dryad40/100

Data from: Linking divergence in phenotypic selection on floral traits to divergence in local pollinator assemblages in a pollination-generalized plant

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publicOct 2024View details →
dryad40/100

Improving wheat yield prediction using secondary traits and high-density phenotyping under heat stressed environments

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publicSep 2021View details →
dryad40/100

Data from: Genetic and environmental effects on morphological traits of social phenotypes in wasps

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publicJul 2024View details →
dryad36/100

Data from: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees

<p>Metabolic rate is often cited as the fundamental rate that determines the rate of all biological processes by shaping energetic availability for the various behavioral and life history traits that contribute to performance. It has therefore been suggested that metabolic rate drives the widely observed covariance among these different levels of phenotypic traits. However, much of the work on this topic has relied on pairwise correlational analysis, thereby leaving an important gap in our understanding regarding the functional links that shape this phenotypic covariance, often referred to as pace-of-life. Using honeybees as an experimental model, we measured a large number of behavioural, life history and physiological traits in individual bees and used a structural equation model to characterize the phenotypic covariance structure among these traits. Following this with a path analysis, we demonstrate that variation in metabolic rate plays a fundamental proximate role in driving this phenotypic covariance structure in honeybees. We discuss the importance of these findings in the context of how interindividual variation in terms of slow-fast phenotypes may drive the phenotype of a group and the functional role metabolic rate might play in shaping division of labour and social evolution.</p>

opencc-zeroOct 2020View details →
zenodo36/100

Does the spatial sorting of dispersal traits affect the phenotype of the non-dispersing stages of the invasive frog Xenopus laevis through coupling?

<p>Over ten weeks, we surveyed the development of <em>X. laevis</em> tadpoles in the French invasive range by&nbsp;conducting&nbsp;experiments in outdoor mesocosms and in laboratory microcosms, from free-swimming larvae to metamorphosis. We tested the effect of the location of the parental pond in the colonised range (core or periphery) on morphological traits related to dispersal (SVL and hind limb length), time to metamorphosis (development) and survival to metamorphosis. This excel spreadsheet contains the metadata and data spreadsheets used in the analysis. In addition to the first metadata sheet, the file contains nine additional sheets each containing data used in the separate analysis as outlined in the manuscript.&nbsp;</p>

opencc-by-4.0Oct 2020View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated 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.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

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.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

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.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

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.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

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.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record