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5,828 results for “traits”
ShareTrait: a data portal for making trait data interoperable and reusable
<p><strong>Scope</strong></p> <p>This dataset provides the SQL version of the ShareTrait database, corresponding to <strong>ShareTrait version 1.2.0</strong>. It represents the structured database equivalent of the previously published dataset, <strong>ShareTrait: a data portal for making trait data interoperable and reusable</strong>, version 1.0.0 (Zenodo, July 12, 2023, <a href="https://doi.org/10.5281/zenodo.8138904" target="_new" rel="noopener">DOI: 10.5281/zenodo.8138904</a>). This version includes the database file, an SQL query, and the resulting output file generated from the SQL query. </p> <p><strong>Dataset content</strong></p> <p>The repository provides:</p> <ul> <li><strong>ShareTrait-database-v1.2.0.db</strong> : the database file.</li> <li><strong>master-query-all.sql</strong> : SQL query used for reconstructing the dataset.</li> <li><strong>master-query-output.csv</strong> : SQL query output file .</li> <li><strong>ShareTrait-dataset-database-mapping.csv</strong> : mapping of attribute fields from the SQL query output to the corresponding attributes in <a href="/records/8138904/files/ShareTrait_MetaData_v1.0.0.csv?download=1">ShareTrait_MetaData_v1.0.0.csv</a>, with relevant column name = "Column_name", version 1.0.0 (<a href="https://doi.org/10.5281/zenodo.8138904" target="_new" rel="noopener">DOI: 10.5281/zenodo.8138904</a>)</li> </ul> <p><strong>Access and usage</strong></p> <p>Files and documentation are available on GitHub: <a href="https://github.com/ShareTraitProject" target="_new" rel="noopener">ShareTrait Project</a>. Users can execute the SQL query by using either SQLiteStudio or SQLite3. Detailed instructions are provided in this repository <strong>README</strong>.</p> <p><strong>Citation</strong></p> <p>When using this dataset, please provide the following citation:</p> <p>Leiva, F., Ellers, J., Berg, M. P., Cuxart-Erruz, R., Barneche, D., Blackburn, T., Castañeda, L. E., Chown, S., Gaitán-Espitia, J. D., Gebauer Mery, P. H., Gomez Isaza, D., Hardy, I., Hermaniuk, A., Hirst, A., Jorissen, S., Keasar, T., Koene, J. M., Le Lann, C., Martorelli, I., Molinet C., Niklitschek E.J., Oliveira B., Olivier B., Orizaola G., Pilakouta N., Shameer K.S., Shokri M., Stoks R., Tougeron K., Tuni C., van de Pol I.L.E., van Dis N.E., Visser B., Vogels J., White C.R., Wu N., and Verberk W. (2025). ShareTrait: a data portal for making trait data interoperable and reusable (version 1.2.0) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.14826294" target="_new" rel="noopener">https://doi.org/10.5281/zenodo.14826294</a></p> <p>For further information, please contact: <a rel="noopener">i.martorelli@vu.nl</a></p>
Zooplankton functional trait database for Canadian lakes
<p>This dataset contains functional traits of 102 crustacean zooplankton taxa sampled in 624 Canadian lakes (Pelagic sample), as well as 58 sub-fossil cladoceran taxa (Sediments sample) sampled in 101 lakes. Lakes were sampled across Canada as part of the NSERC Canadian LakePulse Network. The traits used are: feeding type (B(<em>Bosmina</em>)-filtration, C(<em>Chydorus</em>)-filtration, D(<em>Daphia</em>)-filtration, S(<em>Sidae</em>)-filtration, stationary suspension or raptorial), habitat (littoral, pelagic or intermediate) and trophic group (carnivore, herbivore, omnivore, or a combination of these). Pelagic species length of up to 10 individuals per taxon per lake were measured by BSA Environmental Services (Ohio, U.S.A.), and averaged for each taxon. Sediments sample lengths were either obtained from the literature (Demott & Kerfoot, 1982; Barnett et al., 2007; Griffiths et al., 2019), or from the Pelagic sample length data. Feeding type, habitat and trophic group functional traits were obtained from literature (Demott & Kerfoot, 1982; Barnett et al., 2007; Hébert et al., 2016; Griffiths et al., 2019).</p> <p>References</p> <p>Barnett, A. J., Finlay, K., & Beisner, B. (2007). Functional diversity of crustacean zooplankton communities: Towards a trait-based classification. <em>Freshwater Biology</em>, <em>52</em>(5), 796–813. https://doi.org/10.1111/j.1365-2427.2007.01733.x</p> <p>Demott, W. R., & Kerfoot, W. C. (1982). Competition among cladocerans: nature of the interaction between Bosmina and Daphnia. <em>Ecology</em>, <em>63</em>(6), 1949–1966. https://doi.org/10.2307/1940132</p> <p>Griffiths, K., Winegardner, A. K., Beisner, B. E., & Gregory-Eaves, I. (2019). Cladoceran assemblage changes across the Eastern United States as recorded in the sediments from the 2007 National Lakes Assessment, USA. <em>Ecological Indicators</em>, <em>96</em>, 368–382. 061</p> <p>Hébert, M.-P., Beisner, B. E., & Maranger, R. (2016). A compilation of quantitative functional traits for marine and freshwater crustacean zooplankton. Ecology. https://doi.org/10.1890/15-1275</p>
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 Québec, 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> title={MSPB: a longitudinal multi-sensor dataset with phenotypic trait measurements from honey bees}, </p> <p> author={Yi Zhu and Mahsa Abdollahi and Ségolène Maucourt and Nico Coallier and Heitor R. Guimarães and Pierre Giovenazzo and Tiago H. Falk},</p> <p> year={2023},</p> <p> eprint={2311.10876},</p> <p> archivePrefix={arXiv},</p> <p> 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>
Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.
<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., & Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed explanation of the data.</p>
Genotyping-by-sequencing (GBS) dataset for genome wide associations of growth, phenology and plasticity traits in willow (Salix viminalis (L.))
<p>These vcf-files constitute underlying raw data material for the manuscript "Genome wide associations of growth, phenology and plasticity traits in willow (Salix viminalis (L.))". For more detailed information please consult the README file in the repository.</p>
Functional traits database for North American birds
<p>Estimation of functional diversity in biological communities requires extensive and complete data on numerous functional traits of species or even individuals. When estimating functional diversity at large scales, this fact possesses an issue that may be hard to overcome: for many species, there might not be sufficient data on their functional traits. In such cases, even if there is missing information on functional trait value for one species in a community, this makes the trait impossible to use for the estimation of the functional diversity of a community. On the other hand, there are available datasets on the functional traits of all extant species within certain lineages across the world, but such datasets are often limited to very few functional traits, missing some dimensions of species' ecological niches. In this dataset, I compiled the available data from various sources that describe 23 functional traits of 703 bird species that occur in Canada, the United States, and Mexico. These functional traits include the following: diet type, diurnal and nocturnal feeding, diet items, feeding methods, feeding substrate, nest type, nest substrates, breeding system, chick development at hatching, nest aggregation, clutch size, first breeding age, number of clutches a year, breeding success, adult annual survival, mean biomass, maximum lifespan, hand-wing index, kleptoparasitism, nest parasitism, and the extent of dependency on other species for building a nest.</p>
Priority effects can be explained by competitive traits
<p>Code (updated after review)</p> <p>Traits - Trait values that were measurent and calculated from the individuals grown alone (updated after review).</p> <p>See version 2 for other files </p>
Morpho-anatomical traits explain the effects of bacterial-feeding nematodes on soil bacterial community composition and plant growth and nutrition
<p>Soil Bacterial populations</p> <p>V3-V4, of the 16S rRNA gene using the primers 341F CCTAYGGGRBGCASCAG and 806R GGACTACNNGGGTATCTAAT.</p>
Python code for "Evolutionary epidemiology consequences of trait-dependent control of heterogeneous parasites"
<p>The file contains the Python code used to run the agent-based simulation of the selection-mutation model presented in "Evolutionary epidemiology consequences of trait-dependent control of heterogeneous parasites"</p>
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Supplementary data: Agro-morphological and molecular characterization reveal deep insights in promising genetic diversity and marker-trait associations in Fagopyrum esculentum and F. tataricum
<p>Our study focuses on the global/European buckwheat germplasm collected as part of the ECOBREDD project. The potential of this highly diverse collection for organic buckwheat breeding was evaluated at two complementary levels: phenotypic and genetic. Here, we characterized the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <em>Fagopyrum esculentum</em> and <em>F. tataricum</em> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers (Simple Sequence Repeats) (see publication and info sheet of the data).</p>
Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests
Biodiversity in many areas is rapidly shifting and declining as a consequence of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor, and conserve biodiversity hotspots. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the trait information required to evaluate functional diversity is often lacking and is difficult to harmonize across disparate data sources. Biodiversity hotspots are particularly lacking in this information. To address this knowledge gap, we compiled Frugivoria, a trait database containing dietary, life-history, morphological, and geographic traits, for mammals and birds exhibiting frugivory, which are important for seed dispersal, an essential ecosystem service. Accompanying Frugivoria is an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyze traits in space. This version of Frugivoria contains mammal and bird species found in contiguous moist montane forests and adjacent moist lowland forests of Central and South America– the latter specifically focusing on the Andean states. In total, Frugivoria includes 45,216 unique trait values, including new values and harmonized values from existing databases. Frugivoria adds 23,707 new trait values (8,709 for mammals and 14,999 for birds) for a total of 1,733 bird and mammal species. These traits include diet breadth, habitat breadth, habitat specialization, body size, sexual dimorphism, and range-based geographic traits including range size, average annual mean temperature and precipitation, and metrics of human impact calculated over the range. Frugivoria fills gaps in trait categories from other databases such as diet category, home range size, generation time, and longevity, and extends certain traits, once only a
Regional and local variation in chemical, structural, and physical leaf traits for tree species in the northeastern United States, 2016-2023.
This dataset is a compilation of leaf trait measurements for 25 different Northern American tree species in the northeastern United States collected between 2016 and 2023 by the Terrestrial Ecosystems Analysis Lab at the University of New Hampshire. Currently, this dataset contains measurements for 2,006 samples across 18 chemical, physical, and structural traits. Measured traits include stable isotopes for carbon (C) and nitrogen (N), chlorophyll estimates, leaf and petiole dimensions, and leaf and petiole water content. Traits have been measured at plots spanning a wide range of latitude, longitude, elevation, and forest types. A simple table containing these plot descriptions has been included. Additional leaf physiological and optical traits have been measured concurrently on many of these samples and have been or will be published separately. This is a continuous dataset that will be updated on an as needed basis.
CoRRE Trait Data: A collection of 17 categorical and continuous traits for more than 4000 grassland species worldwide
In our changing world, it is critical to understand and predict plant community responses to global change drivers. Plant functional traits promise to be a key predictive tool for many ecosystems, including grasslands, however their use requires both complete plant community and functional trait data. Yet, representation of these data in global databases is incredibly sparse, particularly beyond a handful of most used traits and common species. Here we present the CoRRE Trait Database, spanning 17 traits (9 categorical, 8 continuous) anticipated to predict species’ responses to global change for 4,079 vascular plant species across 173 plant families present in 390 grassland experiments from around the world. The database contains complete categorical trait records for all 4,079 plant species, obtained from a comprehensive literature search. Additionally, the database contains nearly complete coverage (99.97%) of species mean values for continuous traits for a subset of 2,927 plant species, predicted from observed trait data drawn from TRY and a variety of other plant trait databases using Bayesian Probabilistic Matrix Factorization (BHPMF) and multivariate imputation using chained equations (MICE). These data will shed light on mechanisms underlying population, community, and ecosystem responses to global change in grasslands worldwide.
Understory percent cover, plant traits, canopy LAI, PAR, temperature, and soil moisture data at multiple time points for sites in the burn chronosequence and Indian Point forest at the University of Michigan Biological Station, Pellston, MI (2022-2023)
Community ecology has sought to understand the mechanisms by which plant communities are assembled through time and space. One prominent way to address how communities are assembled is by quantifying functional traits. While there is a tremendous body of literature on functional traits, debate persists about how to account for variation in measured traits. For example, intraspecific trait variation (ITV) can be equal to or greater than interspecific trait variation and ITV has also been found to vary greatly across years. Therefore, there is a need to account for variability in functional trait measures among and within species and through time to improve our understanding of community assembly. Chronosequences are a powerful tool to address temporal changes in community dynamics, however, the inclusion of understory plants in forest chronosequence studies is still relatively uncommon. Previous chronosequence studies have been primarily performed in grasslands or in a limited subset of forest types, so further work is needed in understory plant traits across other ecosystems and climates to improve trait-based understanding of understory plant communities through time. Additionally, because plant traits change as ecosystems age, community interactions are likely to change with ecosystem age. Interactions of particular interest are herbivory, arthropod predation, and the influence of plant traits on arthropod diversity.
Environmental, community and trait data of small water bodies in Zijin Mountain, Nanjing, Jiangsu, China, 2022
Small water bodies (SWBs) are vulnerable to drought and play a vital role in the conservation of aquatic biodiversity. Currently climate change is intensifying the seasonal drought of SWBs in monsoonal east Asia. However, little is known about the response of benthic macroinvertebrates of small ponds and streams that simultaneously suffer from climate-induced extreme drought. This study aimed to explore the taxonomic and functional response of macroinvertebrates in ponds and streams, either respectively or jointly, to extreme summer drought. We calculated taxonomic and functional diversity indices of communities in 11 streams and 12 ponds across three seasons: spring, summer and winter in 2022. We performed a permutational multivariate analysis of variance, Moran’s eigenvector maps, Moran Spectral Randomization based variation partitioning and convex hull analysis of trait space to examine temporal compositional and functional, as well as trait changes, and the contributions of environmental and spatial factors in shaping communities. The responses of taxonomic and functional diversity in ponds and streams were contrasting during the summer drought. Ponds showed increased taxonomic richness (TR), functional richness (FRic), functional richness (FRed) and trait space volume, while streams experienced decreased TR, FRic and trait space volume but increased FRed. The taxonomic and functional increases of ponds were driven by an influx of generalist taxa from streams, while the increase of FRed in streams resulted from the loss of species with strong dispersal and lentic adaptation traits. Dispersal played a more significant role than environmental filtering in shaping community structure during the drought, especially for streams lacking hydrological connectivity. This study provides the first insights into the complex response of macroinvertebrates to summer drought of SWBs in east Asia monsoonal region. Our results underscore the refuge effect of ponds during summer
American Residential Macrosystems - Leaf functional traits and raw data in five major metropolitan areas, 2012-2013
"We used leaf functional traits in residential yards and nearby natural areas to assess biotic ecological homogenization in five cities across the U.S. that span major ecological biomes and climatic regions: Baltimore, MD, Boston, MA, Los Angeles, CA, Miami, FL, and Minneapolis-St. Paul, MN."
Freshwater insect occurrences and traits for the contiguous United States, 2001 - 2018
Freshwater insects comprise 60% of the diversity of freshwater animals and are essential indicators of ecosystem health. Yet our knowledge of the distribution of freshwater insect diversity in the United States is incomplete because we lack comprehensive data on freshwater insect distributions and traits at a continental scale. We fill this knowledge gap by presenting a database of occurrence records and functional traits for freshwater insects in the contiguous US. We compiled over 2.05 million genus occurrence records for 932 genera in the major freshwater insect orders, at 51,044 stream locations sampled between 2001 and 2018 by federal and state biological monitoring programs. We assembled life history, dispersal, morphology, and ecology traits from existing databases, scientific books, and the primary literature, and present traits and trait affinities for 1,072 insect genera. Our freshwater insects CONUS database can be used to map freshwater insect taxonomic and functional diversity, and when paired with environmental data, will provide a powerful resource for quantifying how the environment shapes diversity patterns as well as taxon-specific distributions across the contiguous US.
Species trait tissue chemistry: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Periphyton Abundance and Structural Traits, Diatom Taxa Relative Abundance, and Associated Environmental Data from Samples Collected from the Greater Everglades, Florida, USA from September 2005 - ongoing
This data package contains benthic algae (periphyton) and environmental data collected annually during the wet season between 2005 and 2021 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan (CERP MAP) intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units (LSU) and each year, random coordinates are 'drawn' within each PSU and one draw is visited in each sampleable PSU. Sampled periphyton is processed for aggregate structural traits (i.e., biomass, chlorophyll-a, organic content, and phosphorus concentration) and for diatom taxa. For diatoms, slides are prepared, and at least 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental and spatial data for each sampled draw. In addition to the CERP MAP data, this dataset also includes data on the same variables collected from up to 21 primary sampling units in the Broward County Water Preserve Area beginning in 2020. The data in this package replace and supersede those in package knb-lter-fce.1210 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1210).
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.