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193 results for “trait analysis”
Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes
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Data from: A phylogenetic- and trait-based analysis of community assembly in a subtropical forest in central China
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Data from: Phenotypic integration limits the variation in plant phenotypic plasticity among traits: a meta-analysis
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Data from: Inferring camera trap detection zones for rare species using species- and camera-specific traits: A meta-level analysis
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Data for: Phylogenetically controlled life history trait meta-analysis in cetaceans reveals unexpected negative brain size and longevity correlation
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Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
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Data for Analysis of Keystone Predation - trait based or driven by extrinsic processes?
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Data from: The comparative analysis of lineage-pair traits
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Data from: Comparative analysis of the multivariate genetic architecture of morphological traits in three species of Gomphocerine grasshoppers
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Social selection analysis reveals limited effect of neighbors’ traits in Tree swallows
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Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
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Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis
<p>We provide data and code needed to re-do the analyses and figures presented in our preprint <em>Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent </em>Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ):</p> <p>- data table : <em>data_repetition01.xls</em>, with informations about each column in the file <em>data_repetition_info.pdf</em></p> <p>- data table : <em>data_individual01.xls</em>, with informations about each column in the file <em>data_indivdual_info.pdf</em></p> <p><em>- </em>The R code used to do the analyses : <em>Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R</em></p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters
1. Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). 2. Here we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, e.g., on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. 3. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). 4. The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints i) among communities from different regions, ii) on different traits across similar environmental gradients, and iii) for the same trait across different gradient-types.
Data from: Trait-based functional dietary analysis provides a better insight into the foraging ecology of bats
1. The degree of trophic specialization determines the ability of predators to cope with changing foraging conditions, but in predators that prey on hundreds of species it is challenging to assess, especially when prey identity varies among predator individuals and across space and time. 2. Here, we test the hypothesis that a bat species foraging on flying insects like moths will show ample flexibility in trophic niche, and this irrespective of phylogenetic relationships among moths, so as to cope with a high diversity of prey types that vary across seasons. We predict that individual bats will show functional dietary differences consistent with energetic requirements and hunting skills. 3. We used DNA metabarcoding to determine the diet of 126 Mediterranean horseshoe bats (Rhinolophus euryale) from two different sites during three seasons. Simultaneously, we measured moth availability and characterized the traits of 290 moth taxa. Next, we explored the relationship between phylogeny and traits of all consumed and available moth taxa. Finally, we assessed the relationship between individual traits of bats and traits related to prey profitability, for which we used the RLQ and fourth-corner statistical techniques. 4. Seasonality was the main factor explaining the functional dietary variation in adult bats, with moths consumed irrespective of their phylogenetic relationships. While adults consumed moths with a broad range in wing loading, body mass and echolocation detection ability, juveniles consumed slower, smaller and lighter moths, which suggests that young individuals may undergo some fitness gain and/or psychomotor learning process during which they would acquire more effective foraging skills. 5. Our approach revealed a degree of functional flexibility in the trophic niche previously unknown for an insectivorous bat. R. euryale consumed a wide variety of moth taxa differing in profitability throughout seasons and between ontogenetic stages. We showed the validity of trait-based approaches to gain new insights in the trophic specialization of predators consuming hundreds of species of prey.
Data from: Assessing the vulnerability of Africa's freshwater fishes to climate change: a continent-wide trait-based analysis
Climate change is a key driver of biodiversity loss across the globe, and freshwater fishes are predicted to be among the most vulnerable taxa. African freshwater ecosystems are home to one of the most unique and diverse ichthyo-faunas on the planet, and freshwater fish species provide essential livelihoods for millions of people living in riparian communities across the continent. Although nearly one sixth of African freshwater fishes have been designated as endangered or vulnerable to extinction by the IUCN Red List assessment, the effects of climate change on these species have not been explored on a continent-wide scale. In this study, we present the first trait-based climate change vulnerability assessment (CCVA) comprising the majority (85%) of Africa's currently described freshwater fishes. We assembled data relating to three dimensions of vulnerability including sensitivity, adaptive capacity, and exposure. In addition, we developed an index of 'conservation value' based on traditional conservation metrics including extinction risk, endemism, and provision of ecosystem services. We found that almost 40% of African freshwater fishes are vulnerable to climate change, mostly owing to the many species with highly specialized habitat and life-history requirements, and because of the numerous anthropogenic stressors they face. High proportions of species within the Nothobranchiidae and Cichlidae families were found to be vulnerable. Regions with high frequencies of vulnerable species included the African rift valley lakes, the Congo River drainage, and the coastal rivers of West Africa. Several important data deficiencies were identified relating to species' population sizes, genetic variability, and life history traits, and constitute priority research areas for the future. In addition, we highlighted some cases where traditional conservation approaches overlook species and regions that are predicted to be threatened by climate change.
Data from: Trait correlation network analysis identifies biomass allocation traits and stem specific length as hub traits in herbaceous perennial plants
Correlations among plant traits often reflect important trade‐offs or allometric relationships in biological functions like carbon gain, support, water uptake, and reproduction that are associated with different plant organs. Whether trait correlations can be aggregated to "spectra" or "leading dimensions," whether these dimensions are consistent across plant organs, spatial scale, and growth forms are still open questions. To illustrate the current state of knowledge, we constructed a network of published trait correlations associated with the "leaf economics spectrum," "biomass allocation dimension," "seed dimension," and carbon and nitrogen concentrations. This literature‐based network was compared to a network based on a dataset of 23 traits from 2,530 individuals of 126 plant species from 381 plots in Northwest Europe. The observed network comprised more significant correlations than the literature‐based network. Network centrality measures showed that size traits such as the mass of leaf, stem, below‐ground, and reproductive tissues and plant height were the most central traits in the network, confirming the importance of allometric relationships in herbaceous plants. Stem mass and stem‐specific length were "hub" traits correlated with most traits. Environmental selection of hub traits may affect the whole phenotype. In contrast to the literature‐based network, SLA and leaf N were of minor importance. Based on cluster analysis and subsequent PCAs of the resulting trait clusters, we found a "size" module, a "seed" module, two modules representing C and N concentrations in plant organs, and a "partitioning" module representing organ mass fractions. A module representing the plant economics spectrum did not emerge. Synthesis. Although we found support for several trait dimensions, the observed trait network deviated significantly from current knowledge, suggesting that previous studies have overlooked trait coordination at the whole‐plant level. Furthermore, network analysis suggests that stem traits have a stronger regulatory role in herbaceous plants than leaf traits.
Data from: Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis
Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter – which differentially affects individuals according to their characteristics and shapes species assemblages – and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal by ungulates in fragmented landscapes, comparing eight plant traits and two habitat indicators between dispersed and non-dispersed plants. We found that ungulates dispersed at least 44% of the available plant species. Moreover, some plant traits and habitat indicators increased the likelihood for plant of being dispersed. Persistent or nitrophilous plant species from open habitats or bearing dry or elongated diaspores were more likely to be dispersed by ungulates, whatever the dispersal mechanism. In addition, endozoochory was more likely for diaspores bearing elongated appendages whereas epizoochory was more likely for diaspores released relatively high in vegetation. Hoof-epizoochory was more likely for light diaspores without hooked appendages. Fur-epizoochory was more likely for diaspores with appendages, particularly elongated or hooked ones. We thus observed a gradient of filtering effect among the three dispersal mechanisms. Endozoochory had an effect of rather weak intensity (impacting six plant characteristics with variations between ungulate-dispersed and non-dispersed plant species mostly below 25%), whereas hoof-epizoochory had a stronger effect (eight characteristics included five ones with above 75% variation), and fur-epizoochory an even stronger one (nine characteristics included six ones with above 75% variation). Our results demonstrate that seed dispersal by ungulates is an ecological filter whose intensity varies according to the dispersal mechanism considered. Ungulates can thus play a key role in plant community dynamics and have implications for plant spatial distribution patterns at multiple scales.
Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa
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Source data of the MultiSTAAR manuscript "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies".
<p>This dataset serves as the source data for Figures 2-3 and Extended Data Figures 1-2 of the MultiSTAAR manuscript titled "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies". MultiSTAAR is a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies.<br><br><strong>Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and ncRNA multi-trait analysis of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerids (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Figure 3.</strong> TOPMed genetic region (2-kb sliding window) unconditional multi-trait analysis results of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Extended Data Figure 1.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of fasting glucose (FG) and fasting insulin (FI) using TOPMed data (<em>n</em> = 21,731).<br><br><strong>Extended Data Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of C-reactive protein (CRP), interleukin 6 (IL-6), lipoprotein-associated phospholipase A2 (Lp-PLA2) activity, and lipoprotein-associated phospholipase A2 (Lp-PLA2) mass using TOPMed data (<em>n</em> = 9,380).</p>
Fig. 2 in Gut-content analysis in four species, combined with comparative analysis of trophic traits, suggests an araneophagous habit for the entire family Palpimanidae (Araneae)
Fig. 2 Comparison of relative 1 conspeccfics spcders cnsects 1 frequency of conspecifics (can- A B nibalism), heterospecific spiders 0.9 0.9 (araneophagy), and insects in 0.8 0.8 the gut of P . gibbulus A, P . 0.7 0.7 potteri B , Diaphorocellus C and frequency Otiothops D . Proportions are 0.6 0.6 estimated per all individuals in e 0.5 0.5 a class (male, female, juvenile). 0.4 0.4 Frequency of cannibalism can be overestimated (see "Discus- Rela 0.3 0.3 sion" for more details), thus 0.2 0.2 should be interpreted with 0.1 0.1 caution 0 0 male female female juvencle adult juvencle adult
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.