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5,828 results for “Traits”
Experimental evidence for short term directional selection of epigenetic trait variation
<p>This Arabidosis data folder includes 5 folders providing the data and code associated with the publication entitled "Experimental evidence for short term directional selection of epigenetic trait variation" by Pujol et al. in Peer Community Journal:</p> <p>"in Silico 1000 resampling" folder includes two folders; one for Population 1, and one for Population 2, each including 24 files. Each file presents the 1000 lists of plant IDs that were randomly sampled to build control groups (listrand), and the corresponding lists of plant IDs selected on the basis of trait values to build the corresponding high (Top) and low (Bot) selection lines, for the strong (20) and weak (60) selection intensities.</p> <p>“phenotypic and epiril data” includes two csv files; data_pop1 and data_pop2, respectively for population 1 and 2, and a readme txt file that presents the data included in the files.</p> <p>“scripts R epigenomic selection” includes two R script files: “PCA_arabidopsis”, which includes the R code used to conduct the PCA analysis on epiRIL data and “Arabette_analysis_loop_Epigenotypes_data”, which is used to insert that epigenotype data in the analysis.</p> <p>“scripts R epigenomic validation” includes nine R scripts used to conduct tests of molecular epigenomic data validation and comparison with existing data from the literature: “Script 1 Extract 126 markers from BSMAP ouput files and apply methylkit”, “Script 2 Boxplots of the BS signal distribution for the 126 markers and their correspondence to published HMM classification”, “Script 3 Correlation between EM-seq and BS seq_published_data for the 126 markers”, “Script 4 Correlation between the BS signals of EM-seq and WGBS data for the 126markers”, “Script 5 Hierarchical clustering of the epiRILs EM-seq and published epigenomic data”, “cluster and PCA analysis of Col wt vs 24 sequenced epiRILs”, which filenames are self-explanatory. “methylkit_epiRILs_vs_Col_wt_DMCs” was used to use methylkit in order to identify Differentially Methylated Cytosines between epiRILs and in comparison to Col-0. “methylkit_tiles_script” was used to build the tiles in Methylkit. “verif DMR CHG context” was used to verify differentially methylated regions in the CHG context.</p> <p>“scripts R phenotypic selection” includes four R scripts “Arabette_analysis”, “Arabette_analysis_loop_Phenotypes_data”, “Arabette_analysis_loop_pop1_final”, “Arabette_analysis_loop_pop2_final” that were used to estimate the parameters used for comparing selection treatments, in other words, to estimate means and confidence intervals (“loop” scripts) in population 1 (“pop1” script) and population 2 (“pop2” script)</p>
Data from: Dispersal and establishment traits provide a colonization advantage for a polyploid apomictic plant
<p><span><strong>Premise</strong>: Apomictic plants (reproducing asexually through seed) often have larger ranges and occur at higher latitudes than closely related sexuals, a pattern known as geographical parthenogenesis (GP). Explanations for GP include differences in colonizing ability due to reproductive assurance and direct/indirect effects of polyploidy (most apomicts are polyploid) on ecological tolerances. While life history traits associated with dispersal and establishment also contribute to the potential for range expansion, few studies compare these traits in related apomicts and sexuals. </span></p> <p><span><strong>Methods</strong>: We investigated differences in early life history traits between diploid-sexual and polyploid-apomictic <em>Townsendia hookeri </em>(Asteraceae), which displays a classic pattern of GP. Using lab and greenhouse experiments, we measured seed dispersal traits, germination success, and seedling size and survival in sexual and apomictic populations from across the range. </span></p> <p><span><strong>Key Results</strong>: While theory predicts that trade-offs between dispersal and establishment traits should be common, this was largely not the case in <em>T. hookeri</em>. Apomictic seeds had both lower terminal velocity (staying aloft longer when dropped) and higher germination success than sexual seeds. While there were no differences in seedling size between reproductive types, apomicts did, however, have slightly lower seedling survival than sexuals. </span></p> <p><span><strong>Conclusions</strong>: These differences in early life history traits, combined with reproductive assurance conferred by apomixis, suggest that apomicts achieve a greater range through advantages in their ability to both spread and establish. </span></p>
Data - Krieg et al. (2023) Functional Traits and Trait Co-ordination Change Over the Life of a Leaf in a Tropical Fern Species. AJB.
<p>Summary of the data set used in Krieg et al. (2023) Functional Traits and Trait Co-ordination Change Over the Life of a Leaf in a Tropical Fern Species. AJB.</p>
Trait-dependent diversification in angiosperms: Patterns, models and data
<p>Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to dataset properties – trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.</p>
Molecular mapping of quantitative trait loci (QTL) for resistance to early blight in tomato
<p>Molecular mapping of quantitative trait loci (QTL) for resistance to early blight in tomato (1135884)</p>
Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
<p>1. Crop diversification offers a promising solution to meet expanding global food demands while maintaining ecosystem services. Diversification strategies that employ mixed planting to reduce pest damage (e.g., intercropping), termed "associational effects" (AE) in the ecological literature, can decrease (associational resistance) or increase (associational susceptibility) herbivore abundance on a focal plant. While application of AE to agroecosystems typically reduces pest abundance, the range of outcomes varies widely.</p> <p>2. We conducted a meta-analysis using 272 estimates of insect herbivore abundance on crops neighbored by a conspecific or heterospecific from 44 studies undertaken on six continents. We focus on four agricultural crops well-represented from sites across the globe to test hypotheses related to understanding how herbivore traits (diet breadth, feeding guild, origin), plant traits (crop type, phylogenetic distance to neighbor), and environmental context (climate, experimental design) contribute to variation in the outcomes of associational effects.</p> <p>3. Overall, bicultures provided a strong reduction of insect abundance on the focal crop. Climate and interactions between herbivore traits, particularly diet breadth and origin, and plant traits or environmental context mediated the strength of associational effects.</p> <p>4. Bicultures provided the strongest reductions in insect abundance at low latitudes and this effect decreased at higher latitudes, but only for insects with certain traits. Abundance of generalist herbivores and globally distributed pests tended to be most strongly negatively affected by bicultures, under certain contexts, whereas specialist herbivores and native pests were less affected by neighbors.</p> <p>5. Synthesis and application. This meta-analysis highlights that variability in AE is determined in part by the interactive effects of herbivore traits and environmental context and provides guidance for incorporating beneficial ecological interactions into integrated pest management strategies.</p>
Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests
<p><span>1. Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity. </span></p> <p><span>2. We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at twenty-four plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for: (1) nutrient-based species sorting due to contrasting trait-environment relationships; (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy; and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability.</span></p> <p><span>3. We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient-based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at the site level. At a plot level soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister-species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades. </span></p> <p><span>4. Synthesis. Our results demonstrate that soil nutrient-based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.</span></p>
Global intraspecific trait-climate relationships for grasses are linked to a species' typical form and function
<p>Plant traits are useful for predicting how species may respond to environmental change and/or influence ecosystem properties. Understanding the extent to which traits vary within species and across climatic gradients is particularly important for understanding how species may respond to climate change. We explored whether climate drives spatial patterns of intraspecific trait variation for three traits (specific leaf area (SLA), plant height, and leaf nitrogen content (Nmass)) across 122 grass species (family: Poaceae) with a combined distribution across six continents. We tested the hypothesis that the sensitivity (i.e., slope) of intraspecific trait responses to climate across space would be related to the species' typical form and function (e.g., leaf economics, stature, and lifespan). We observed both positive and negative intraspecific trait responses to climate with the distribution of slope coefficients across species straddling zero for precipitation, temperature, and climate seasonality. As hypothesized, variation in slope coefficients across species was partially explained by leaf economics and lifespan. For example, acquisitive species with nitrogen-rich leaves grew taller and produced leaves with higher SLA in warmer regions compared to species with low N<sub>mass</sub>. Compared to perennials, annual grasses invested in leaves with higher SLA yet decreased height and N<sub>mass</sub> in regions with high precipitation seasonality. Thus, while the influence of climate on trait expression may at first appear idiosyncratic, variation in trait-climate slope coefficients is at least partially explained by the species' typical form and function. Overall, our results suggest that a species' mean location along one axis of trait variation (e.g., leaf economics) could influence how traits along a separate axis of variation (e.g., plant size) respond to spatial variation in climate.</p>
High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude
<p>Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion, and calculated seven complementary indices of functional diversity for 144 species of marine ray-finned fishes along large-scale depth (50 m – 1200 m) and latitudinal gradients (29° – 51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo-Video systems and museum specimens. We partitioned functional variation into intra- and inter-specific components for the first time using a PERMANOVA approach. We also implemented two tree-based diversity metrics in a functional distance-based context for the first time: namely, the variance in pairwise functional distance, and the variance in nearest-neighbour distance. Functional alpha diversity increased with increasing depth, and decreased with increasing latitude. More specifically, the dispersion and mean nearest-neighbour distances among species in trait space, and intra-specific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion and regularity indices all decreased with increasing latitude; however, intra-specific trait variation increased with latitude, suggesting that intra-specific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multi-dimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.</p>
Raw data drosophila parasitoids sampled in 2008 life history traits
<p>Sampling of parasitoids in 2008 and 2011</p> <p>Life history and physiological traits measurements at different temperatures : developement time, fecundity, mass, metabolic rate, etc.</p> <p> </p>
CanFlyet: Habitat zone and diet trait dataset for Diptera species of Canada and Greenland
<p>True flies (Diptera) are an ecologically important group that play a role in agriculture, public health, and ecosystem functioning. As researchers continue to investigate this order, it is beneficial to link the growing occurrence data to biological traits. However, large-scale ecological trait data are not readily available for fly species. While some databases and datasets include fly data, many ecologically relevant traits for taxa of interest are not included. In this dataset we provide ecological traits (habitat and diet) for fly species of Canada and Greenland having occurrence records on the Barcode of Life Data Systems (BOLD). Trait data were compiled based on literature searches conducted from April 2021 - January 2023 and assigned at the lowest taxonomic level possible. The dataset contains traits for 983 species across 380 genera, 25 subfamilies, and 61 families. This dataset allows for assignment of traits to occurrence data for Diptera species and can be used for further research into the ecology, evolution, and conservation of this order. </p>
Global dataset for "Global leaf-trait mapping based on optimality theory "
<p>This repository contains Global data used for “<em>Global leaf-trait mapping based on optimality theory</em><strong>” </strong>published in GEB.</p> <ol> <li>Global_Maps_SLA represents climatology of published Global SLA used for comparison (details products see table 1 and figure 4).</li> <li>Global_Maps_Na represents climatology of published Global Narea used for comparison (details see table 1 and figure 4).</li> <li>Global_Maps_Nmass represents climatology of published Global Nmass used for comparison (details see table 1 and figure 4).</li> <li>TS_SLA is simulated time-series of <em>SLA</em> based on optimality theories from 1992 to 2015</li> <li>TS_Na is simulated time-series of <em>Narea </em>based on optimality theories from 1992 to 2015</li> <li>TS_Nmass is simulated time-series of <em>Nmass </em>based on optimality theories<em> </em> from 1992 to 2015</li> <li>TS_LMA_decidudous is simulated time-series of deciduous <em>LMA</em> based on optimality theories from 1982 to 2016</li> <li>TS_LMA_evergreen is simulated time-series of evergreen <em>LMA</em> based on optimality theories from 1982 to 2016</li> <li>TS_Vcmax25 is simulated time-series of Vcmax25 based on optimality theories from 1982 to 2016</li> </ol>
Metadata for various molecular traits included in the eQTL Catalogue
<p>Metadata for various molecular traits included in the eQTL Catalogue. </p> <p>Metadata files for the Leafcutter datasets can be found <a href="https://doi.org/10.5281/zenodo.7850746">here</a>.</p> <p>The tab-separated files contain the following columns:</p> <ul> <li><strong>phenotype_id</strong> - ID of the molecular trait that has been quantified. This can be either the gene ID (RNA-eq eQTLs), probe ID (microarray eQTLs), transcript ID (full-length transcript usage QTLs), splice junction ID (Leafcutter), exon id (exon-level QTLs) or any other molecular trait that has been quantified.</li> <li><strong>quant_id</strong> - Used to quantify relative transcript usage or relative transcriptional event usage (in txrevise). </li> <li><strong>group_id</strong> - Used for transcript usage and splicing phenotypes. Overlapping phenotypes whose relative expression is quantified belong to the same group (e.g. alternative spliced exons form clusters in Leafcutter). QTLTools permutation p-values are calculated accross all phenotypes within a group and only the phenotype with the smallest permutation p-value is reported.</li> <li><strong>gene_id</strong> - Ensembl gene id</li> <li><strong>chromosome</strong> - Chromosome of the gene</li> <li><strong>gene_start</strong> - End coordinate of the gene (GRCh38)</li> <li><strong>gene_end</strong> - Start coordinate of the gene (GRCh38)</li> <li><strong>strand</strong> - Strand of the gene</li> <li><strong>gene_name</strong> - Gene name extracted from Ensembl biomart.</li> <li><strong>gene_type</strong> - Gene type extracted from Ensembl biomart.</li> <li><strong>gene_gc_content</strong> - Percentage GC content of the gene. Extracted from Ensembl biomart and used as a covariate in cqn normalisation. Calculated with bedtools nuc for exons.</li> <li><strong>gene_version</strong> - Ensembl gene version</li> <li><strong>phenotype_pos</strong> - Genomic position used to determine the centre point of the <em>cis-</em>window for QTL mapping. By default this is the beginning of the gene (either gene start or gene end, depending on the strand of the gene).</li> <li><strong>phenotype_length</strong> - (optional) - Length of the gene or exon in basepairs. Required to properly normalise featureCounts quantification results with cqn.</li> </ul>
Herbarium specimens reveal century-long trait shifts in poison ivy due to anthropogenic CO2 emissions
<p>Dataset for manuscript entitled "Herbarium specimens reveal century-long trait shifts in poison ivy due to anthropogenic CO<sub>2</sub> emissions." Contains one spreadsheet file ("Ng et al 2023 Poison Ivy trait data.xlsx"). Note that metadata can be found in first tab.</p>
Data from: N-dimensional hypervolumes in trait-based ecology: does occupancy rate matter?
<p>Many methods for estimating functional diversity of biological communities rely on measuring geometrical properties of n-dimensional hypervolumes in a trait space. To date, these properties are calculated from individual hypervolumes or from their pairwise combinations. Our capacity to detect functional diversity patterns due to the overlap of multiple hypervolumes is thus limited.</p> <p>Here, we propose a new approach for estimating functional diversity from a set of hypervolumes. We rely on the concept of occupancy rate, defined as the mean or absolute number of hypervolumes enclosing a given point in the trait space. Furthermore, we describe a permutation test to identify regions of the trait space in which the occupancy rate of two sets of hypervolumes differs.</p> <p>We illustrate the utility of our approach over existing methods with two examples on aquatic macroinvertebrates. The first example shows how occupancy rate relates to the stability of trait space utilisation due to increased flow intermittency and allows the identification of taxa in regions of the trait space with low occupancy rates. The second example shows how the permutation test based on occupancy rates can detect differences in trait space utilisation due to river morphology variation even with a high degree of overlap among input hypervolumes.</p> <p>Our newly developed approach is particularly suitable in functional diversity analysis when investigating patterns of overlap among multiple hypervolumes. We thus emphasise the need to consider analyses based on occupancy rate into functional diversity estimation.</p>
Hummingbird blood traits track oxygen availability across space and time
<p>Predictable trait variation across environments suggests shared adaptive responses via repeated genetic evolution, phenotypic plasticity, or both. Matching of trait-environment associations at phylogenetic and individual scales implies consistency between these processes. Alternatively, mismatch implies that evolutionary divergence has changed the rules of trait-environment covariation. Here we tested whether species adaptation alters elevational variation in blood traits. We measured blood for 1,217 Andean hummingbirds of 77 species across a 4,600 m elevational gradient. Unexpectedly, elevational variation in hemoglobin concentration ([Hb]) was scale independent, suggesting that physics of gas exchange, rather than species differences, determine responses to changing oxygen pressure. However, mechanisms of [Hb] adjustment did show signals of species adaptation: Species at either low or high elevations adjusted cell size, whereas species at mid-elevations adjusted cell number. This elevational variation in red blood cell number-versus-size suggests that genetic adaptation to high altitude has changed how these traits respond to shifts in oxygen availability.</p>
Figure 3 in Sublethal effects of spiromesifen on life table traits ofTetranychus urticae (Acari: Tetranychidae) andNeoseiulus californicus (Acari: Phytoseiidae)
Figure 3 Age-stage life expectancy (exj) of two generations of Tetranychus urticaeexposed to LC20 of spiromesifen.
Figure 6 in Sublethal effects of spiromesifen on life table traits ofTetranychus urticae (Acari: Tetranychidae) andNeoseiulus californicus (Acari: Phytoseiidae)
Figure 6 Age-stage survival rate (sxj) and age specific survival rate (lx), fecundity (mx), and net maternity l(xmx) of Neoseiulus californicus exposed to LC20 of spiromesifen.
Figure 2 in Sublethal effects of spiromesifen on life table traits ofTetranychus urticae (Acari: Tetranychidae) andNeoseiulus californicus (Acari: Phytoseiidae)
Figure 2 Age specific survival rate (lx), fecundity (mx), and net maternity l(xmx) of two generations of Tetranychus urticaeexposed to LC20 of spiromesifen.
Data from: Transgressive segregation in mating traits drives hybrid speciation
<p><span>Hybridization can instantaneously generate novel genetic variation, which can promote ecological speciation by creating novel adaptive phenotypes. However, it remains unclear how hybridization, creating novel mating phenotypes (e.g., mating season, genitalia shapes, sexual displays, mate preferences), affects speciation especially when the phenotypes do not confer adaptive advantages. Here, based on individual-based evolutionary simulations, we propose that transgressive segregation of mating traits can drive incipient hybrid speciation. Simulations demonstrated that incipient hybrid speciation occurred most frequently when the hybrid population received moderate continued immigration from parental lineages</span><span> causing </span><span>recurrent episodes of hybridization. Recurrent hybridization constantly generated genetic variation, which </span><span>promoted</span> <span>the rapid stochastic evolution of mating phenotypes</span><span> in a hybrid population.</span><span> The stochastic evolution continued until a novel mating phenotype came to dominate the hybrid population, which reproductively isolates the hybrid population from parental lineages. However, too </span><span>frequent hybridization rather hindered the evolution of reproductive isolation by inflating the variation of mating phenotypes to produce phenotypes allowing mating with parental lineages. Simulations also revealed conditions for long-term persistence of hybrid species after their incipient emergence. </span><span>Our results suggest that recurrent transgressive segregation of mating phenotypes can offer a plausible explanation for hybrid speciation and radiations that involved little adaptive ecological divergence.</span></p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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