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193 results for “trait analysis”
Minimal dataset for the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".
<p>Dataset "lin2024-sex_combined_interaction-association_signifincant_in_one_or_more_tests-summary.txt" is a minimal dataset to reproduce the figures and tables in the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank". </p> <p><br>To generate this dataset, see "https://github.com/BoxiLin/t2meta" Steps 0, 1.</p> <p>This dataset is the input for Steps 2, 3, 4, 5 to generate Figures 1-3 and Table 2-3.</p> <p> </p> <p>##### Column information ########################</p> <p>The following columns are annotations on each variant in the GWAS, calculated across the analysis subset of 361,194 samples by the Neale lab:</p> <p>code: Phenotype identifier in the form of "[UKB Data field]_raw"<br>variant: Unique variant identifier in the form "chr:pos:ref:alt", where "ref" is aligned to the forward strand.<br>chr: Chromosome of the variant.<br>pos: Position of the variant in GRCh37 coordinates.<br>rsid: rs ID<br>ref: Reference allele on the forward strand.<br>alt: Alternate allele (not necessarily minor allele).<br>p_hwe: Hardy-Weinberg p-value.<br>info: Imputation INFO score as provided by UK Biobank.</p> <p> </p> <p>The following columns are sex-stratified test statistics calculated by the Neale lab:</p> <p>minor_allele.x: Minor allele (AF < 0.5) in the female GWAS <br>minor_AF.x: Minor allele frequency in the female GWAS <br>beta.x: Estimated effect size of alt allele in the female GWAS <br>se.x: Estimated standard error of beta in the female GWAS<br>tstat.x: t-statistic of beta estimate (= beta/se) in the female GWAS <br>pval.x: p-value of beta significance test in the female GWAS </p> <p>minor_allele.y: Minor allele (AF < 0.5) in the male GWAS <br>minor_AF.y: Minor allele frequency in the male GWAS <br>beta.y: Estimated effect size of alt allele in the male GWAS <br>se.y: Estimated standard error of beta in the male GWAS <br>tstat.y: t-statistic of beta estimate (= beta/se) in the male GWAS <br>pval.y: p-value of beta significance test in the male GWAS </p> <p> </p> <p><br>The following columns are sex-combined test statistics calculated in our analysis:</p> <p>T.I: test statsitic for interaction effect-only <br>p.T.I: p-value of the interaction effect-only test <br>TSG.L: test statsitic for inverse variance weighted meta-analysis<br>p.TSG.L: p-value of the inverse variance weighted meta-analysis<br>TSG.Q: test statsitic for the omnibus meta-analysis<br>p.TSG.Q: p-value for the omnibus meta-analysis</p>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
Supplementary data: Effect of genotype by environment interaction (GEI) analysis for potato tuber yield and their quality traits in organic multi-environment domains of Poland
<p>Climate and raw data supplementary to the related publication in the journal Agriculture (ISSN 2077-0472).</p>
Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
<p><span><b>Aim: </b>Animal movement determines home range patterns, which in turn affect individual fitness, population dynamics and ecosystem functioning. Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data.</span></p> <p><span><b>Location</b>: Northern America and Europe.</span></p> <p><span><b>Time period</b>: 1988 – 2016.</span></p> <p><span><b>Major taxa studied</b>: Bats.</span></p> <p><span><b>Methods</b>: We compiled data on home range size and mean daily distance between roosts and foraging areas at both colony and individual levels from 166 studies of 3,129 radiotracked individuals of 49 bat species. We calculated multi-scale habitat composition and configuration in the surrounding landscapes of the 165 studied roosts. Using mixed models, we examined the effects of habitat availability and spatial arrangement on bat movements, while accounting for body mass, aspect ratio, wing loading and habitat specialization.</span></p> <p><span><b>Results:</b><i> </i>We found a significant effect of landscape composition on home range size and mean daily distance at both colony and individual levels. On average, home ranges were up to 42% smaller in the most habitat-diversified landscapes while mean daily distances were up to 30% shorter in the most forested landscapes. Bat home range size significantly increased with body mass, wing aspect ratio and wing loading, and decreased with habitat specialization.</span></p> <p><span><b>Main conclusions: </b>Promoting bat movements through the landscape surrounding roosts at large spatial scales is crucial for bat conservation. Forest loss and overall landscape homogenization lead temperate bats to fly farther to meet their ecological requirements, by increasing home range sizes and daily foraging distances. Both processes might be more detrimental for smaller, habitat-specialized bats, less able to travel increasingly longer distances to meet their diverse needs.</span></p>
Data for "Meta-analysis of induced anti-herbivore defence traits in plants from 647 manipulative experiments with natural and simulated herbivory"
<p>Data used in analysis in "Meta-analysis of induced anti-herbivore defence traits in plants from 647 manipulative experiments with natural and simulated herbivory" in Journal of Ecology. </p> <p>Code used for analysis are included as Supplementary Material of the main article. </p> <p> </p>
Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
<p>Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.</p>
A global analysis of aerial displays in passerines revealed an effect of habitat, mating system and migratory traits
<p><span>Aerial displaying is a flamboyant part of the sexual behaviour of several volant animal groups, including birds. Nevertheless, little attention has been focused on identifying correlates of large-scale diversity in this trait. In this study, we scored the presence and absence of aerial displays in males of 1,732 species of passerine birds (Passeriformes) and employed Bayesian phylogenetically informed mixed models to test for associations between aerial displays and a set of life-history and environmental predictors. Our multivariate models revealed that species with males that perform aerial displays inhabited open rather than closed (forested) habitats. These species also exhibited higher levels of polygyny, had more elongated wings, migrated over longer distances and bred at higher latitudes. When we included species where the sexual function of displays has not been explicitly described but is likely to occur, we found that aerial displaying was also associated with smaller body size and increased male plumage colouration. Our results suggest that both sexual selection and natural selection have been important sources of selection on aerial displays in passerines.</span></p>
FUNCTIONAL ANALYSIS OF GENES FOR REPRODUCTIVE TRAITS IN PIGS: FROM GWAS TO POST-GWAS
<p>Reproductive traits, such as number of teats, uniformity and litter size, are essential for animal breeding programs due to the importance for the production chain, since they influence the maternal ability of sow and can affect the number of weaned piglets. Our objective was to identify candidate genes associated with reproductive traits in pigs, using GWAS data, from a systematic review combined with sequencing data, to build networks of biological processes and Gene-TFs (transcription factors networks from the identified genes in order to highlight the most candidate genes for litter size, uniformity and number of teats. In the systematic review only peer-reviewed articles were used, with descriptors related to the evaluated traits, and selected based on eligibility criteria. Fourteen papers were selected and classified into groups for functional analysis of gene networks with 2077 candidate genes identified. After combining with the list of genes presenting known structural variants in the 5'UTR and/or coding region, 306 genes remained to be used to build the networks of biological processes and TFs gene networks, highlighting processes associated with litter size (e.g., ionotropic glutamate receptor signaling pathway and blastocyte growth) and teats number (e.g., growth hormone receptor, regulation of the BMP - Bone Morphogenetic Proteins signaling pathway and blood vessel proliferation). Three most candidate genes for litter size trait (<em>GRID2</em>and <em>PALB2</em>) and six most candidate genes (<em>GHR, IFT80,</em> <em>FSTL3, SKOR1, SMURF1</em> and <em>AKT3</em>) for teats number were prioritized. TF associated with candidate genes were also identified for litter size (<em>PALB2</em> and <em>GRID2</em>) and teat number (<em>RIN, LTBP2</em> and <em>COL6A6</em>). Thus, it is suggested that the genes and TFs presented in this study may play an important role in the traits studied, being important for genetic studies and animal breeding. The highlighted genes may bring new considerations to the current knowledge of the genetic architecture of these traits, since the markers associated with these genes can be assigned higher weights in genomic selection and validated in specific populations.</p>
Organisation of gene programs revealed by unsupervised analysis of diverse gene-trait associations
<p>Data used for manuscript 'Organisation of gene programs revealed by unsupervised analysis of diverse gene-trait associations'.<br> </p> <p> </p> <p> </p>
Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes
<p>Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate phenotypes can be represented in reduced dimensional space using principal component analysis with 77.7% of the variance captured by two orthogonal axes, here termed a 'trait-scape'. Furthermore, this trait-scape can be recovered with a reduced set of traits. Plastic responses to the new environments expanded phenotypic trait values and the trait-scape, however, the overall pattern of response to the new environments was similar between strains and many trait correlations remained constant. These findings demonstrate that trait-scapes can be used to reveal common constraints on multi-trait plasticity in phytoplankton with divergent underlying phenotypes. Understanding how to integrate trait correlational constraints and trade-offs into theoretical frameworks like biogeochemical models will be critical to predict how microbial responses to environmental change will impact elemental cycling now and into the future.</p>
Social selection analysis reveals limited effect of neighbors' traits in Tree swallows
<p>Social interactions are ubiquitous in nature and can shape fitness of individuals through social selection. This type of selection arises when phenotypes of neighbors influence the fitness of a focal individual. Quantifying social selection is crucial to better characterise the overall selective landscape. For example, if intraspecific competition is strong, traits that are beneficial for an individual could be detrimental for competitors. In this study, we quantified social selection acting on four key ecological traits (body mass, wing length, laying date and clutch size) in wild Tree swallow (<em>Tachycineta bicolor)</em> females. We used reproductive success measured at three stages throughout the breeding season as fitness proxies to assess selection acting at those decisive moments. We also quantified the effects of environment on selection using measures of conspecifics' density, type of agricultural landscape and presence of interspecific competitors. Overall, we found no strong evidence of social selection on these traits in our study system, although there were marginally non-significant selection gradients suggesting positive effect of larger neighbors. Environmental variables affected reproductive success but did not affect social selection gradients. Our study calls for more social selection estimates to be reported across environments to better understand its importance in wild populations.</p>
Supplementary Table S1. Combined analysis of variance containing the degrees of freedom (DF), mean squares (MS), P value (P val.), mean, coefficient of experimental variation (CEV%) and selective accuracy (SA) for the traits of luminosity (L*), chromaticity a* (a*), chromaticity b* (b*), grain length (length, mm), grain width (width, mm), grain thickness (thickness, mm), mass of 100 grains (Mass, g), normal grains (Ng, %), water absorption (absorption, %), cooking time (Ct, min:s), and concentrations of potassium (K, g kg-1 dry matter - DM), phosphorus (P, g kg-1 DM), calcium (Ca, g kg-1 DM), magnesium (Mg, g kg-1 DM), iron (Fe, mg kg-1 DM), zinc (Zn, mg kg-1 DM), and copper (Cu, mg kg-1 DM) obtained in 25 common bean cultivars evaluated in four experiments carried out from 2019 to 2021
<p><strong><span>Table S1.</span></strong><span> Combined analysis of variance.</span></p> <p><strong><span>Indirect selection for multiple technological and nutritional traits in common bean cultivars under different degrees of multicollinearity</span></strong></p> <p><strong><span>Bragantia, 2024.</span></strong></p>
100 Years of Penaeids Domestication and Meta-analysis of Breeding Traits
<p><strong>Additional files</strong></p> <p><strong>Additional file 1 Table S1</strong></p> <p>Format: csv file</p> <p>Title: Quantitative genetic publications for penaeids genetic improvement programs from 1997 to 2024.</p> <p><strong>Additional file 2 Table S2</strong></p> <p>Format: csv file</p> <p>Title: Summary of heritability estimates on breeding traits in penaeids selective breeding programs.</p> <p><strong>Additional file 3 Table S3</strong></p> <p>Format: csv file</p> <p>Title: Analysis of heritability estimates in penaeids selective breeding programs for disaese resistance, feeding efficiency, growth traits, morphological traits, quality traits, reproductive traits, stress tolerance and survival.</p>
melian009/Mispark: Preliminary analysis mutualistic networks in space, rarefaction, sierra size and sampling individuals, species, and traits
<p>Mutualistic networks in space, morphological traits and colors, or how to put all together to understand rare and common species in rapidly changing landscapes</p>
Data for: Phylogenetically controlled life history trait meta-analysis in cetaceans reveals unexpected negative brain size and longevity correlation
<p>The identification of patterns in trait evolution is essential to understand the interaction of evolutionary forces, and provides useful information for species management. Cetaceans are a phylogenetically well-resolved infraorder that exhibit distinct trait variation across behavioural, molecular and life history dimensions, yet few researchers have applied a meta-analytic or comparative approach to these traits. To understand cetacean trait evolution, we used a phylogenetic generalised least squares approach to examine the cognitive buffer hypothesis (CBH). A large brain should buffer individuals against environmental challenges through increasing survival rates, and a longer lifespan should buffer individuals against the cost of extended development for larger brains according to the CBH, leading to an expected positive correlation between brain size and lifespan. In contrast to this expectation, previously observed in taxa including primates, we found a negative correlation between brain size and lifespan in cetaceans. This suggests cetaceans experience selective pressures different from most other mammals in these traits but may be more similar to some social mammalian carnivores that display alloparenting. We also provide a comprehensive dataset to explore additional aspects of trait evolution but which would greatly benefit from studies on behavioural ecology across cetaceans and increased focus on data-deficient species. </p>
Data from: Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
<p>The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection, or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.</p>
Data and analysis result for "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics"
<p>Data set and analysis results from our paper "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics" (pre-print). This file contains GWAS summary statistics of 2,483 traits and 51,399 SNP variants from European individuals, originally downloaded and processed from Pan-UK Biobank (https://pan.ukbb.broadinstitute.org/). Additionally, we include results of 100 pleiotropic factors inferred by our method and tSVD as comparison. Please see README for detailed breakdown.</p>
Data and analysis scripts for: Asymmetrical reproductive barriers in sympatric Jewelflowers: are floral isolation, genetic incompatibilities, and floral trait displacement connected?
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A global analysis of aerial displays in passerines revealed an effect of habitat, mating system and migratory traits
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Data from: Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
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