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138 results for “complex traits”
Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits
<p>This (zipped) folder contains 3 sub-folders:</p> <p>#**********************************************************************************************************<br>The "bin" folder contains fuctions and gentic maps needed for analyes<br>bin \<br> predLink.R - function to predict linkage <br> sibREML_v0.1.1.R - function to run SibREML<br> sim-sib-array.R - script to simulate sib-pairs from parental haplotypes<br> Summarised_genetic_map_bcf.txt - genetic map per 0.5-cM long segments, based on map from bcftools <br> (BCFtools: https://samtools.github.io/bcftools/bcftools.html)<br> Summarised_genetic_map_OMNI.txt - genetic map per 0.5-cM long segments, based on OMNI map <br> (https://github.com/joepickrell/1000-genomes-genetic-maps/tree/master/interpolated_OMNI)<br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "SIM" folder contains the simulation pipeline (scripts 01-15) as well as IBD sharing and simulated phenotypes for Simulated sib-pairs.<br>SIM \<br> 01_sim-sib-array.sh *pre-run*<br> 02_bed_recode_bcf_map.sh *pre-run*<br> 03_make_merlin.R *pre-run*<br> 04_error_merlin.sh *pre-run*<br> 05_merlin_IBD.sh *pre-run*<br> 06_sample_causal_snps.R *pre-run*<br> 07_simulate_pheno.sh *pre-run*<br> 08_bhat_gwas.R *can be run using provided data* <br> 09_Linkage_VH.R *can be run using provided data* <br> 10_predLink.R *can be run using provided data*<br> 11_phi_hat.R *can be run using provided data*<br> 12_IBD_Mb.R *can be run using provided data*<br> 13_IBD_cM_recombrate_stratified.R *can be run using provided data*<br> 14_SibREML.R *can be run using provided data*<br> 15_SibREML_stratified_Q4.R *can be run using provided data*<br> causal_snps \ *provided causal SNPs*<br> IBD_results \ *provided IBD-probabilities for 1000 simulated sib-pairs*<br> Linkage_VH_results \ <br> pheno \ *provided simulated phenotypes (h2=1) for 8 genetic architectures*<br> Phi_hat_results.txt<br> predicted \<br> README<br> SibREML_results.txt<br> SibREML_stratified_Q4.txt</p> <p>The data can be used to run Linkage analysis, predict linkage, estimate phi_hat, <br>as well as estimate non-stratified and recombination rate stratified sib-heritability (h2_FS and c).<br>The README is provided within the folder. <br>#**********************************************************************************************************</p> <p> </p> <p>#**********************************************************************************************************<br>The "HT_BMI" folder contains data and scripts to predict linkage and estimate phi_hat for height and BMI.<br>HT_BMI \<br> 01_predLink_HT_BMI.R<br> 02_phi_hat_HT_BMI.R<br> gws_sumstats \ *provided summary GWAS summary statistics to predict linkage for height and BMI*<br> Linkage_results \ *provided linkage meta-analysis results for height and BMI from this study*<br> Phi_hat_results_HT_BMI.txt<br> PREDLINK_bmi.txt<br> PREDLINK_height.txt<br> README<br>The README is provided within the folder.<br>#**********************************************************************************************************</p> <p><strong> </strong></p>
Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits
<p>Supporting data associated with the manuscript "Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits". These include:</p> <ul> <li><strong>StringTie2.438.GEUVADIS.gtf.gz</strong> - Assembled transcriptome using RNA-seq from 438 samples from the GEUVADIS project by StringTie2</li> <li><strong>puQTL_nominal_output.txt.gz</strong> - puQTL results from QTLtools nominal pass</li> <li><strong>puQTL_conditional_output.txt.gz</strong> - puQTL results from QTLtools conditional pass</li> <li><strong>eQTL_nominal_output.txt.gz</strong> - eQTL results from QTLtools nominal pass</li> <li><strong>eQTL_conditional_output.txt.gz</strong> - eQTL results from QTLtools conditional pass</li> </ul> <p>See <a href="https://qtltools.github.io/qtltools/">https://qtltools.github.io/qtltools/</a> for column descriptions of QTL mapping results.</p>
Summary statistics - Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits
<p>Summary statistics for all trans-acting/target gene pairs tested in our manuscript.</p> <p>Preprint available: <a href="https://doi.org/10.1101/471748">https://doi.org/10.1101/471748</a></p>
COJO ARG variants from "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits"
<p>These are COJO ARG variants accompanying the manuscript "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits". For more details, view the README.md file and refer to our manuscript.</p>
Data for: "Generative prediction of causal gene sets responsible for complex traits"
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Complex multi-trait responses to multivariate environmental cues in a seasonal butterfly
<p>Dataset for 'Complex multi-trait responses to multivariate environmental cues in a seasonal butterfly'.</p>
Data from: Between predators and parasitoids: complex interactions among shelter traits, predation, and parasitism in a shelter-building caterpillar community
<ol> <li>Shelter building is widespread in the animal world and such shelters often influence the success of their builders. Shelters built by caterpillars influence the likelihood of attacks by natural enemies, but how particular shelter traits influence caterpillar survival is not known. Furthermore, the differential effects of certain shelter traits on some natural enemies, such as predators, may lead to "enemy-free space" for other natural enemies (parasitoids). The parasitoid enemy-free space hypothesis has not been directly tested for shelter-building caterpillars.</li> <li>To understand how shelter traits influence caterpillar survival, shelter traits, predation, and parasitism were measured simultaneously for 24 caterpillar morphospecies (1465 caterpillars) in a tropical dry forest and analyzed in a phylogenetic context.</li> <li>Shelter type, shelter openness, and whether shelters accumulated frass had different amounts of phylogenetic signal, with frass accumulation displaying the most and shelter openness the least.</li> <li>All three traits affected the frequency with which caterpillar species experienced predation. Predation was elevated in two shelter types (leaf folds and leaf rolls) compared to cut-and-fold shelters. Combinations of shelter openness and frass accumulation also affected predation, with closed frass-free shelters having the lowest predation and closed frass-filled shelters having the highest.</li> <li>Parasitism was not affected by shelter traits but was strongly correlated with evolutionary history and negatively correlated with predation.</li> <li>These results confirm a trade-off between predation and parasitism and demonstrate that predation can be more frequent than parasitism. Different shelter types result in different amounts of predation. These defensive shelter traits and their effectiveness also vary phylogenetically. Together, our results suggest that predation and parasitism determine the success of shelter-building caterpillars, and that success is a function of the specific shelter they construct. More generally, our results demonstrate the importance of considering the effects of defensive traits on both predators and parasitoids when investigating interactions between herbivores and natural enemies.</li> </ol>
Probabilistic inference of the genetic architecture of functional enrichment of complex traits
<p>We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.</p>
Complex floral traits shape pollinator attraction to ornamental plants
<p><strong>Background and Aims </strong>Ornamental flowering plant species are often used in managed greenspaces to attract and support pollinator populations. In natural systems, selection by pollinators is hypothesized to result in convergent multimodal floral phenotypes that are more attractive to specific pollinator taxa. In contrast, ornamental cultivars are bred via artificial selection by humans, and exhibit diverse and distinct phenotypes. Despite their prevalence in managed habitats, the influence of cultivar phenotypic variation on plant attractiveness to pollinator taxa is not well resolved.</p> <p><strong>Methods </strong>We used a combination of field and behavioural assays to evaluate how variation in floral visual, chemical and nutritional traits impacted overall attractiveness and visitation by pollinator taxonomic groups and bee species to 25 cultivars of five herbaceous perennial ornamental plant genera.</p> <p><strong>Key results</strong> Despite significant phenotypic variation, cultivars tended to attract a broad range of pollinator species. Nonetheless, at the level of insect order (bee, fly, butterfly, beetle), attraction was generally modulated by traits consistent with the pollination syndrome hypothesis. At the level of bee species, the relative influence of traits on visitation varied across plant genera, with some floral phenotypes leading to a broadening of the visitor community, and others leading to exclusion of visitation by certain bee species.</p> <p><strong>Conclusions </strong>Our results demonstrate how pollinator choice is mediated by complex multimodal floral signals. Importantly, the traits that had the greatest and most consistent effect on regulating pollinator attraction were those that are commonly selected for in cultivar development. Though variation among cultivars in floral traits may limit the pollinator community by excluding certain species, it may also encourage interactions with generalist taxa to support pollinator diversity in managed landscapes.</p>
Data from: Sexually discordant selection is associated with trait specific morphological changes and a complex genomic response
<p>Sexes often have differing fitness optima, potentially generating intra-locus sexual conflict, as each sex bears a genetic 'load' of alleles beneficial to the other sex. One strategy to evaluate conflict in the genome is to artificially select populations discordantly, against established sexual dimorphism, reintroducing attenuated conflict. We investigate a long-term artificial selection experiment reversing sexual size dimorphism in <em>Drosophila melanogaster</em> during ~350 generations of sexually discordant selection. We explore morphological and genomic changes to identify loci under selection between the sexes in discordantly and concordantly size selected treatments. Despite substantial changes to overall size, concordant selection maintained ancestral sexual dimorphism. However, discordant selection altered size dimorphism in a trait-specific manner. We observe multiple, possible soft selective sweeps in the genome, with size related genes showing signs of selection. Patterns of genomic differentiation between the sexes within lineages identified potential sites maintained by sexual conflict. One discordant selected lineage shows a pattern of elevated genomic differentiation between males and females, on chromosome 3L, consistent with the maintenance of sexual conflict. Our results suggest visible signs of conflict and differentially segregating alleles between the sexes due to discordant selection.</p>
Complex trait‒environment relationships underlie the structure of forest plant communities
<p>Traits differentially adapt plant species to particular conditions generating compositional shifts along environmental gradients. As a result, community-scale trait values show concomitant shifts, termed trait‒environment relationships. Trait‒environment relationships are often assessed by evaluating community-weighted mean (CWM) traits observed along environmental gradients. Regression-based approaches (CWMr) assume that local communities exhibit traits centered at a single optimum value and that traits do not covary meaningfully. Evidence suggests that the shape of trait‒abundance relationships can vary widely along environmental gradients—reflecting complex interactions—and traits are usually interrelated. We used a model that accounts for these factors to explore trait‒environment relationships in herbaceous forest plant communities in Wisconsin (USA). We built a generalized linear mixed model (GLMM) to analyze how abundances of 185 species distributed among 189 forested sites vary in response to four functional traits (vegetative height-VH, leaf size-LS, leaf mass per area-LMA, and leaf carbon content), six environmental variables describing overstory, soil, and climate conditions, and their interactions. The GLMM allowed us to assess the nature and relative strength of the resulting 24 trait‒environment relationships. We also compared results between GLMM and CWMr to explore how conclusions differ between approaches. The GLMM identified five significant trait‒environment relationships that together explain ~40% of variation in species abundances across sites. Temperature appeared as a key environmental driver, with warmer and more seasonal sites favoring taller plants. Soil texture and temperature seasonality affected LS and LMA; seasonality effects on LS and LMA were nonlinear, declining at more seasonal sites. Though often assumed for CWMr, only some traits under certain conditions had centered optimum trait‒abundance relationships. CWMr more liberally identified (13) trait‒environment relationships as significant but failed to detect the temperature-seasonality‒LMA relationship identified by the GLMM. Synthesis. Although GLMM represents a more methodologically complex approach than CWMr, it identified a reduced set of trait‒environment relationships still capable of accounting for the responses of forest understory herbs to environmental gradients. It also identified separate effects of mean and seasonal temperature on LMA that appear important in these forests, generating useful insights and supporting broader application of GLMM approach to understand trait‒environment relationships.</p>
Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals: GWAS summary statistics
<p>Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories as well as complex trait architectures remain hidden due to the lack of Big Data. To fill this gap, the Mexican Biobank project genotyped 1.8 million markers in 6,057 individuals from 32 states and 898 sampling localities across Mexico with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Through a suite of state-of-the-art methods for ancestry deconvolution and inference of identity-by-descent (IBD) segments, we inferred detailed ancestral histories for the last 200 generations in different Mesoamerican regions, unravelling native and colonial/post-colonial demographic dynamics. We observed large variations in runs of homozygosity (ROH) among genomic regions with different ancestral origins reflecting their demographic histories, which also affect the distribution of rare deleterious variants across Mexico. We analysed a range of biomedical complex traits and identified significant genetic and environmental factors explaining their variation, such as ROH found to be significant predictors for trait variation in BMI and triglycerides.<br> ======================================</p> <p>This dataset contains GWAS summary statistics for the Mexico Biobank Project. Summary statistics for 22 binary and quantitative traits are provided from the full cohort of 5721 individuals from across Mexico, and a subset of 1061 individuals inferred to have more than 90% Native American ancestry.</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>
Trans-eQTL effects on risk of type 1 diabetes: a test of the sparse effector (omnigenic) hypothesis of complex trait genetics (supplementary data)
<p>This repository contains summary-level data generated by performing <a href="https://github.com/molepi-precmed/trans-qtls">Genomewide aggregated trans- effects (GATE) analysis</a> in case-control study of Type 1 Diabetes (T1D).</p>
Data from: Between predators and parasitoids: complex interactions among shelter traits, predation, and parasitism in a shelter-building caterpillar community
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Complex trait‒environment relationships underlie the structure of forest plant communities
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Data from: Sexually discordant selection is associated with trait specific morphological changes and a complex genomic response
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Data from: Behavioural vs. physiological adaptation: which contributes more to the evolution of complex traits in a warming climate?
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Complex floral traits shape pollinator attraction to ornamental plants
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Data from: An integrative approach to prioritize candidate causal genes for complex traits in cattle
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.