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1,161 results for “Drosophila melanogaster”
Formatting hemiclone Drosophila melanogaster genotype data for GWAS
<p>Data and code for generating filtering and formatting of Drosophila melanogaster genotype data, from the Sussex LHM hemiclone population sample.</p>
Population genomics of Sussex LHM Drosophila melanogaster
<p>Input data, code, output data, summary plots, and run logs for investigation of the population genetics of the Drosophila melanogaster Sussex LHM sample.</p> <p>For output graphs, see popgen_plots.png</p> <p>Input data are 'plink binary' format.</p> <p>Code is a unix/linux shell script containing commands for Plink to perform population genetic tests.</p> <p>The two R scripts contain i. a short command for making a subpopulation file, ii. commands for plotting the output data. Both are initated in the shell script.</p> <p>Platform and version information are available in the log files. Other information available in the shell and R scripts.</p> <p>Broad observations are that the allele frequency disibribution is normal except a few humps around MAF 0.2-0.3 in the autosomes.</p> <p>Linkage disequilbrium, on average, levels-out after ~200bp but there can still be some at distances of 300Kb.</p> <p>The population appears to be divided into four genetically distinct groups (on the IBD-PCA scatter plot), with Fst analysis indicating that this is caused by genetic variation around the centromeres. This is possibly caused by historic admixture, and low centromeric recombination.</p>
Phenotype data for Sussex LHM Drosophila melanogaster reproductive fitness GWAS
<p>Input data, code, logs, graphs and output data for the Sussex LHM Drosophila melanogaster hemiclones.</p> <p>Aim is to generate single, standardised values of female and male reproductive fitness for each hemiclone genome, for using in genome-wide association test using Plink software.</p> <p>Notes on how to run are provided in the code.</p>
Gene co-ordinates, expression levels; SNP identifiers and functions for Drosophila melanogaster (Sussex LHM population)
<p>Data for SNP context information to add to GWAS results. Specifically, SNP functions, sex-bias in gene expression, official SNP idenfiers from NCBI dbSNP, and gene positions and names (from UCSC Genome Browswer). Most of the input files are on-line and their URLs are stated in the code (make_dmel_accessory_data.sh). Also includes code, logs, and exploratory graphs.</p>
Bivariate GWAS for female and male fitness in Drosophila melanogaster (Sussex, LHm)
<p>Code, logs, results and graphs for genome-wide association study of reproductive fitness in D.melanogaster hemiclone lines, using the R package 'Mulitphen'.</p>
Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation
<p>Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred <em>Drosophila melanogaster</em>strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.</p> <p>See the README.txt file to get a description of the uploaded files. Scripts.zip contains annotated command lines and scripts for the project (see internal README.txt file).</p>
Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster - ethoscope dataset
<p>Ethoscope dataset for Vicent et al 2022, PLoS Pathogens</p> <p>Original preprint available at: https://www.biorxiv.org/content/10.1101/2021.08.24.457493v1</p> <p> </p>
Linkage-independent SNPs in the Drosophila melanogaster Sussex LHM sample
<p>Unix code for running Plink program for generating a list of SNPs (single-nucleotide polymorphisms) which are independent of linkage diseqiulibrium. Used for later statistical analyses incorporating the number of independent tests made across the genome.</p>
Separate-sex GWAS for reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>Code, data, logs, and graphs for GWAS on seperate-sex reproductive fitness in Drosophila melanogaster, Sussex LHM population sample.</p> <p>The shell script, code_drive_basic_gwas.sh, downloads input data files from the internet, drives Plink to select LD-independent SNPs, and then perform a genome-wide association test against female and male fitness, separately. Plink is also used to assign functions and gene names to SNPs. Bash/Unix code is used for formatting/compatibility adjustments, and also to add NCBI-dbSNP IDs to results. The shell script starts an R script that generates basic diagnostic graphs. This updated version differs from the first in that three large unconfirmed snRNA genes have been omitted to improve assignment of SNPs to genes.</p> <p>See https://f1000research.com/articles/5-2644/v3 and http://www.sussex.ac.uk/lifesci/morrowlab/</p>
False discovery rate calculations for genome-wide association study of reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>R code and results of applying false discovery (FDR) rate calculations to establish statistical signficance in a genome-wide association study of reproductive fitness in Drosophila melanogaster. Phenotype values were generated on hemiclone female and male lines from an outbred, laboratory adapted population. Thus, GWAS were previously performed seperately on the phenotype values for each sex, and also using a bivariate GWAS implemented in the R package multiPhen.</p> <p>FDR calculations were performed using the R package 'fdrtool' on all SNPs, and on LD-independent SNPs, the latter of which was used to determine p-value thresholds for genome-wide significance when all SNPs were considered.</p> <p>This version differs from the original in that: i) Some gene positions/names have been reassigned for accuaracy in the input data. ii) A file containing the p-value thresholds corresponding to an FDR of 0.1 has been added. The 95% credible intervals for each SNP association have been added to the results data files.</p>
Orthologs for Homo Sapiens and Drosophila Melanogaster from the Roundup Orthology Database Version 4
<p>This dataset contains orthologs for Homo sapiens and Drosophila melanogaster, computed with the Reciprocal Smallest Distance algorithm using a divergence threshold of 0.8 and an e-value threshold of 1e-5. The orthologs were downloaded from version 4 of the Roundup database, which is no longer available.</p>
Data from: Genetic and environmental canalization are not correlated among altitudinally varying populations of Drosophila melanogaster
<p>Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves is limited, despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as a correlated response to environmental canalization (congruence model). Yet, empirical evidence has not consistently supported predictions of a correlation between genetic and environmental canalization. In a recent study, a population of <em>Drosophila </em>adapted to high altitude showed evidence of genetic decanalization relative to those from low altitudes. Using strains derived from these populations, we tested if they varied for multiple aspects of environmental canalization We observed the expected differences in wing size, shape, cell (trichome) density and mutational defects between high- and low-altitude populations. However, we observed little evidence for a relationship between measures of environmental canalization with population or with defect frequency. Our results do not support the predicted association between genetic and environmental canalization.</p>
Drosophila melanogaster template brains
<p>Male and female symmetric averaged templates (18 and 14 brains, respectively) and intersex template brain for <em>Drosophila melanogaster</em>. Voxel size: (0.461, 0.461, 1) micron.</p>
A dataset of 3D fly (Drosophila melanogaster) flight trajectories to study the role of neuropeptide degradation in visuo-motor behaviors.
<p>As part of a wide study on the role of neuropeptides in the visuo-motor behavior of Drosophila melanogaster, we exposed three fly strains with impaired neuropeptide degradation function, and corresponding controls, to different visual stimuli.</p> <p>Find further details in the provided README.</p>
Read-mapping for next-generation sequencing data (Drosophila melanogaster)
<p>Code, logs and quality-control data for whole-genome resequencing of Sussex-LH<sub>M</sub> and RG <em>Drosophila melanogaster</em>.</p> <p>Mapping code is in the archive lhm_mapping_scripts.zip</p> <p>Mapping logs are in the in the archive lhm_mapping_logs.zip</p> <p>Other zip archives contain the quality control data.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Genome-wide estimation of linkage disequilibrium-independent SNPs in Drosophila melanogaster (Sussex LHM).
<p>Uses R to create SNP density across each chromosome arm. Uses Plink 1.9 to select independent SNPs with step sizes corresponding to chromosome density. Output data is combined_chromosomes_lhm_indep.txt a list of SNP IDs.<br> </p>
A re-analysis of an existing Drosophila melanogaster dataset reveals a new set of genes involved in post-mating response
<p>The figures and tables presented here are part of a manuscript submitted for publication by Chloe J. Bennett and Rodolfo Aramayo entitled:</p> <p><strong>"A re-Analysis of an existing <em>Drosophila melanogaster</em> dataset reveals a new set of genes involved in post-mating response"</strong></p> <p><strong>Abstract</strong></p> <p>RNA sequencing (RNA-seq) is a commonly used method to identify changes in gene expression between two conditions. The analysis of RNA-seq output is complicated, with the possibility of getting different results from the same raw data. We developed and deployed four parallel pipelines to reanalyze an existing dataset of two female Drosophila melanogaster tissue types before and after mating. The Drosophila post-mating response (PMR) is a well-characterized suite of changes that occur after mating, accompanied by a flux in gene expression. In comparing our study with the previous analysis of this dataset, we find our results to be more stringent, though we do identify a number of significant genes not found before. We also found variation among our own separate experiments, with gene-to-transcript isoform number and index building playing important roles in outcome. Finally, we identified a set of genes found by our pipeline that were not identified by the previous study and proposed potential roles for these genes in post-mating biology. Together, this work presents a critique of current RNA-seq analysis techniques and proposes multiple workflow adjustments that can increase the sensitivity, specificity, and stringency of differential gene expression studies.</p>
Desiccation stress acts as cause as well as cost of dispersal in Drosophila melanogaster
<p>Environmental stress is one of the important causes of biological dispersal. At the same time, the process of dispersal itself can incur and/or increase susceptibility to stress for the dispersing individuals. Therefore, in principle, stress can serve as both a cause and a cost of dispersal. We studied these potentially contrasting roles of a key environmental stress (desiccation) using Drosophila melanogaster. By modulating water and rest availability, we asked whether: (a) dispersers are individuals that are more susceptible to desiccation stress, (b) dispersers pay a cost in terms of reduced resistance to desiccation stress, (c) dispersal evolution alters the desiccation cost of dispersal, and (d) females pay a reproductive cost of dispersal. We found that desiccation was a clear cause of dispersal in both sexes, as both male and female dispersal propensity increased with increasing duration of desiccation. However, the desiccation cost of dispersal was male-biased, a trend unaffected by dispersal evolution. Instead, females paid a fecundity cost of dispersal. We discuss the complex relationship between desiccation and dispersal, which can lead to both positive and negative associations. Furthermore, the sex differences highlighted here may translate into differences in movement patterns, thereby giving rise to sex-biased dispersal patterns.</p>
A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster
<p>Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects - PIGEs) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important, since they have the capacity to contribute to evolutionary change. Here we use Drosophila genetics to construct a breeding design that allows testing nearly complete haploid genomes (>99%) for PIGEs. Using this technique, we estimate the variance in male lifespan due to PIGEs among four populations and compare this to the total paternal genetic variance (the sum of paternal indirect and direct genetic effects). Our results indicate that a substantial part of the total paternal genetic variance results from PIGEs. A screen of 38 haploid genomes, randomly sampled from a single population, suggests that PIGEs also influence variation in lifespan within populations. Collectively, our results demonstrate that PIGEs may constitute an underappreciated source of phenotypic variation.</p>
Data from: Pre-copulatory reproductive behaviours are preserved in Drosophila melanogaster infected with bacteria
<p>The activation of the immune system upon infection exerts a huge energetic demand on an individual, likely decreasing available resources for other vital processes, like reproduction. The factors that determine the trade-off between defensive and reproductive traits remain poorly understood. Here, we exploit the experimental tractability of the fruit fly <em>Drosophila melanogaster</em> to systematically assess the impact of immune system activation on pre-copulatory reproductive behaviour. Contrary to expectations, we found that male flies undergoing an immune activation continue to display high levels of courtship and mating success. Similarly, immune-challenged female flies remain highly sexually receptive. By combining behavioural paradigms, a diverse panel of pathogens and genetic strategies to induce the fly immune system, we show that pre-copulatory reproductive behaviours are preserved in infected flies, despite the significant metabolic cost of infection.</p>
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OpenNeuro
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