Data from: Population genetic evidence for cold adaptation in European Drosophila melanogaster populations

Bozicevic V, Hutter S, Stephan W, Wollstein A

Date Published: November 9, 2015

DOI: http://dx.doi.org/10.5061/dryad.20t9v

 

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Title Gene Ontology data
Downloaded 48 times
Description A list of ClueGO terms enriched with candidate genes for latitude, the overlap with terms enriched with candidate genes of Fabian et al. (2012), and the results of GO enrichment using Gowinda.
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Title Inversion analysis data
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Description Candidate genes and their distances from the breakpoints of cosmopolitan inversions.
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Title Climate data
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Description Climate data retrieved from the World Meteorological Organization and other environmental variables.
Download Climate.xlsx (14.07 Kb)
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Title Bayenv2 environment file
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Description Standardised environmental variables in file format used for the Bayenv2 analysis.
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Title SNP data - autosomes
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Description Genotypes of autosomal SNPs used in the analysis.
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Title SNP chromosomal coordinates - autosomes
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Description Each line in the file lists the chromosome (autosome) and the absolute coordinate for the SNPs used in the analysis.
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Title SNP data - chromosome X
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Description Genotypes of X chromosome SNPs used in the analysis.
Download chrx.geno (59.82 Mb)
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Title SNP chromosomal coordinates - chromosome X
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Description Each line in the file lists the absolute coordinates for the X chromosome SNPs used in the analysis.
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Title Pairwise FST estimates for autosomal SNPs
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Description A Matlab file containing 3663890 autosomal SNPs, their pairwise FST estimates, and P-values for each SNP derived from coalescent simulations.
Download pairwise_fst_autos.mat (237.7 Mb)
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Title Pairwise FST estimates for the X chromosome SNPs
Downloaded 25 times
Description A Matlab file containing 867049 X chromosome SNPs, their pairwise FST estimates, and P-values for each SNP derived from coalescent simulations.
Download pairwise_fst_chrX.mat (52.22 Mb)
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Title Bayenv2 results - autosomes
Downloaded 10 times
Description A Matlab file containing the Bayes factors of 313972 autosomal SNPs, as calculated using Bayenv2. File also contains P-values for each SNP estimated from coalescent simulations, including the FDR adjustment (Benjamini and Hochberg 1995).
Download bfautos_bh.mat (54.19 Mb)
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Title Bayenv2 results - chromosome X
Downloaded 9 times
Description A Matlab file containing the Bayes factors of 39304 X chromosome SNPs, as calculated using Bayenv2. File also contains P-values for each SNP estimated from coalescent simulations, including the FDR adjustment (Benjamini and Hochberg 1995).
Download bfX.mat (5.894 Mb)
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Title Polygenic trait forward simulations script
Downloaded 8 times
Description A Matlab script to conduct forward simulations of multiple loci of a quantitative trait setting, and run Bayenv2 on final frequencies.
Download multi_locus_simu.m (5.553 Kb)
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Title Power analysis - simulations with sel. coeff. of 0.1
Downloaded 6 times
Description A Matlab file containing data related to the power analysis. Simulations of the evolution of a polygenic trait with the multilocus selection coefficient set at 0.1 (de Vladar and Barton 2014).
Download multi_locus_simu_drift_ldex_S0.1.mat (207.6 Mb)
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Title Power analysis - simulations with sel. coeff. of 0.05
Downloaded 7 times
Description A Matlab file containing data related to the power analysis. Simulations of the evolution of a polygenic trait with the multilocus selection coefficient set at 0.1 (de Vladar and Barton 2014).
Download multi_locus_simu_drift_ldex_S0.05.mat (208.0 Mb)
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Title Demographic estimation data - s9649
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Description A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.
Download abc_gen_s9649.mat (27.39 Mb)
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Title Demographic estimation data - s9481
Downloaded 9 times
Description A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.
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Title Demographic estimation data - s8148
Downloaded 6 times
Description A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.
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Title Demographic estimation data - s48101
Downloaded 8 times
Description A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.
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Title Demographic estimation data - s7061
Downloaded 6 times
Description A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.
Download abc_gen_s7061.mat (27.32 Mb)
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Title Bayes factors from Bayenv2 - all chromosomes
Downloaded 6 times
Description A Matlab file containing SNP coordinates for all 353276 SNPs and their associated Bayes factors (BFs) obtained by means of Bayenv2. Contains minimum BFs over 10 independent runs of Bayenv2, as well as median BFs that were used in the downstream analyses.
Download bf.mat (27.28 Mb)
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Title Bayenv2 intermediate file - raw BFs
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Description An intermediate Matlab file containing raw Bayes factors from Bayenv2.
Download bayenv2mat.mat (12.63 Mb)
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Title Demographic estimation data - simulated FST autosomes
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Description A Matlab file containing FST estimated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains autosomal SNPs.
Download abc_fst_in_sim_autos.mat (3.879 Mb)
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Title Demographic estimation data - simulated FST chromosome X
Downloaded 8 times
Description A Matlab file containing FST estimated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains X chromosome SNPs.
Download abc_fst_in_sim_chrX.mat (837.6 Kb)
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Title Demographic estimation data - simulated BFs autosomes
Downloaded 8 times
Description A Matlab file containing Bayes factors calculated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains autosomal SNPs.
Download abc_bayenv2_sim_autos.mat (963.1 Kb)
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Title Demographic estimation data - simulated BFs chromosome X
Downloaded 6 times
Description A Matlab file containing Bayes factors calculated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains X chromosome SNPs.
Download abc_bayenv2_sim_chrX.mat (968.6 Kb)
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Title Demographic estimation data - summarized (autosomes)
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Description A Matlab file with summarized data from demographic estimation analysis by means of Approximate Bayesian Computation (autosomes).
Download abc_summarized_data_autos.mat (668.1 Kb)
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Title Ensembl gene IDs
Downloaded 10 times
Description A Matlab file containing Flybase (FBgn) gene IDs, their names and chromosomal locations. Retrieved from Ensembl.
Download enshgnc.mat (415.4 Kb)
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Title Ensembl gene ontology annotation
Downloaded 7 times
Description A Matlab file containing Flybase (FBgn) gene IDs, their gene ontology annotation and chromosomal locations. Retrieved from Ensembl.
Download ensgo.mat (271.3 Kb)
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Title ABC rejection data - autosomes
Downloaded 9 times
Description A Matlab file containing the Approximate Bayesian Computation rejection matrix (autosomes).
Download abc_reject_autos.mat (73.23 Kb)
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Title ABC rejection data - X chromosome
Downloaded 5 times
Description A Matlab file containing the Approximate Bayesian Computation rejection matrix (X chromosome).
Download abc_reject_chrX.mat (60 Kb)
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Title Genome annotations script
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Description A script to generate a Matlab file with genome annotations.
Download annotdbmat.m (5.233 Kb)
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Title Reformat FUNC GO results script
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Description A script to reformat results from the FUNC GO analysis.
Download go_process_out.m (5.159 Kb)
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Title ABC rejection script
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Description A script to apply the ABC rejection algorithm to simulated data.
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Title ABC generate polymorphism data script
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Description A script to generate polymorphism data from reasonable priors using coalescent simulations.
Download abc_gen.m (3.301 Kb)
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Title Export sets for FUNC script
Downloaded 7 times
Description A script to export gene sets for GO analysis with FUNC (Prüfer et al. 2007).
Download go_export_func.m (2.914 Kb)
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Title ABC simulate BFs script - autosomes
Downloaded 7 times
Description A script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (autosomes).
Download abc_bayenv2_sim_autos.m (2.224 Kb)
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Title ABC simulate BFs script - X chromosome
Downloaded 4 times
Description A script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (X chromosome).
Download abc_bayenv2_sim_chrX.m (2.21 Kb)
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Title ABC simulate FSTs script
Downloaded 9 times
Description A script to simulate FST values from a given demographic model.
Download abc_fst_in_sim.m (2.205 Kb)
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Title ABC combine ms results script
Downloaded 6 times
Description A script to gather ms simulation results into one Matlab file.
Download abc_ms2mat.m (1.802 Kb)
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Title ABC apply regression script
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Description A script to apply a weighted regression in the space of summary statistics as proposed by Beaumont et al. (2002).
Download abc_regression.m (2.474 Kb)
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Title ABC run ms script
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Description A script to run Hudson's ms and return structure with haplotype matrices.
Download abc_runms.m (2.393 Kb)
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Title ABC summarize data script
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Description A script to summarize data provided as a Matlab file.
Download abc_summarize_data.m (1.794 Kb)
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Title ABC summarize struct. script
Downloaded 8 times
Description A script to summarize data in struct. of haplotype matrices.
Download abc_summarize_struct.m (1.34 Kb)
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Title ABC apply summary stats script
Downloaded 9 times
Description A script to apply summary statistics to a single haplotype matrix.
Download abc_summarize.m (2.134 Kb)
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Title Demographic estimation data - chromosome X
Downloaded 9 times
Description A Matlab file with summarized data from demographic estimation analysis by means of Approximate Bayesian Computation (chromosome X).
Download abc_summarized_data_chrX.mat (1.601 Kb)
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Title Calculate aSFS script
Downloaded 6 times
Description A script to calculate the absolute site frequency spectrum from Drosophila genotypes.
Download aSFS_fromdata.m (1.311 Kb)
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Title Calculate aSFS from simulations script
Downloaded 6 times
Description A script to calculate the absolute site frequency spectrum from simulations.
Download aSFSm.m (1.172 Kb)
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Title Bayenv2 batch script
Downloaded 7 times
Description A script to initiate Bayenv2 runs.
Download bayenv2_batch.m (2.168 Kb)
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Title Bayenv2 export SNPs for Cov matrix script
Downloaded 9 times
Description A script to export randomly sampled SNPs for covariance matrix generation in Bayenv2.
Download bayenv2_export_matrixgen.m (2.182 Kb)
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Title Bayenv2 export polymorphisms script
Downloaded 8 times
Description A script to export polymorphic SNPs for testing in Bayenv2.
Download bayenv2_export.m (2.631 Kb)
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Title Bayenv2 export independent SNPs for Cov matrix generation
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Description A script to export a random number of equally distant SNPs for matrix generation in Bayenv2.
Download bayenv2_simu_matrixgen.m (1.448 Kb)
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Title Bayenv2 simulation wrapper script
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Description A script to provide Bayenv2 values for simulated frequencies given in a matrix file and environmental files.
Download bayenv2_simuwrapper.m (2.901 Kb)
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Title Bayenv2 haplotypes wrapper script
Downloaded 3 times
Description A script to provide Bayenv2 values for haplotypes given in a matrix file and environmental files.
Download bayenv2_wrapper.m (2.889 Kb)
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Title Bayenv2 matrix batch script
Downloaded 7 times
Description Bayenv2 matrix batch script, outputs bf.mat file.
Download bayenv2mat_batch.m (1.487 Kb)
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Title Bayenv2 matlab export script - autosomes
Downloaded 5 times
Description A script to export the output of Bayenv2 into a Matlab file (autosomes).
Download bayenv2mat.m (2.386 Kb)
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Title Bayenv2 matlab export script - chromosome X
Downloaded 7 times
Description A script to export the output of Bayenv2 into a Matlab file (X chromosome).
Download bayenv2matX.m (2.197 Kb)
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Title Clean db script
Downloaded 8 times
Description A script to clean Drosophila genetic data structure.
Download cleandb.m (1.953 Kb)
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Title Provide P-values for SNPs from demographic simulations
Downloaded 5 times
Description A script to provide empirical P-values for FST estimates: inputs a Matlab file with FST values and a Matlab file with demographic simulations and outputs a Matlab file including empirical P-values for individual SNPs corrected for multiple testing (Benjamini and Hochberg 1995).
Download empPvalsFst.m (1.772 Kb)
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Title Estimate pairwise FST script
Downloaded 8 times
Description A script to estimate the population pairwise FST. Inputs genotypes as a Matlab file and exports FST values as another Matlab file.
Download pairwise_fst.m (1.819 Kb)
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Title Forward simulations of polygenic traits
Downloaded 8 times
Description A script to conduct forward simulations according to de Vladar and Barton (2014) on multiple loci of a polygenic trait. Inputs the selection coefficient, the mutation rate, effect sizes of SNPs, the phenotypic optimum, initial frequencies, number of steps, and population size.
Download nlocfwd.m (2.338 Kb)
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Title Merge country script
Downloaded 4 times
Description A Matlab script to merge country-wise and exclude populations.
Download merge_country.m (1.103 Kb)
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Title Read ms output script
Downloaded 8 times
Description A script to read output from ms (Hudson et al. 2002).
Download msread.m (1.895 Kb)
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Title Fold SFS script
Downloaded 4 times
Description A Matlab script to fold a given unfolded site frequency spectrum.
Download fold.m (1.274 Kb)
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Title Exclude populations given in popids
Downloaded 5 times
Description A Matlab script to exclude the unwanted populations.
Download excludepops.m (1.322 Kb)
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When using this data, please cite the original publication:

Bozicevic V, Hutter S, Stephan W, Wollstein A (2015) Population genetic evidence for cold adaptation in European Drosophila melanogaster populations. Molecular Ecology 25(5): 1175–1191. http://dx.doi.org/10.1111/mec.13464

Additionally, please cite the Dryad data package:

Bozicevic V, Hutter S, Stephan W, Wollstein A (2015) Data from: Population genetic evidence for cold adaptation in European Drosophila melanogaster populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.20t9v
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