DOI: 10.5061/dryad.20t9v
title: Data from: Population genetic evidence for cold adaptation in European Drosophila melanogaster populations

description: We studied Drosophila melanogaster populations from Europe (the
 Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic
 evidence of adaptation to cold. We present here four lines of evidence for
 genes involved in cold adaptation from four perspectives: (1) the
 frequency of SNPs at genes previously known to be associated with
 chill-coma recovery time (CCRT), startle reflex (SR), and resistance to
 starvation stress (RSS) vary along environmental gradients and therefore
 among populations; (2) SNPs of genes that correlate significantly with
 latitude and altitude in African and European populations overlap with
 SNPs that correlate with a latitudinal cline from North America; (3) at
 the genome-wide level, the top candidate genes are enriched in gene
 ontology (GO) terms that are related to cold tolerance; (4) GO enriched
 terms from North American clinal genes overlap significantly with those
 from Africa and Europe. Each SNP was tested in 10 independent runs of
 Bayenv2, using the median Bayes factors to ascertain candidate genes. None
 of the candidate genes were found close to the breakpoints of cosmopolitan
 inversions, and only four candidate genes were linked to QTLs related to
 CCRT. To overcome the limitation that we used only four populations to
 test correlations with environmental gradients, we performed simulations
 to estimate the power of our approach for detecting selection. Based on
 our results we propose a novel network of genes that is involved in cold
 adaptation.
description: Gene Ontology
 dataA
 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.Gowinda_vs_lat.xlsxInversion analysis dataCandidate genes and their distances from the breakpoints of cosmopolitan inversions.inversion_analysis.xlsxClimate dataClimate data retrieved from the World Meteorological Organization and other environmental variables.Climate.xlsxBayenv2 environment fileStandardised environmental variables in file format used for the Bayenv2 analysis.environmental_variables_standardized.txtSNP data - autosomesGenotypes of autosomal SNPs used in the analysis.autos.genoSNP chromosomal coordinates - autosomesEach line in the file lists the chromosome (autosome) and the absolute coordinate for the SNPs used in the analysis.autos.mapSNP data - chromosome XGenotypes of X chromosome SNPs used in the analysis.chrx.genoSNP chromosomal coordinates - chromosome XEach line in the file lists the absolute coordinates for the X chromosome SNPs used in the analysis.chrx.mapPairwise FST estimates for autosomal SNPsA Matlab file containing 3663890 autosomal SNPs, their pairwise FST estimates, and P-values for each SNP derived from coalescent simulations.pairwise_fst_autos.matPairwise FST estimates for the X chromosome SNPsA Matlab file containing 867049 X chromosome SNPs, their pairwise FST estimates, and P-values for each SNP derived from coalescent simulations.pairwise_fst_chrX.matBayenv2 results - autosomesA 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).bfautos_bh.matBayenv2 results - chromosome XA 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).bfX.matPolygenic trait forward simulations scriptA Matlab script to conduct forward simulations of multiple loci of a quantitative trait setting, and run Bayenv2 on final frequencies.multi_locus_simu.mPower analysis - simulations with sel. coeff. of 0.1A 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).multi_locus_simu_drift_ldex_S0.1.matPower analysis - simulations with sel. coeff. of 0.05A 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).multi_locus_simu_drift_ldex_S0.05.matDemographic estimation data - s9649A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.abc_gen_s9649.matDemographic estimation data - s9481A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.abc_gen_s9481.matDemographic estimation data - s8148A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.abc_gen_s8148.matDemographic estimation data - s48101A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.abc_gen_s48101.matDemographic estimation data - s7061A Matlab file containing data related to demographic parameter estimation by means of Approximate Bayesian Computation.abc_gen_s7061.matBayes factors from Bayenv2 - all chromosomesA 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.bf.matBayenv2 intermediate file - raw BFsAn intermediate Matlab file containing raw Bayes factors from Bayenv2.bayenv2mat.matDemographic estimation data - simulated FST autosomesA Matlab file containing FST estimated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains autosomal SNPs.abc_fst_in_sim_autos.matDemographic estimation data - simulated FST chromosome XA Matlab file containing FST estimated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains X chromosome SNPs.abc_fst_in_sim_chrX.matDemographic estimation data - simulated BFs autosomesA Matlab file containing Bayes factors calculated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains autosomal SNPs.abc_bayenv2_sim_autos.matDemographic estimation data - simulated BFs chromosome XA Matlab file containing Bayes factors calculated on simulated data from the demographic estimation analysis by means of Approximate Bayesian Computation. Contains X chromosome SNPs.abc_bayenv2_sim_chrX.matDemographic estimation data - summarized (autosomes)A Matlab file with summarized data from demographic estimation analysis by means of Approximate Bayesian Computation (autosomes).abc_summarized_data_autos.matEnsembl gene IDsA Matlab file containing Flybase (FBgn) gene IDs, their names and chromosomal locations. Retrieved from Ensembl.enshgnc.matEnsembl gene ontology annotationA Matlab file containing Flybase (FBgn) gene IDs, their gene ontology annotation and chromosomal locations. Retrieved from Ensembl.ensgo.matABC rejection data - autosomesA Matlab file containing the Approximate Bayesian Computation rejection matrix (autosomes).abc_reject_autos.matABC rejection data - X chromosomeA Matlab file containing the Approximate Bayesian Computation rejection matrix (X chromosome).abc_reject_chrX.matGenome annotations scriptA script to generate a Matlab file with genome annotations.annotdbmat.mReformat FUNC GO results scriptA script to reformat results from the FUNC GO analysis.go_process_out.mABC rejection scriptA script to apply the ABC rejection algorithm to simulated data.abc_reject.mABC generate polymorphism data scriptA script to generate polymorphism data from reasonable priors using coalescent simulations.abc_gen.mExport sets for FUNC scriptA script to export gene sets for GO analysis with FUNC (Prüfer et al. 2007).go_export_func.mABC simulate BFs script - autosomesA script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (autosomes).abc_bayenv2_sim_autos.mABC simulate BFs script - X chromosomeA script to simulate Bayenv2 Bayes factors from 10 best demographic simulations (X chromosome).abc_bayenv2_sim_chrX.mABC simulate FSTs scriptA script to simulate FST values from a given demographic model.abc_fst_in_sim.mABC combine ms results scriptA script to gather ms simulation results into one Matlab file.abc_ms2mat.mABC apply regression scriptA script to apply a weighted regression in the space of summary statistics as proposed by Beaumont et al. (2002).abc_regression.mABC run ms scriptA script to run Hudson's ms and return structure with haplotype matrices.abc_runms.mABC summarize data scriptA script to summarize data provided as a Matlab file.abc_summarize_data.mABC summarize struct. scriptA script to summarize data in struct. of haplotype matrices.abc_summarize_struct.mABC apply summary stats scriptA script to apply summary statistics to a single haplotype matrix.abc_summarize.mDemographic estimation data - chromosome XA Matlab file with summarized data from demographic estimation analysis by means of Approximate Bayesian Computation (chromosome X).abc_summarized_data_chrX.matCalculate aSFS scriptA script to calculate the absolute site frequency spectrum from Drosophila genotypes.aSFS_fromdata.mCalculate aSFS from simulations scriptA script to calculate the absolute site frequency spectrum from simulations.aSFSm.mBayenv2 batch scriptA script to initiate Bayenv2 runs.bayenv2_batch.mBayenv2 export SNPs for Cov matrix scriptA script to export randomly sampled SNPs for covariance matrix generation in Bayenv2.bayenv2_export_matrixgen.mBayenv2 export polymorphisms scriptA script to export polymorphic SNPs for testing in Bayenv2.bayenv2_export.mBayenv2 export independent SNPs for Cov matrix generationA script to export a random number of equally distant SNPs for matrix generation in Bayenv2.bayenv2_simu_matrixgen.mBayenv2 simulation wrapper scriptA script to provide Bayenv2 values for simulated frequencies given in a matrix file and environmental files.bayenv2_simuwrapper.mBayenv2 haplotypes wrapper scriptA script to provide Bayenv2 values for haplotypes given in a matrix file and environmental files.bayenv2_wrapper.mBayenv2 matrix batch scriptBayenv2 matrix batch script, outputs bf.mat file.bayenv2mat_batch.mBayenv2 matlab export script - autosomesA script to export the output of Bayenv2 into a Matlab file (autosomes).bayenv2mat.mBayenv2 matlab export script - chromosome XA script to export the output of Bayenv2 into a Matlab file (X chromosome).bayenv2matX.mClean db scriptA script to clean Drosophila genetic data structure.cleandb.mProvide P-values for SNPs from demographic simulationsA 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).empPvalsFst.mEstimate pairwise FST scriptA script to estimate the population pairwise FST. Inputs genotypes as a Matlab file and exports FST values as another Matlab file.pairwise_fst.mForward simulations of polygenic traitsA 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.nlocfwd.mMerge country scriptA Matlab script to merge country-wise and exclude populations.merge_country.mRead ms output scriptA script to read output from ms (Hudson et al. 2002).msread.mFold SFS scriptA Matlab script to fold a given unfolded site frequency spectrum.fold.mExclude populations given in popidsA Matlab script to exclude the unwanted populations.excludepops.m