DOI: 10.5061/dryad.vs264
title: Data from: Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

description: We used whole-genome resequencing data from a population of Drosophila
 melanogaster to investigate the causes of the negative correlation between
 the within-population synonymous nucleotide site diversity (πS) of a gene
 and its degree of divergence from related species at nonsynonymous
 nucleotide sites (KA). By using the estimated distributions of mutational
 effects on fitness at nonsynonymous and UTR sites, we predicted the
 effects of background selection at sites within a gene on πS and found
 that these could account for only part of the observed correlation between
 πS and KA. We developed a model of the effects of selective sweeps that
 included gene conversion as well as crossing over. We used this model to
 estimate the average strength of selection on positively selected
 mutations in coding sequences and in UTRs, as well as the proportions of
 new mutations that are selectively advantageous. Genes with high levels of
 selective constraint on nonsynonymous sites were found to have lower
 strengths of positive selection and lower proportions of advantageous
 mutations than genes with low levels of constraint. Overall, background
 selection and selective sweeps within a typical gene reduce its synonymous
 diversity to ∼75% of its value in the absence of selection, with larger
 reductions for genes with high KA. Gene conversion has a major effect on
 the estimates of the parameters of positive selection, such that the
 estimated strength of selection on favorable mutations is greatly reduced
 if it is ignored.
description: BGS-modelsPrograms to run the BGS models. Executables in Fortran (Summation-BGS-model-prog.rtf, Integral-BGS-model-prog.rtf and Data-analysis-1lineage-prog.rtf), specimen input files (Integral-BGS-model-datafile.rtf and Summation-BGS-model-datafile.rtf) and specimen output files (Summation-BGS-model-OP1.rtf and Integral-BGS-model-OP1.rtf).Data-analysesThese are the programs and specimen results for analysing the original data. Executables in Fortran: Data-analysis-1lineage-prog.rtf and Data-analysis-2species-prog.rtf. Specimen input files: Data-analysis-2species-datafile.rtf and Data-analysis-1lineage-datafile.rtf. Specimen output files: Data-analysis-2species-OP1.rtf and Data-analysis-1lineage-OP1.rtf.Sweep-effectsPrograms to calculate selective sweep effect for nonsynonymous sites (sweeps-NS sites-prog.rtf) and UTRs (sweeps-UTRsites-prog.rtf) gene using the summation method. Specimen input files: sweeps-NSsites-datafile.rtf and sweeps-UTRsites-datafile.rtf. Specimen output files: sweeps-NSsites-OP1.rtf and sweeps-UTRsites-OP1.rtf.Data for correlation analyses-1lineageData for correlation analyses-2speciesBootstrap-analysisBootstrap analysis files. Executables in fortran: Bootstrap-analysis-1lineage-prog.rtf and Bootstrap-analysis-2species-prog.rtf. Specimen input files: Bootstrap-analysis-2species-datafile.rtf and Bootstrap-analysis-1lineage-datafile.rtf. Specimen output files: Bootstrap-analysis-2species-OP1.rtf and Bootstrap-analysis-1lineage-OP1.rtf.Table_S2APopulation genomic statistics for NS sites for each bin of KA values for mel-yak.Table_S2BPopulation genomic statistics for NS sites for each bin of KA values for mel.Table_S3AUTR population genomic statistics for each bin of KA values for mel-yak.Table_S3BUTR Population genomic statistics for each bin of KA values for mel.