Files and scripts used in Pervasive suppressors halt the spread of selfish Segregation Distorter in a natural population by Chang, Handler, et al.

All_filtered_snps_2019.vcf: This file contains variant calls referenced in Chang, Handler et al. 2026 (https://doi.org/10.1093/genetics/iyag108). We applied the GATK4 best practice pipeline to map and call SNPs in the DGRP (POPLIN et 206 al. 2018) using the Drosophila melanogaster R6 genome assembly (HOSKINS et al. 2015). In short, we mapped Illumina reads from DGRP and Iso-1 to the Flybase R6 reference using bwa mem 208 (v0.7.15; (LI AND DURBIN 2010)) and marked the duplicates using GATK MarkDuplicates with default settings (v4.1.2; http://broadinstitute.github.io/picard/). We integrated known indel data from the DGRP (MACKAY et al. 2012) and DPGP1 (LANGLEY et al. 2012) to optimize our SNP calling in GATK.Files in /scripts folder contain R scripts used to create figures and run analyses for Chang, Handler et al. 2026. Scripts are labeled by figures 1-4. All files required to run scripts are in the directory and referenced in each script.File names and descriptions:Fig1_v3.R: Code for Figure 1- Distribution of Rsp copy number in the DGRP. Code and files to create histograms and run PCA analyses. Associated files: fig1_pheno3.txt, fig1_pca_covar.txt, fig1_pca_covar_v2.txt.Fig2_v2.R: Code for Figure 2- High frequency of suppressors on autosomes and the X chromosome across DGRP strains. Code and files to plot k value distributions. Associated files: fig2_SD_compare_v2.txt.Fig3_v2.R: Code for Figure 3 -Rsp copy number is associated with drive strength and explains GWAS signals near the centromere of chromosome 2. Code and files to run GWAS analyses.Fig4_v2.R: Code and Files for Figure 4- One major locus contributes to the suppressing effect of Su(SD)X by rescuing sperm with sensitive Rsp alleles. Associated files: fig4_genotype_phenotype_v2.csv, fig4_Recombine.txt.FigS1_v2.R: Code and files for Figure S1- Surveys of dominant suppressors or intermediate sensitive Rsp on individual autosomes form DGRP. Associated files: figS1_SuSD2.txt, figS1_SuSD3.txt.FigS2_v2.R: Code and files for Figure S2 - The positive correlation of k values and Rsp numbers using different methods across DGRP strains.FigS3_S4_S5_v2.R: Code and files for Figure S3 - Quantile-quantile (Q-Q) plots from genome-wide association studies using DGRP strains under different conditions.Files for association studies:no_covar_0.05_DGRPX.assoc.linearno_covar_0.05_noX_nocovar.assoc.linearno_covar_DGRPX.assoc.linearno_covar_noX.assoc.linearqPCR_0.05_DGRPX.assoc.linearqPCR_0.05_noX.assoc.linearqPCR_DGRPX.assoc.linearqPCR_noX.assoc.linearshort_0.05_read_DGRPX.assoc.linearshort_0.05_read_noX.assoc.linearshortread_DGRPX.assoc.linearshortread_noX.assoc.linearslot_blot_0.05_DGRPX.assoc.linearslot_blot_0.05_noX.assoc.linearslotblot_DGRPX.assoc.linearslotblot_noX.assoc.linear