Data from: Ecology shapes epistasis in a genotype-phenotype-fitness map for stick insect colour

The following files are included in this data archive: 2019_Tchumash_transplant_table.csv = csv text file with data from the release-recapture selection experiment. The files includes one row per individual with data on treatment, block, survival (binary) and color. selectionGradBayes.R = R script with code for fitting selection gradients with Bayesan methods. bayes_glm and bayes_hglm = JAGS models required by selectionGradBayes.R. spectra.chumash.zip = zip compressed directory with the raw color spectra data. 2020Tchumash_quantum_catch_epistasis.R = R script to make graphs summarizing the spectra data. Tchumash.spectra.epistasis.txt and Tchumash.list.epistasis.txt = Text file tables required to run 2020Tchumash_quantum_catch_epistasis.R. filtered2x_tchum_mel_gbs_2019.vcf.gz = gzip compressed vcf file. This has the variant (SNP) data used in this study. This version of the file has been filtered as described in the manuscript. mod_g_epi_tchum.txt, mod_g_tchum_AC.txt, mod_g_tchum_MM.txt, mod_g_tchum.txt = geno format text files for gemma. These files contain the genotype data (posterior mean estimates of genotypes) used for fitting BSLMMs with gemma. The AC and MM files contain only individuals in the AC or MM treatment, respectively. mod_g_tchum.txt contains all individuals. mod_g_epi_tchum.txt contains all individuals and includes the epsitatic effects (genotype products) for SNPs showing evidence of marginal epistasis based on the MAPIT analysis. pheno_MM, pheno_AC, pheno_color = pheno format text files for gemma. pheno_MM and pheno_AC contains survival and sex as phenotypes (binary), whereas pheno_color has the color data. These are input for the BSLMM fit with gemma. pheno_rg_cv.txt and pheno_gb_cv.txt = pheno format text files for cross-validation with gemma. Here, each color phenotype (RG or GB) has been repeated across multiple columns with missing data for subsets of individuals. models.R = main R script for analyzing expected fitness as a function of color-associated SNPs. Various versions of this analysis are included. tchumSnpTable.txt = text file with one row per SNP with columns for LG, scaffold and position. This file is required by models.R cvScript*R = set of R scripts for cross-validation analyses under different conditions, that is based on survival or expected fitness as the response and with additive effects only, or including dominance or epistasis. cvSummary.R = R script to summarize cross-validation analyses. ld.R = R script used to summarize patterns of LD among color-associated SNPs. runMapitColor.R and runMapitSurv.R = R scripts used to run the MAPIT analyses (tests for marginal epistasis) with color and survival as responses. calcBV.R = R script used to calculate genomic-estimated breeding values for RG and GB color traits with and without allowing for epistasis. pleoitropy.R = R script used to run the core pleiotropy analyses. nullSims.R and nullSimsPl.R = R script used to perform null simulations fitting the Bayes model selection/model averaging models to sets of random SNPs with or without allowing for pleiotropy.