RAD_cydmelhec_data.geno: Space delimited tabular file giving the genotype calls used this paper. They were filtered from the .vcf files (generated by GATK unified genotyper) and represent all bases that were called with a genotype quality >=30 in multiple individuals. Individuals are in columns and genome positions in rows. Missing data are given as "N". This file was filtered for the relevant individuals and all sites with missing data removed prior to running analyses with any of the given scripts. geno_to_haplo_54.pl: Perl script used to go from genotype calls to haplotype calls (not phased). This was done before running the Fst scripts but not AMOVAs. clumpy.py: python script used to split the single calls file(s) into individual RAD loci. The output consists of multiple files - one for each locus found - all in the same format as the original calls input file, and a comma separated values file with the start and end positions in the genome and length of each RAD locus. Fst.r: R script used to calculate the Fst values for the major race and species comparisons discussed in the paper. Inputs are the indidividual RAD locus haplotpe files and the summary statistics file generated by clump.py Fst_spcorr.r: R script used to calculate correlations between Fst values at increasing genomic distances. Input is the output from above. Fst2.r: R script used to calculate Fst between all pairs of populations. Inputs are as Fst.r. amova1.r: R script used to perform AMOVA analyses. Generates a distance matrix based to genotype calls and used the ade4 package to run Amovas. Inputs are the indidividual RAD locus genotype files and the summary statistics file generated by clump.py and character matrix files (see below). genotype_matrix.csv: A starting genotype matrix assuming sepatare genotypes for each individual that is modified by the above script. population_matrix_CP.csv: A file giving colour pattern groupings for each population for the AMOVA analysis population_matrix_geo.csv: As above giving geographic groupings population_matrix_taxon.csv: As above giving taxonomic groupings Hmel_chromosomes_dec_2011_OLD_HOX_no_header_filtered.agp: A file relating the scaffolds to chromosomes (inferred from RAD mapping from The Heliconius Genome Consortium 2012). This was used to generate genome-wide plots.