README ############################### File 1: "snp_table_DRYAD.txt" This is the filtered SNP table analyzed in the paper. It is a text file with 18 columns and 109707 rows. Each row provides data for an individual SNP. Columns are: 1. "chr": chromosome (nuclear chromosomes chr1-chr16, as well as chrmito) 2. "pos": non-cumulative position along each chromosome (matches UCSC Genome Browser) 3. "ref": reference allele in the S288C genome 4. "alt": non-reference allele 5. "maf_A1": frequency of the alternate allele in founder DBVPG6765 6. "maf_A2": frequency of the alternate allele in founder DBVPG6044 7. "maf_B3": frequency of the alternate allele in founder YPS128 8. "maf_B4": frequency of the alternate allele in founder Y12 9. "alt_4S_0": count of alternate allele in 4X pop cycle 0 10. "ref_4S_0": count of reference allele in 4X pop cycle 0 11. "alt_4S_6": count of alternate allele in 4X pop cycle 6 12. "ref_4S_6": count of alternate allele in 4X pop cycle 6 13. "alt_4S_12": count of alternate allele in 4X pop cycle 12 14. "ref_4S_12": count of alternate allele in 4X pop cycle 12 15. "alt_4S_12H": count of alternate allele in 4X pop cycle 12H 16. "ref_4S_12H": count of alternate allele in 4X pop cycle 12H 17. "cyc0_cyc12_FET": -log10(p) of Fisher's Exact Test comparing cycle 0 - cycle 12 18. "cyc12_cyc12H_FET": -log10(p) of Fisher's Exact Test comparing cycle 12 - cycle 12H ############################### File 2: "hap_freqs_DRYAD.txt" This is the table of estimated haplotype frequencies analyzed in the paper. It is a text file with 14 columns and 11482 rows. Haplotypes were estimated across 30kb windows using a 1kb step size, using the R script haplotype.limSolve.code.R (https://github.com/tdlong/yeast_SNP-HAP). Columns are: 1. "chr": chromosome (nuclear chromosomes C01-C16) 2. "pos": non-cumulative position along each chromosome (matches UCSC Genome Browser) 3. "cyc0_A1": haplotype frequency of founder DBVPG6765 at cycle 0 4. "cyc0_A2": haplotype frequency of founder DBVPG6044 at cycle 0 5. "cyc0_B3": haplotype frequency of founder YPS128 at cycle 0 6. "cyc12_B4": haplotype frequency of founder Y12 at cycle 0 7. "cyc12_A1": haplotype frequency of founder DBVPG6765 at cycle 12 8. "cyc12_A2": haplotype frequency of founder DBVPG6044 at cycle 12 9. "cyc12_B3": haplotype frequency of founder YPS128 at cycle 12 10. "cyc12_B4": haplotype frequency of founder Y12 at cycle 12 11. "cyc12H_A1": haplotype frequency of founder DBVPG6765 at cycle 12H 12. "cyc12H_A2": haplotype frequency of founder DBVPG6044 at cycle 12H 13. "cyc12H_B3": haplotype frequency of founder YPS128 at cycle 12H 14. "cyc12H_B4": haplotype frequency of founder Y12 at cycle 12H