Figure SI 1. Large genomic regions respond at both temperatures. ;Figure SI 2. Histograms of parental gene expression differences per gene at 18°C (blue) and at 29°C (purple). ;Figure SI 3. Influence of the window size (1, 50, 250, 500 SNP(s)) and FDR threshold (x-axis, 0.05, 0.1, 0.15) for the partitioning of the genomic windowś diagnostic (y-axis, color code indicated in the legend).;Figure SI 4. Correlation between ancestral gene expression and genomic response after 20 generations. ;Table SI 1. Partition of the genome per class.

We estimated the median size of genomic regions with pronounced linkage at F20 by the autocorrelation in allele frequency between non-overlapping windows of 250 SNPs as in Burny et al, 2021. The distance between windows where the autocorrelation is no longer significant is used as measure of association. In the jittered boxplots, one dot represents one chromosome and a given replicate (18°C, blue; 29°C, purple).;The dashed lines represent at 18°C and 29°C the median absolute logFC S/O (0.37 at 18°C and 0.50 at 29°C, B; p-value paired Wilcoxon one-sided test=5×10-148).;Individual chromosomes and genome-wide estimates are shown.;Left. The temperature effect on the gene expression differences between the two parental genotypes (Samarkand and Oregon-R, y-axis) is plotted against the temperature effect of the allele frequency changes (x-axis). Each data point corresponds to a gene. The Spearman correlation (ρ) coefficient is reported. Right. The correlation between gene expression differential (logFC S/O 29°C - logFC S/O 18°C) and allele frequency differential (AFC 29°C - AFC 18°C) are measured in bins containing an increasing number of genes, which are ranked by expression (red) or allele frequency (black) differential.;The class definition is indicated in column 3 where the conditioning is made on p-values corrected with the Benjamini-Hochberg procedure for either neutrality tests at 18°C and 29°C (p.adjw18°C neutral and p.adjw29°C neutral) or from the linear model on the non-neutral windows (p.adjwLM) (see Methods). The percentage of windows affected in each class is reported in column 4 per chromosome and average genome-wide (GW), obtained with an False Discovery Rate (FDR) threshold of 5%, 10% and 15% (1st, 2nd and 3rd sub-row) and for non-overlapping windows of 250 SNPs