PMC

Genome-wide L2FC per population. Using DESeq2 [] the log2 fold-change (L2FC) in expression between rec90 and RT was calculated for 13803 genes with sufficient read count in both populations separately for African and European flies. Genes were then grouped into distinct bins according to their L2FC. Bin size is 0.2. The area where the African and European histograms overlap is depicted in dark red. a All genes, b genes with an absolute L2FC > 0.6

Transcriptome overview: PCA. PCA was calculated using the built-in methods provided by DESeq2 [42] for variance stabilizing transformation of read counts and PCA on the 500 genes with the highest overall expression variance. Note that samples are clearly separated according to continent and condition with the exception of RT and CS samples, which cluster tightly together in both populations such that symbols partly overlap

CCRT for the eight focal strains. Chill coma recovery time (CCRT) was determined following a 7 h cold shock in an ice-water bath. Depicted values are averaged over both sexes and a multitude of independent experiments. Strains originate from Umea, Sweden (SU07, SU08, SU58), Leiden, the Netherlands (E14), Siavonga, Zambia (ZI197, ZI216, ZI418), and Lake Kariba, Zimbabwe (A157)

Amount of highly plastic genes per strain. Genewise L2FC between rec90 and RT was calculated for each strain after normalization of raw counts using the TPM method [, ]. All genes with zero read count in one sample were excluded resulting in 12617 genes in total. Depicted are only genes with an absolute L2FC > 1 with no respect to up- or down-regulation