Figure 2.

Dispersed genomic architecture of parallel adaptation and enrichment for old genetic variation. (a) Signatures of selective sweeps across the stickleback adaptive radiation on Haida Gwaii are distributed throughout the genome. Vertical gray bars indicate outlier regions enriched for both iHS (blue) and H12 (green) outliers (black points) at Bonferroni‐corrected alpha <0.001, with iHS and H12 outliers exceeding 99.9% quantiles of neutral demographic expectations. Several blocks of old standing variation, indicated by a large range in absolute divergence (d _XY) between population pairs (purple area), overlap such outlier regions. Color codes below each chromosome indicate d _XY range quantiles shown in panel c. Roman numerals are chromosome names; letters correspond to outlier regions (see Table S2). (b) Genotype distribution of Haida Gwaii stickleback for known large inversions: “marine” haplotypes are found in several freshwater populations, in particular in fully plated freshwater populations (DA, DW, SY). First principal components of SNP genotypes in the indicated genomic interval are shown, with the percentage of variation explained in brackets. (c) Distribution of d _XY ranges in 100‐kb windows based on all pairwise d _XY values between the 29 individuals, with quantiles indicated by colors. (d) Outlier regions are enriched for old standing genetic variation: 16% of the outlier regions fall into genomic regions containing old genetic variation.