Extended Data Fig. 3: Measures of differentiation and divergence for linkage groups with supergenes.
As a complement to the patterns of temporal divergence shown in Figure 4, differentiation and divergence across linkage groups with supergenes were also quantified as Fst (a-h) and dxy (i-p). As in Figure 4, the two measures were calculated in sliding windows with a length of 250 kbp, for predefined groups of populations that separated those with the ancestral and derived supergene orientations. Both measures are plotted across linkage groups of the gadMor2 assembly (a-d, i-l) and chromosomes of the newer gadMor341 (e-h, m-p) assembly. Note that gadMor3 chromosome 2 is inverted relative to gadMor2 LG 2 (see Supplementary Figure 1). Comparable results were obtained by Barth et al.37 for gadMor2 LGs 2, 7 and 12, using a different dataset and shorter window sizes of 50 and 100 kbp.
