Fig. 3
Genetic divergence along the genome between individuals representing the pure species. Each dot represents the average FST of a 200 kb window, with a stepping size of 100 kb. The red lines show smoothed divergence trends along chromosomes as inferred from a generalised additive model. Unanchored scaffolds are not represented as only one of them was longer than the window length of 200 kb. Note that there is no exceptionally strong divergence along chromosomes 2 and 3 on which most large-effect loci were identified by GWAS (see Fig. 2)