Fig. 2: Detection of a supergene in chromosome 2.
Panel (A): sliding windows analysis of the proportion of variance explained by the first axis of a PCA computed on chromosome 2 in NWA samples. Each dot corresponds to a window. Panel (B): local PCA within the supergene region (17,000,000-48,000,000) of chromosome 2 including only NWA individuals. Panel (C): proportion of heterozygotes within the supergene region for HB/HB (N = 9), HB/HS (N = 2) and HS/HS (N = 10) genotypes. The line within the boxplot represents the median value with the lower and upper hinges being the first (Q1) and third (Q3) quartiles. The upper whisker goes from the hinge to the largest value no further than 1.5 times the distance between Q1 and Q3 and the lower whisker from the hinge to the lowest value no further than 1.5 times the distance between Q1 and Q3. Data beyond the whisker are represented as points. Panel (D): heatmap of the pairwise linkage disequilibrium between SNPs. Color gradient represents the value of the r2 correlation between SNPs. Panel (E): sliding window FST between HB/HB and HS/HS individuals from NWA. Panel (F): local PCA within the supergene region including all individuals. Dot shape in Panels B and F represents the sampling location and colour represents the genotype at the supergene: HS/HS (purple), HB/HS (red) and HB/HB (yellow).
