Figure 2: Supergene-mediated differential gene expression. (A) Volcano plot of gene expression differences between SB/SB andSB/Sb gynes, independent of organ and social-environment effects (multifactorial-model). Aqua dots represent statistically significant differences (FDR < 0.01). (B) Volcano plot of gene expression differences between SB/SB and Sb/Sb gynes. (C) UpSet plot showing organ-specific patterns of differential gene expression associated with differences in social chromosome genotype in polygyne-reared gynes. The pattern of genes common to different comparisons is indicated by the dots below the vertical bar plot. Numbers in parentheses indicate the genes remaining in a category after elimination of cusp cases (genes with FDR = 0.01-0.1 in other contexts, described in Methods). (D) Heatmap of the distribution of differentially expressed genes across the linkage-mapped genome in polygyne-reared gynes. The region spanned by the lg16 Sb supergene is marked in green. Labels to the right of the heatmap refer to candidate genes in each of the categories described in panel C.