Figure 1: Experimental design.Monogyne colonies (large blue box) have a single, unwinged reproductive queen, sterile workers, and, seasonally, winged unmated queens (gynes), all with the SB/SB genotype ( BB’ in figure). Polygyne colonies (large red box) contain multiple, unwinged reproductive queens with the SB/Sb genotype (‘Bb’ in figure). The gynes in polygyne colonies can have a SB/SB, SB/Sb, or Sb/Sb genotype, although Sb/Sb gynes are rare because the Sb haplotype recessively induces early mortality of females. Polygyne workers are a mixture of SB/SB and SB/Sb individuals (Sb/Sbworkers are also rare). Pupae from monogyne colonies were cross-fostered in both monogyne and polygyne units (blue arrows and small blue boxes) while pupae from polygyne colonies were cross-fostered in polygyne units (red arrows and small red boxes). In the experimental samples, the color of the box border around the workers indicates whether individuals were raised in monogyne (blue) or polygyne (red) colonies until pupation. The color of the worker indicates whether individuals were raised in monogyne (blue) or polygyne (red) colonies from pupation until 14 days into adulthood. Brains and ovaries of gynes and brains and gasters of workers (marked in gold) were collected for RNA-seq analyses (data for gynes are from (Arsenault et al., 2020)). Sample sizes are included next to each tissue/caste.
Figure 2: Direct and indirect genetic effects on gene expression.For each pairwise comparison, the sample types are illustrated at the top of the figure (as described in Figure 1). (A , B ,C , D ) The numbers of differentially expressed genes (DEGs) in each pairwise comparison are plotted at multiple significance levels. (E, F , G , H ) Log2-transformed gene expression ratios. Directionality of each plot mirrors the directionality of the schematic for that comparison at the top of the figure (positive values indicate higher expression in SB/Sb individuals in panel E and the polygyne social environment in panel F ). Each plot includes a box plot showing the ratios for all genes, including those that are not significant (whiskers show observations within 1.5 * IQR of the lower and upper quartiles). Each dot represents a DEG (FDR < 0.1). Significant directional bias in differential expression is indicated with * (chi-squared test; P < 0.05). (I , J ,K , L ) Log2-transformed ratio of overrepresentation within rather than outside the supergene region (observed / expected) for significant DEGs (FDR < 0.1). Positive values indicate a higher proportion of DEGs found within the supergene versus the rest of the genome. Statistical significance of enrichment is indicated with * (chi-squared test; P < 0.05).