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).