Gene expression variation in the brains of harvester ant foragers is associated with collective behavior

Abstract

Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.

Fig. 1. Colony variation in collective behavior, physiology, and forager brain gene expression.

a Colony traits for the nine colonies profiled in this study. The top Y axis reflects colony sensitivity of foraging activity to humidity, in units of the number fewer foraging trips made per degree decrease in daily humidity (Methods). The bottom Y axis is forager brain dopamine-to-serotonin ratio (Methods), a measure of colony variation in neurophysiology. Bars are group means ± s.e.m. b The axes are the first three principal components of the single-forager brain transcriptome, capturing 37% of variation among samples. Each point is a single-forager brain transcriptomic sample, the point of the color represents colony. c Linear Discriminant Analysis on first 30 PCA dimensions (77% of variation). A point is a single-forager brain transcriptomic sample, the point of the color represents colony.

Fig. 2. Gene expression correlations with colony behavior and physiological traits.

The distribution of correlation coefficients are shown transcriptome-wide a, c and for candidate loci lists b, d, between colony traits and forager brain gene expression (N = 85). a Histogram of correlation coefficients between the expression of each gene in the P. barbatus transcriptome and sensitivity of foraging activity to humidity. b Expression correlation with colony sensitivity of foraging activity to humidity for the different candidate loci categories (**P < 0.001; one-sample t test). c Transcriptome-wide expression correlations with colony average forager brain dopamine-to-serotonin ratio. Bar color reflects the top (blue) 50% of correlation values used for the omnibus gene ontology enrichment test. The bottom 50% is not highlighted since no significant enrichments were detected. d Correlation with forager brain dopamine-to-serotonin ratio (DA:5HT) for the different candidate locus groups. (no tests with P < 0.01; one sample t test).

Fig. 3. Summary of weighted gene correlation network analysis (WGCNA).

a Dendrogram of hierarchically clustered genes, based on expression levels. “Leaves” along “branches” represent individual loci. The Y axis represents network distance as determined by 1 – topological overlap (TO), values closer to 0 indicate greater similarity of expression profiles between samples. The first color band denotes the coexpression module assignments for the loci directly above. Modules are named by color. The second color band represents Pearson correlations between gene expression profiles and module eigengenes (kME); the darker the shade of red, the closer the correlation value is to 1. The third and fourth color bands represent Pearson correlations between gene expression profiles and colony-level traits; sensitivity of foraging activity to humidity and forager brain dopamine to serotonin (DA:5HT) ratio, where darker the color of red, the closer the correlation value is to 1 and −1. The final color band represents the dN/dS decile for loci in the dendrogram such that darker the shade of red, the lower the dN/dS decile is for that gene (WGCNA Methods). b Correlation between gene expression level and sensitivity of foraging activity to humidity (Y axis) for individual loci (dots), plotted against the dN/dS decile (X axis) for the same loci. All 7085 loci in the dendrogram are shown. The red line is the best-fit linear regression and the blue line represents the regression slope among the 11 coexpression modules of module average dN/dS vs. average expression correlation with the sensitivity of foraging activity to humidity. c Relationship between module centrality of each locus (X axis) and dN/dS decile (Y axis). d Correlation between gene expression level and sensitivity of foraging activity to humidity (Y axis) for individual loci (dots) in the “green” coexpression module, plotted against their module centrality (X axis, expression correlation with green module eigengene). The red line is the best-fit linear regression. Genes that are more central to the module tend to have stronger correlations with colony behavioral traits (Pearson r = 0.52, p < 3e-42).