Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies

Abstract

For social animals, the genotypes of group members affect the social environment, and thus individual behavior, often indirectly. We used genome-wide association studies (GWAS) to determine the influence of individual vs. group genotypes on aggression in honey bees. Aggression in honey bees arises from the coordinated actions of colony members, primarily nonreproductive "soldier" bees, and thus, experiences evolutionary selection at the colony level. Here, we show that individual behavior is influenced by colony environment, which in turn, is shaped by allele frequency within colonies. Using a population with a range of aggression, we sequenced individual whole genomes and looked for genotype-behavior associations within colonies in a common environment. There were no significant correlations between individual aggression and specific alleles. By contrast, we found strong correlations between colony aggression and the frequencies of specific alleles within colonies, despite a small number of colonies. Associations at the colony level were highly significant and were very similar among both soldiers and foragers, but they covaried with one another. One strongly significant association peak, containing an ortholog of the Drosophila sensory gene dpr4 on linkage group (chromosome) 7, showed strong signals of both selection and admixture during the evolution of gentleness in a honey bee population. We thus found links between colony genetics and group behavior and also, molecular evidence for group-level selection, acting at the colony level. We conclude that group genetics dominates individual genetics in determining the fatal decision of honey bees to sting.

Keywords: GWAS; aggression; behavioral genetics.

Fig. 1.

Genome-wide associations of aggression at the group level. (A) Distribution of colony aggression phenotypes derived using dimensional reduction of response to experimental threat and postthreat behavioral screening assay for all colonies used in the study; the map illustrates the original geographic source for all of the colonies, with colors highlighting intensity of response or exclusion (if gray). (B) Network diagram of kinship structure derived from a sparse matrix of coefficient of relationships (r) retaining only the degrees of relationship above first cousin (0.125). Circle vertices identify foragers, square vertices identify soldiers, and color of vertices matches colony response from A. Green hexagons identify queen samples, and edges highlight kinship associations within (solid) and between (dotted) colonies. Grouping was achieved with the Fruchterman–Reingold algorithm. (C) Association of colony-level MAF across the genome to colony aggression phenotype; the dashed line shows significance threshold (Bonferroni corrected α = 7.67E⁻¹⁰).

Fig. 2.

Signatures of selection and admixture in loci associated with colony aggression. (A) Gray dots show selection signatures [the natural log ratio of decay in LD, ln(Rsb)] across the genome for variants between gAHBs and AHBs (data from ref. 21). Those that show both statistically significant selection and statistically significant association between colony-level genotype and colony aggression phenotype in the present study are colored according to significance of the group genotype–phenotype association. The association and selection studies used different samples of individuals. Adjacent to the y axis, simplified box plots for all of the haplotype blocks (gray) and those with overlap (black) identify the extremes, interquartile range, and median of the ln(Rsb) distribution. The dark rectangle highlights a span of notable, significant overlap in LG 07. (B) Region within the rectangle of A, expanded to show selection, association, and admixture. (Top) The ln(Rsb) signal from Fig. 2A. (Middle) The colony genome-wide association signal from Fig. 1C. (Bottom) The proportional contribution of EHB (yellow) and AHB (magenta) reference populations from ref. . Proportional contribution was derived via RFMix ancestry determination analysis and ranges from zero to one (y axis). The x axes for all three plots correspond to base pair coordinates of the span within LG 07.