Gene ontology enrichment analyses
Gene ontology enrichment analyses were performed with topGO (Alexa, A. et al., 2006), using Drosophila melanogaster orthologs of honey bee genes converted via a one-to-one reciprocal best hit BLAST (Table S15). We focused our assessment (Tables 3-4) on the more specific and highly enriched terms through sorting each resulting GO term list by percent coverage (defined as the proportion of genes associated with a GO term represented among the differentially expressed genes in each phenotype contrast) and selecting the top quartile, and then by GO term rank (defined as the number of child terms per GO term) and selecting the bottom quartile. Thus, Tables 3-4 represent the significantly enriched GO categories that had the largest proportion of DEGs and the most specific biological functions.