The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the production of new queens by removing the current colony queen, and we used RNA sequencing to study the gene expression profiles of both developing larvae and their caregiving nurses before and after queen removal. By comparing the gene expression profiles of queen-destined versus worker-destined larvae as well as nurses observed feeding these two types of larvae, we identified larval and nurse genes associated with caste development. Of 950 differentially expressed genes associated with caste, 82% were expressed in larvae with putative direct effects on larval caste, and 18% were expressed in nurses with putative indirect effects on caste. Estimated selection coefficients suggest that both nurse and larval genes putatively associated with caste are rapidly evolving, especially those genes associated with worker development. Altogether, our results suggest that indirect effect genes play important roles in both the expression and evolution of socially influenced traits such as caste.
Counts of mapped reads per gene for each of the 12 samples
Table showing counts of mapped reads (from htseq-count) per gene for each of the 12 samples. Further output from htseq-count per sample is shown at the bottom of the table, summarizing the total number of mapped reads, reads that were not mapped, and the proportion of total mapped reads. The first table column, "genes" refers to the A. mellifera Official Gene Set 3.2 accession numbers (Elsik et al. 2014). The remaining 12 columns refer to the 12 samples: "wg" = pooled HPG tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wg" = pooled HPG tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qg" = pooled HPG tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wh" = pooled head tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wh" = pooled head tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qh" = pooled head tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wm" = pooled MG tissue from nurses collected from queenright colonies while feeding worker-destined larvae; "Wm" = pooled MG tissue from nurses collected from queenless colonies while feeding worker-destined larvae; "Qm" = pooled MG tissue from nurses collected from queenless colonies while feeding queen-destined larvae; "wl" = pooled 4th instar worker-destined larvae from queenright colonies; "Wl" = pooled 4th instar worker-destined larvae from queenless colonies; "Ql" = pooled 4th instar queen-destined larvae from queenless colonies
allcounts.csv
raw hive observation data
Table of raw observation data of individually-marked bees observed interacting with worker and queen cells in two replicate observation hives. The inferred age of each bee is also shown. "day" = the day of the study following queen removal; "hive" = whether the observation came from replicate hive B or D; "tag color" and "tag #" = the color and number on the tag glued to the mesosoma of the individually-marked bee; "abdomen" = color of paint mark on the abdomen of the individually-marked bees. Together the mesosoma tag and abdomen paint mark were unique and enabled individual identification; "behavior" the observed behavior of the individually-marked bee; "time" the time of the observation; "Observer" = the initials or first name of the observer, see contributors in author list and Acknowledgements; "age" = the inferred age of the individually-marked bee, based on the date it was added as a newly-emerged bee to the observation hive plus the number of days that had elapsed.
raw hive observations 7May2011.csv
