I hesitate to stick my toe into this conflagration of evolutionary mysteries, but as long as we've come around to phenotypic plasticity, I'll put in a couple cents.  BTW, thanks everyone for the recent contributions.

When investigating regulation of genetic expression, there is no question epigenetic factors come into play (see attached), but backing up a little, we need to remember that there are no genes "for" anything... epigenetic or otherwise.  That's not how it works.  We've come a long ways since Mendel. It's well known that a vast majority of the genome does not actually code for phenotypic traits, and that the functionality of the non-coding regulatory logic extends from the developing stages of an organism throughout its physiological life via the successive engagement of elaborate and multi-dimensional molecular machinery involving gene regulatory networks. The gene regulatory networks operate along with the attendant Cis-regulatory "elements" which contain binding sites for the transcription factors produced by the regulatory networks. It's basically many huge sequence specific multi-dimensional Boolean networks that all feed inputs and outputs back and forth to each other.  Plus... insect genomes are actually even more complex than mammalian ones mainly due to post transcriptional processing of the mRNA that finally leaves the nucleus to go out and actually make something happen.  Ok... so what? And what's this have to do with honey bees epigenetics (?) 

So anyway...  having a genomic sequence in hand, really doesn't tell us anything. It's taking apart all these regulatory networks and identifying all the various "nodes" that begin to provide clues as to how things work. This has only recently been possible. (Obviously still a long ways to go)  But as far as addressing the "queen/worker" developmental issue, a recent investigation (last year) did begin to layout (for the first time) multiple levels of epigenetic regulation in honey bees that are implicated in establishing and maintaining the two female castes. It's an intriguing read. They even found some conserved genes that are related to our well studied fruit flies that help explain such things as larger eye size in the drones, etc. Please enjoy: 

Lowe, R. et al. (2022) ‘Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms’, Nucleic Acids Research, 50(20), pp. 11550–11562. Available at: https://doi.org/10.1093/nar/gkac992.

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