While two organisms may be genetically identical, the way the genes are expressed allows for very large differences. Epigenetics describes the mechanisms by which individual genes are either expressed or inhibited. It is as though each gene is associated with a dimmer switch that can either attenuate or amplify its importance, (i.e. its impact on the phenotype), according to changes in the organism's external and internal environment. For queen bees, the transformational environmental changes are linked to the ingestion of royal jelly.

Royal jelly is composed of 67% water, 12.5% crude protein including a variety of amino acids, 11% simple sugars and 5% fatty acids. It also contains multiple trace minerals, enzymes and vitamins. All larvae are fed royal jelly for the first three days, however the queen feasts on it for a lifetime – and in great quantities. But the catalyst behind queen differentiation is a specific component of the protein called 57-kDa, better known as Royalactin. Royalactin increases body size and ovary development and shortens the developmental time in honeybees. The difference between queen and worker castes is one of the most striking examples found in the nature of phenotypic polymorphism due to epigenetic factors.

 

Queen	Workers
Fed royal jelly during lifetime (food quantities = 10x more than workers)	Fed royal jelly for 3 days, then downgraded mixture of pollen and honey
Rapid growth: 200mg final weight	100 mg final weight
Lifetime = 3 years	Lifetime = 1 month
Maturation of reproductive organs (up to 2000 eggs per day)	Rudimentary, inactive ovaries

At the cellular level, the phenotypic polymorphism of honeybees is mediated by a process called CpG methylation. CpG methylation is able to establish and maintain diverse patterns of gene expression from the same genome under specific temporal, spatial and environmental conditions—the internal and external environment pressures mentioned above. This non-reproductive modification of genomic DNA provides a link between genomes and the environment and may result in a phenotypic change that is heritable, independently of DNA mutation. Paradoxically, it was only relatively recently that the process of genomic methylation was established in invertebrates. This was because the technology was not yet available to detect modifications (methylomes) with very low methylation levels.