My chief concern is that epigenetics is becoming a catch all phrase for what we can't account for in our understanding of genetics. There are a lot of factors at work, not the least of which is environmental, and of course, organisms such as honey bee colonies are capable of modifying their own environment (the nest) which is the environment into which subsequent generations are born.

> Epigenetic mechanisms are invoked to address the 'missing heritability' problem in genome-wide association studies (GWAS), which show that most traits with high heritabilities (such as height, intelligence quotient, personality traits and many common diseases) cannot be explained by association with common genetic variants.

> Epigenetic processes are a potential answer to this problem because they allow non-genetic information to be inherited across generations. But there is a great deal of variation in epigenetic mechanisms. They are present in many taxa, and multiple epigenetic mechanisms are proposed to affect development and disease (including DNA methylation, histone modifications and non-coding RNA).

> The erasure of epigenetic marks at the germline and embryogenesis in vertebrates is quite extensive and makes it a difficult topic to study.  At the very least, the potential for epigenetic transgenerational inheritance appears limited. Moreover, quantitative genetic evidence shows that epigenetic variation itself is influenced by genetic variation. 

> ... this study demonstrated that the most heritable epigenetic sites were those correlated with functional genome regions, indicating that function-specific epigenetic indicators were under the strongest genetic control.

> Evidence suggests that epigenetic systems are themselves phenotypes, and their genes are subject to natural selection, drift and all else.

source: The extended evolutionary synthesis and the role of soft inheritance in evolution
Thomas E. Dickins and Qazi Rahman. Proc. R. Soc. B (2012) 279, 2913–2921

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