At its broadest sense, to say that a phenotype is epigenetic suggests that it occurs without changes in DNA sequence, yet is heritable through cell division and occasionally from one organismal generation to the next. Since gene regulatory changes are oftentimes in response to environmental stimuli and may be retained in descendent cells, there is a growing expectation that one's experiences may have consequence for subsequent generations and thus impact evolution by decoupling a selectable phenotype from its underlying heritable genotype. But the risk of this overbroad use of “epigenetic” is a conflation of genuine cases of heritable non-sequence genetic information with trivial modes of gene regulation. A look at the term “epigenetic” and some problems with its increasing prevalence argues for a more reserved and precise set of defining characteristics. Additionally, questions arising about how we define the “sequence independence” aspect of epigenetic inheritance suggest a form of genome evolution resulting from induced polymorphisms at repeated loci (e.g., the rDNA or heterochromatin). 1. Epigenetics and Evolution The importance of sequence polymorphisms in evolution is fundamental and irrefutable. The contribution of epigenetic gene regulation is considerably less well established. In this perspective, I will not attempt to summarize all the studies that have contributed to our current understanding of epigenetics; instead, I will thread together a handful of salient studies, taken particularly but not exclusively from Drosophila research, to illuminate how common and consequent “epigenetic” gene regulation may result from induced polymorphism. Inclusion of induced polymorphism in the panoply of epigenetic gene regulatory mechanisms may force us to reconsider our definitions, but is in accord with current and historic uses of “epigenetics,” and may provide a new mechanism to understand how stable changes in gene expression can be established and maintained. To understand the role of epigenetics in evolution, it is necessary to consider definitions of both evolution and epigenetics. For the purpose of any discussion linking the two, “evolution” must expand to include the change of frequency of phenotypic variants irrespective of underlying allelic variants. This is a mild departure from a sequence-centric view of changes in allele frequencies in evolving populations, but is ironically more aligned with the original use of “epigenetic” to describe the abstract processes that produce a phenotype from a genotype prior to the elucidation of the central
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