Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions. With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can now be addressed. Here, we review epigenetic phenomena in aphids and recent progress toward elucidating the molecular basis of epigenetics in aphids. The discovery of a functional DNA methylation system, functional small RNA system, and expanded set of chromatin modifying genes provides a platform for analyzing these pathways in the context of aphid plasticity. With these tools and further research, aphids are an emerging model system for studying the molecular epigenetics of polyphenisms. 1. Introduction While the genome has been portrayed as a “blueprint” instructing the development of an adult organism, the articulation of genotype into phenotype is a more complex phenomenon. Context-dependent development and environment-dependent phenotypic variation have been observed for decades [1]. Like the changes in gene expression that intrinsically occur in development, environment can affect gene expression and alter developmental trajectories [2]. If these developmental responses to the environment, and plasticity itself, can increase fitness and are heritable, then morphology, physiology, behavior, or life history strategies can evolve elements of adaptive phenotypic plasticity [1, 3]. This can result in the production of continuous or discrete phenotypic variation (polyphenism). The possibility for nongenetic heritable effects of environment on development raises doubts about the “blueprint” view of the genome [4]. Waddington originally defined “epigenetics” as the study of phenomena that act to produce phenotype from genotype all within in a framework of evolutionary biology [5–7]. Waddington’s view of epigenetics now largely encompasses the fields of developmental biology and evolutionary developmental biology, which describe, in part, how patterns of gene expression change during ontogeny and through evolution [8]. The modern field of epigenetics examines how patterns of gene
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