Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms

Abstract

Epigenetics research in evolutionary biology encompasses a variety of research areas, from regulation of gene expression to inheritance of environmentally mediated phenotypes. Such divergent research foci can occasionally render the umbrella term "epigenetics" ambiguous. Here I discuss several areas of contemporary epigenetics research in the context of evolutionary biology, aiming to provide balanced views across timescales and molecular mechanisms. The importance of epigenetics in development is now being assessed in many nonmodel species. These studies not only confirm the importance of epigenetic marks in developmental processes, but also highlight the significant diversity in epigenetic regulatory mechanisms across taxa. Further, these comparative epigenomic studies have begun to show promise toward enhancing our understanding of how regulatory programs evolve. A key property of epigenetic marks is that they can be inherited along mitotic cell lineages, and epigenetic differences that occur during early development can have lasting consequences on the organismal phenotypes. Thus, epigenetic marks may play roles in short-term (within an organism's lifetime or to the next generation) adaptation and phenotypic plasticity. However, the extent to which observed epigenetic variation occurs independently of genetic influences remains uncertain, due to the widespread impact of genetics on epigenetic variation and the limited availability of comprehensive (epi)genomic resources from most species. While epigenetic marks can be inherited independently of genetic sequences in some species, there is little evidence that such "transgenerational inheritance" is a general phenomenon. Rather, molecular mechanisms of epigenetic inheritance are highly variable between species.

Keywords: DNA methylation; adaptation; epigenetics; evolution; histone modification; phenotypic plasticity.

Fig. 1.

A modified version of the “epigenetic landscape” in Waddington (1957). Stem cell populations (near the top of the landscape) experiencing different epigenetic modifications follow different “paths” toward more differentiated states, resulting in populations of cells that harbor distinct epigenetic marks from other cell populations. Each population of differentiated cells is specialized for distinct cellular niches. Figure is modified from Yi (2017).