More Like this

1. Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms

   https://doi.org/10.1093/molbev/msae170  

   Yi, Soojin V (September 2024, Molecular Biology and Evolution)

   Gaut, Brandon (Ed.)

   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. 

   more » « less
2. Rapid Epigenetic Adaptation in Animals and Its Role in Invasiveness

   https://doi.org/10.1093/icb/icaa023  

   Carneiro, Vitor Coutinho; Lyko, Frank (April 2020, Integrative and Comparative Biology)

   Abstract Invasive species represent a serious ecological threat for many ecosystems worldwide and provide a unique opportunity to investigate rapid adaptation and evolution. Genetic variation allows populations of organisms to be both robust and adaptable to different environmental conditions over evolutionary timeframes. In contrast, invasive animals can rapidly adapt to new environments, with minimal genetic diversity. Thus, the extent to which environmental effects can trigger epigenetic responses is particularly interesting for understanding the role of epigenetics in rapid adaptation. In this review, we provide a brief overview of the different epigenetic mechanisms that control gene expression, and emphasize the importance of epigenetics for environmental adaptation. We also discuss recent publications that provide important examples for the role of epigenetic mechanisms in environmental adaptation. Furthermore, we present an overview of the current knowledge about epigenetic modulation as an adaptive strategy for invasive species. A particularly interesting example is provided by the marbled crayfish, a novel, monoclonal freshwater crayfish species that has colonized diverse habitats within a few years. Finally, we address important limitations of current approaches and highlight the potential importance of less well-known mechanisms for non-genetic organismal adaptation. 

   more » « less
3. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

   https://doi.org/10.1093/gbe/evae022  

   Bogan, Samuel N; Yi, Soojin V (February 2024, Genome Biology and Evolution)

   Hoffmann, Federico (Ed.)

   Abstract There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations. 

   more » « less
4. Diverse state‐level marine aquaculture policy in the United States: Opportunities and barriers for industry development

   https://doi.org/10.1111/raq.12631  

   Lester, Sarah E.; Gentry, Rebecca R.; Lemoine, Hayley R.; Froehlich, Halley E.; Gardner, Luke D.; Rennick, Mae; Ruff, Elizabeth O.; Thompson, Kimberly D. (November 2021, Reviews in Aquaculture)

   Abstract Marine aquaculture (mariculture) plays a relatively small role in the United States’ domestic seafood production, despite considerable scope for industry development and high volumes of imported farmed seafood resulting in a significant trade deficit. Currently, most mariculture in the United States occurs in nearshore waters or land‐based tanks and is regulated and guided using state‐level policy, with a relative absence of national coordinating mechanisms to link the patchwork of state policies. There is no comprehensive evaluation showing how different state policies may be enabling or impeding mariculture development. In response, we provide the first systematic overview of state‐level mariculture policy for the 23 coastal marine states in the United States. We compiled information for 16 aquaculture and mariculture policy attributes, including legislation, regulations and management characteristics, particularly those that could enable mariculture development. We found considerable heterogeneity in how states govern and regulate mariculture. As examples, 48% of states have an aquaculture development act, 35% have spatial zoning specifically for mariculture and only 26% have a government‐provided mariculture best management practices document. We examined the relationship between enabling policies and metrics of mariculture output (e.g. production value, number of farms), and while the effect of enabling policy is often equivocal, certain features stand out as important (e.g. government‐provided best management practices). Overall, this policy synthesis suggests approaches that may be influential in enabling mariculture development, which could inform new state‐level policies, an effective overarching federal policy in the United States, or policies in other countries seeking to support an expanded mariculture industry. 

   more » « less
5. Epigenetics in Ecology, Evolution, and Conservation

   https://doi.org/10.3389/fevo.2022.871791  

   Lamka, Gina F.; Harder, Avril M.; Sundaram, Mekala; Schwartz, Tonia S.; Christie, Mark R.; DeWoody, J. Andrew; Willoughby, Janna R. (April 2022, Frontiers in Ecology and Evolution)

   Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology. 

   more » « less