As the Earth progresses through the Anthropocene Epoch, human-caused environmental changes continually impact the natural world. Some of the largest changes occur through land-use change or the development and improper disposal of pollutants. This dissertation aims to present the use of genome-wide molecular tools across two systems to investigate the potential implications and future consequences of these anthropogenic changes. The first of these investigations involves the use of population genomic tools to determine the effects of land-use change in the development of large, ground-mounted solar energy facilities in desert ecosystems. Sensitive arid land ecosystems are the second most common land-cover type for solar energy development globally, so it is necessary to understand existing diversity within desert plant populations to understand spatiotemporal effects of solar energy siting and design. I sampled Mojave milkweed (Asclepias nyctaginifolia) in and around the Ivanpah Solar Electric Generating Station (ISEGS) in the Mojave Desert of California to understand the species’ population structure, standing genetic variation, and the intersection of this biodiversity with solar development. Using Restriction-site Associated Sequencing (RADseq), I found clear population structure over small spatial scales, suggesting each site sampled was a genetically distinct population of Mojave milkweed. This work suggests that the effects of land-cover change, especially those impacting core desert habitat, may impact long-term genetic diversity and persistence by increasing risks of genetic diversity loss or population extirpation. This highlights the need to consider the genetic diversity of species when predicting the impact and necessary conservation measures of large-scale land-cover changes. My second investigation utilized genome-wide RNA and methylation analyses to understand the impacts of microplastics pollution on aquatic organisms. Microplastics exposure correlates with evolutionary and ecological impacts across species, affecting organisms’ development, reproduction, and behavior along with contributing to genotoxicity and stress. To gain a better understanding of organismal responses to microplastics, I performed an experiment using fathead minnows (Pimephales promelas) in different microplastic treatments. I tested two microplastic concentrations, reflecting both current and predicted future conditions, of pre-consumer, pristine plastic and environmentally exposed plastic gathered from Lake Ontario. I raised an F1 generation in the control treatment (no microplastic exposure) to determine intergenerational effects. I used directional mRNA and methylation sequencing to evaluate differences among treatments, sexes, and generations. I found evidence of metabolic stress-response changes in the fish exposed to microplastics compared to the controls. The effect of microplastics on gene expression was stronger in female minnows compared to males, but in epigenomic analyses the origin of the plastic had a larger effect in female minnows whereas the effect of concentration was stronger in males. Many of the differentially expressed or methylated genes interact with estrogenic chemicals associated with plastic. I observed intergenerational effects on gene methylation, highlighting a heritable mechanism in which parents can pass on the effects of microplastic exposure to their offspring. This study is among the first to highlight the persistent impacts of microplastic pollution on gene regulation in freshwater systems. As fathead minnows are an important toxicological model species, our hope is that the results of this study will have implications across aquatics species and ecosystems and highlights the importance of understanding the impact of microplastic exposure across levels of biological organization, from the cellular to population level. Altogether, my investigations in these two systems highlight the diverse ways in which anthropogenic change effects organisms across levels of molecular control and provides context for the ecological and evolutionary implications of these modifications.
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