Many factors, including gene networks, developmental processes, and the environment mediate the link between the activity of genes and complex phenotypes in higher organisms. While genetic variants are the raw material for evolution, these other factors are critical for determining which variants are actually exposed to natural selection. In this dissertation, I describe three projects in which I investigate how developmental mechanisms and the environment interact to shape phenotypic variation. In each project, I use gene expression as a window into the activity of genes, and as a tool to measure variation in and among developmental mechanisms. Two projects are experimental, focusing on early development in sea urchins, and how environmental stress caused by climate change impacts the expression of genetic variation in phenotypic traits. In these projects, I explicitly incorporate information about the biochemical functions of genes and how they interact in development, and test how such mechanisms shape the impact of genetic and environmental perturbations to development. The third project is methodological, in which I propose a unified statistical framework for inferring previously unknown developmental constraints that may underlie gene expression phenotypes. Together, these projects demonstrate that an understanding of developmental mechanisms can enhance our understanding of the processes that shape variation in populations, and can help predict the biological effects of climate change.
