Vertebrate species use the musculoskeletal system as the framework for stability and locomotion; differing environmental conditions and organismal needs select for the optimal, relevant morphology. For about 55 million years since the divergence of the jerboa and house mouse from their last common ancestor, jerboas have evolved disproportionately elongated hind feet to help them traverse their environment and lost all muscle within these feet. These morphological changes occurred due to selection on phenotypic variance, and these same phenotypes are also sensitive to environmental variance. As such, my lab is interested in understanding if environmentally sensitive systems share a genetic basis with the evolutionary genetics of musculoskeletal morphology. I first addressed the development of skeletal proportion by determining that mice are unfortunately not an appropriate model to test if nutritionally sensitive genes are among the genes that drove the evolution of skeletal proportion. In chapter two, I built upon the work of a previous PhD student to gain a better understanding of the molecular mechanisms underlying jerboa foot muscle loss. Using a more complete genome and new tools for improved orthology annotation, I identified a set of key genes and pathways likely related to jerboa foot-muscle loss. In the final chapter, I developed an image processing tool that can automatically quantify cell aggregates from images such as chondrogenic micromasses. This new tool and the knowledge gathered from my thesis research will assist future studies to determine the genetic framework of limb development.