UC San Diego

The vertebrate skeletal system exemplifies the intricate relationship between genetic regulation and evolutionary adaptation. This thesis investigates the genetic mechanisms underlying the evolution of skeletal proportion and development, focusing on the Lesser Egyptian Jerboa (Jaculus jaculus), a rodent with extremely elongated hindlimbs. By integrating comparative genomics, developmental biology, and advanced gene editing technologies, we aimed to better understand the complex cis-regulatory landscapes driving these morphological changes. Here, I present work that identified thousands of putative cis-regulatory regions exhibiting opposing but complimentary evolutionary patterns in the vertebrate limb, underscoring the scale and complexity of evolution within cis-regulatory sequences driving the development of different skeletal forms. I also explore the feasibility of CRISPR/Cas9-mediated gene conversion to facilitate the study of complex genetic traits. Despite challenges in achieving high conversion efficiency, our findings emphasize the importance of precise temporal control of Cas9 activity in the rodent germline. Additionally, we leveraged a conditional knockout strategy using hemizygous transgenes and tissue-specific Cre systems, focusing on the Bone Morphogenic Protein (BMP) signaling pathway. This approach reveals the complexity of genetic redundancy and compensatory mechanisms, providing new insights into skeletal maintenance and homeostasis. This work collectively advances the understanding of macroevolutionary processes and genetic complexity, offering powerful tools for studying the genetic basis of trait evolution. The integration of these methodologies not only enhances our knowledge of vertebrate skeletal diversity but also holds potential for practical applications in conservation biology and biomedical research. This thesis emphasizes the importance of viewing evolutionary biology through the lens of comparative genomics and functional genetics, which will undoubtedly facilitate future discoveries in the field.