A central goal in evolutionary biology is to understand the molecular changes responsible for phenotypic differences between species, in particular those that have arisen among mammals. Phenotypic evolution is thought to be largely founded on developmental gene regulatory changes, which determine species-specific tissue morphologies and thus lay the foundation for their typical physiological properties. We recently performed the first cross-mammalian transcriptome comparisons for adult organs, providing many insights into the molecular evolution of organ physiologies, but the evolution of developmental transcriptomes remains largely unstudied. I propose to generate comprehensive RNA sequencing data for a collection of adult tissues and developmental precursors from many mammals and tetrapod outgroup species (birds, reptiles, amphibians). The data will include dense ontogenetic time courses for key reference species, covering embryonic stages and, for mammals, placental tissues. We will identify coding and noncoding genes constituting core ancestral tissue transcriptomes and assess relative contributions of gene expression changes and the emergence of new genes to the evolution of phenotypically relevant expression patterns. We will also empirically evaluate global models of evolutionary conservation patterns during embryogenesis and placentation. To understand the dynamics of functional and regulatory interactions of different gene types and their evolutionary relevance, we will reconstruct evolutionary transcription networks and assess associated regulatory mechanisms. Overall, this inter-disciplinary “evo-devo” project will unveil ontogenetic and adult gene expression programs underlying shared (ancestral) and lineage-specific morphological and physiological phenotypes. It will thus substantially advance our understanding of the molecular basis of phenotypic evolution.