The vertebrate skeleton is shaped by reciprocal signalling between embryonic tissues layers, and by spatial “codes” of patterning information that arise downstream of these signalling interactions. We use cell lineage tracing approaches to resolve the embryonic tissue origins of the vertebrate skeleton, and experimental embryological manipulations to discover the molecular mechanisms that control the polarity, shape and identity of individual elements. By testing for the redeployment, conservation and divergence of skeletal patterning mechanisms between and within taxa, we may better understand the evolution of skeletal morphology and the origin of anatomical novelty.