Conserved and lineage-specific mechanisms drive chromatophore differentiation in reptiles.

The mechanisms by which novel differentiation pathways evolve to produce new cell types are still not fully understood. Chromatophores, the pigmented cells in the skin, offer an ideal paradigm because each type independently develops from neural crest cells to produce a distinct colour using well-characterised biosynthetic pathways. Here we show, using single-cell gene expression analyses, that canonical chromatophores develop in the embryonic skin of corn snakes and bearded dragon lizards. Yet, we identify previously undescribed chromatophore subtypes in the bearded dragon. These populations co-express progenitor and mature markers and possibly contribute to embryonic skin patterning, as revealed by whole-mount in situ hybridisation. Comparative analyses uncover that while mature chromatophores show cross-species similarity reflecting shared pigmentary function, progenitor states differ in transcription factor usage, including species-specific deployment of MITF, PAX7, and TFEC. Integration with teleost and amphibian datasets confirms that diversification of pigmentation arises through distinct progenitor trajectories converging on similar mature states.