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This opens up new possibilities to study the evolution of cell types and infer molecular properties of organisms inaccessible to experimental research. In this thesis, I explore these two applications in the context of early mammalian development and vertebrate brain evolution. I first detail efforts to construct a single-cell atlas of rabbit gastrulation, which offers a new window into human embryogenesis and provides a resource for validating therapeutic targets, or observations from mice, in a non-rodent system. I then present three new approaches to visualise and compare single-cell transcriptomics data from multiple species. These methods overcome challenges of relating gene features and cell types, which may be applicable to contexts beyond the cross-species setting. Finally, I apply comparative single-cell analyses to trace networks of neural development across deuterostomes. 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