The misplaced mouse Pax6 interneuron subclass: A cross-species transcriptomic reassignment

Subclass cell types are strongly conserved across mammalian brains, making the systemic absence of a caudal ganglionic eminence (CGE) Pax6 interneuron subclass in mouse transcriptional atlases unexpected. Through cross-species transcriptomic analysis, we identify a Pax6 subclass homolog in mouse and uncover primate-specific divergence in the Sncg subclass. Analyses of electrophysiological and spatial datasets reveal limited subclass-specific structure in either modality, emphasizing the superior resolving power of transcriptomics for subclass distinctions. Our results highlight the pitfalls of relying on small sets of marker genes in cell-type annotation and provide evolution-aware annotations and marker sets to support robust cross-mammal interneuron comparisons.