Despite our emphasis on discrete borders between subtypes, we also detected continuous gradients of gene expression. Cosine similarity between nuclei indicated that DS-derived clusters were more like other DS clusters compared to VS-derived clusters, and vice versa (Figure 3D) (p < 0.0001, Permutation tests, STAR Methods). Consistent with this and with previous studies in mouse,15,16 the crystallin mu and the cannabinoid receptor genes, CRYM and CNR1, respectively, reflect continuous gradients on the dorsal-ventral axis of the mouse striatum (Figure 3E). Archetypal analysis indicated that this gradient is reflected in the D1/D2-hybrid population (Figure 3F; Table S2), and across subtype pairs that were divided between the DS and VS (Figure 3G). This results highlights that gene expression gradients that define position on the dorsal and ventral axis are conserved between species. The primate DS is divided into the Cd and Pt by the internal capsule. Compared to the differences between the DS and VS, the Cd and Pt appeared more similar. Indeed, cosine similarities between the striosome and matrix showed that striosome nuclei in the Cd were far more similar to
