Gene family evolution underlies cell type diversification in the hypothalamus of teleosts

Hundreds of cell types form the vertebrate brain, but it is largely unknown how similar cellular repertoires are between or within species or how cell type diversity evolves. To examine cell type diversity across and within species, we performed single-cell RNA sequencing of ~130,000 hypothalamic cells from zebrafish (Danio rerio) and surface- and cave-morphs of Mexican tetra (Astyanax mexicanus). We found that over 75% of cell types were shared between zebrafish and Mexican tetra, which diverged from a common ancestor over 150 million years ago. Shared cell types displayed shifts in paralog expression that were generated by sub-functionalization after genome duplication. Expression of terminal effector genes, such as neuropeptides, was more conserved than the expression of their associated transcriptional regulators. Species-specific cell types were enriched for the expression of species-specific genes, and characterized by the neo-functionalization of expression patterns of members of recently expanded or contracted gene families. Comparisons between surface- and cave-morphs revealed differences in immune repertoires and transcriptional changes in neuropeptidergic cell types associated with genomic differences. The single-cell atlases presented here are a powerful resource to explore hypothalamic cell types, and reveal how gene family evolution and shifts in paralog expression contribute to cellular diversity.