Genomic evolution reshapes cell-type diversification in the amniote brain

Over 320 million years of evolution, amniotes have developed complex brains and cognition through largely unexplored genetic and gene expression mechanisms. We created a comprehensive single-cell atlas of over 1.3 million cells from the telencephalon and cerebellum of turtles, zebra finches, pigeons, mice, and macaques, employing single-cell resolution spatial transcriptomics to validate gene expression patterns across species. Our study identifies significant species-specific variations in cell types, highlighting their conservation and diversification in evolution. We found pronounced differences in telencephalon excitatory neurons (EXs) and cerebellar cell types between birds and mammals. Birds predominantly express SLC17A6 in EX, whereas mammals express SLC17A7 in the neocortex and SLC17A6 elsewhere, possibly due to loss of function of SLC17A7 in birds. Additionally, we identified a bird-specific Purkinje cell subtype (SVIL+), implicating the lysine-specific demethylase 11 (LSD1)/KDM1A pathway in learning and circadian rhythms and containing numerous positively selected genes, which suggests an evolutionary optimization of cerebellar functions for ecological and behavioral adaptation. Our findings elucidate the complex interplay between genetic evolution and environmental adaptation, underscoring the role of genetic diversification in the development of specialized cell types across amniotes.