Cross-species single-cell transcriptomics reveals neuronal similarities and heterogeneity in amniote pallium

The amniote pallium, a vital component of the forebrain, exhibits considerable evolutionary divergence across species and mediates diverse functions, including sensory processing, memory formation, and learning. However, the relationships among pallial subregions in different species remain poorly characterized, particularly regarding the identification of homologous neurons and their transcriptional signatures. In this study, we utilized single-nucleus RNA sequencing to examine over 130 000 nuclei from the macaque ( Macaca fascicularis) neocortex, complemented by datasets from humans ( Homo sapiens), mice ( Mus musculus), zebra finches ( Taeniopygia guttata), turtles ( Chrysemys picta bellii), and lizards ( Pogona vitticeps), enabling comprehensive cross-species comparison. Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium. Notable similarities were observed among cell subtypes, particularly within PVALB ⁺ inhibitory neurons, which exhibited species-preferred subtypes. Furthermore, correlations between pallial subregions and several transcription factor candidates were identified, including RARB, DLX2, STAT6, NR3C1, and THRB, with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts. These results highlight the conserved nature of inhibitory neurons, remarkable regional divergence of excitatory neurons, and species-specific gene expression and regulation in amniote pallial neurons. Collectively, these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.