Genomic sequence evolution underlying human neocortical interareal diversification

BACKGROUND: Neocortical expansion and diversification in primates, especially humans, underpin advanced cognitive abilities, yet the molecular and cellular bases of neocortical area specification remain incompletely understood. RESULTS: Here, we perform an integrative multimodal analysis combining single-nucleus multiomic and spatial transcriptomic sequencing, morphological and electrophysiological profiling, and secondary comparisons across humans, macaques, and mice. We uncovered enhanced area-specific cellular diversification in primates, including distinct upper-layer projection neuron and interneuron subtypes, increased electrophysiological and morphological complexity, and enriched cell connectivity and crosstalk. Notably, this increased interareal heterogeneity coincides with the expansion of evolutionarily young DNA sequences in primates, especially Hominoidea, which are enriched for transposable elements (TEs). We deduce that TEs are likely to contribute to areal specification by acting as cis-regulatory elements and by diversifying the transcriptome. Specifically, TEs harbor evolutionarily novel area-specific transcription factor binding sites for species- and/or area-specific transcription factors in human genome, correlating with the expression of diverse gene biotypes across neocortical areas. Furthermore, our findings reveal that the expression of TE transcripts distinguishes the upper-layer neurons in the frontal cortex, likely enhancing cellular diversification through mechanisms beyond protein-coding gene expression. CONCLUSIONS: These findings illuminate genomic and cellular mechanisms contributing to human neocortical reorganization during evolution, providing insights into the molecular underpinnings of primate brain specialization.