Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types in cerebral cortex

Variations in size and complexity of the cerebral cortex result from differences in neuron number and composition, which are rooted in evolutionary changes in direct and indirect neurogenesis (dNG and iNG) mediated by radial glial progenitors and intermediate progenitors, respectively. How dNG and iNG differentially contribute to cortical neuronal number, diversity, and connectivity are unknown. Establishing a genetic fate-mapping method to differentially visualize dNG and iNG in mice, we found that while both dNG and iNG contribute to all cortical structures, iNG contributes the largest relative proportions to the hippocampus and neocortex compared to insular and piriform cortex, claustrum, and the pallial amygdala. Within the neocortex, whereas dNG generates all major glutamatergic projection neuron (PN) classes, iNG differentially amplifies and diversifies PNs within each class; the two neurogenic pathways generate distinct PN types and assemble fine mosaics of lineage-based cortical subnetworks. Our results establish a ground-level lineage framework for understanding cortical development and evolution by linking foundational progenitor types and neurogenic pathways to PN types. Highlights- A genetic strategy for differential visualization of direct and indirect neurogenesis in the same animal. - dNG and iNG differentially contribute to piriform cortex, basolateral amygdala, hippocampus, and neocortex - Whereas dNG generates all major PN classes, iNG differentially amplifies and diversifies PNs within each class - dNG and iNG construct distinct cortical projection subnetworks.