Distinct neurogenic pathways shape the diversification and mosaic organization of cortical output channels

A hallmark of the mammalian cerebral cortex is its vast and diverse efferent projections across cortical areas mediated by extratelencephalic (ET) neurons that broadcast to myriad subcortical regions. ET neurons are generated from two fundamentally distinct neurogenic pathways: direct neurogenesis (dNG-ETd) from radial glia progenitors and indirect neurogenesis (iNG-ETi) from intermediate progenitors, but the contribution of ETd and ETi to the organization of cortical output channels is unknown. Leveraging a novel lineage-based genetic strategy enabling differential viral access to ETd and ETi in the same mouse, we show that iNG-ETi massively amplifies and diversifies dNG-ETd across the cortex. While ETd projections are largely restricted to the forebrain and midbrain structures, ETi greatly amplifies and diversifies these projections and overwhelmingly dominates the innervation of hindbrain and spinal cord. This is exemplified in an area-specific pattern by ETi dominance to brainstem and spinal action diversification and execution centers from motor areas, to major sensory processing stations along lemniscal pathways from sensory areas, and to pallial, hypothalamic and neuromodulatory structures from high order areas. Corticofugal subpopulations in multiple areas are derived from only ETi, indicating the generation of novel projection types by iNG over dNG. Furthermore, area-specific ETi, but not ETd, spinal projection pattern is sculpted from the massive pruning of an early cortex-wide population during postnatal development. Together, these results uncover that two foundational neurogenic pathways with distinct evolutionary history differentially shape the area-specific diversification and mosaic organization of cortical output channels.