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

The cerebral cortex broadcasts its output to subcortical regions through the projections of diverse extratelencephalic (ET) neurons derived from either direct (dNG-ET^d) or indirect (iNG-ETⁱ) neurogenesis, but the differential contributions of these neurogenic pathways to cortical output organization remain unknown. Establishing a lineage-based viral targeting strategy in mice, we uncover that ETⁱ massively amplifies and diversifies ET^d projections across the cortex. Whereas ET^d primarily targets the forebrain and midbrain, ETⁱ dominates the hindbrain (e.g., brainstem/spinal action centers and lemniscal sensory stations), hypothalamic, and neuromodulatory regions with cortical area-specific projections. Numerous corticofugal subpopulations derive solely from iNG-ETⁱ. Area-specific spinal projections of ETⁱ, but not of ET^d, emerge from the postnatal pruning of an initial cortex-wide population. In the motor cortex, ET^d or ETⁱ activation induced distinct movements: either head-trunk or, additionally, coordinated orofacial-forelimb movements, respectively. Thus, two foundational neurogenic pathways with distinct evolutionary histories differentially shape the area-specific diversification of cortical output channels.