The region of the neural tube posterior to the midbrain undergoes a dramatic series of morphogenetic changes that transform it into the rhombencephalon. The most noticeable event is the establishment of a series of repeated bulges and grooves along the anterior/posterior axis that constitute a series of transient domains referred to collectively as rhombomeres. The neural stem cells in each rhombomere acquire distinct patterns of gene expression based upon their location. These distinctions then facilitate local genesis of motor neurons that give rise to the cranial motor nerves, and to sensory neurons that provide the targets for peripheral cranial sensory inputs to the brainstem (including the cerebellum/pons, also known as the metencephalon, and the medulla oblongata, also known as the myelencephalon). The relationship between rhombomeres and the developing structures of the head is quite precise. Indeed, the neural crest that emerges from the neural tube in the region of each rhombomere (note that there is no neural crest associated with the prosencephalon) establishes cranial target structures that are often innervated by motor neurons generated in the same rhombomere. Similarly, cranial ganglia derived from neural crest that migrates from distinct rhombomeres have a specific relationship with target nuclei generated within the relevant rhombomere.
Within an additional 8 days of development (36 days), the basic topography of the entire nervous system has been established, as have most of the component regions that will then grow and differentiate throughout the balance of embryogenesis. The prosencephalon becomes further subdivided into two telencephalic vesicles (collectively called the telencephalon) that will give rise to the bilaterally symmetric structures of the forebrain: the cerebral cortical hemispheres, the hippocampi, the basal ganglia, basal forebrain nuclei, and the olfactory bulbs. The remainder of the prosencephalon, posterior to the telencephalic vesicles, becomes the diencephalon, which will generate the epithalamus (dorsal structures known as the habenula), thalamus (the relay nuclei that project to the cerebral cortex), and hypothalamus (motor/endocrine control nuclei that regulate visceral and reproductive function and homeostasis). The mesencephalon, rhombencephalon, and myelencephalon become further differentiated, and the cranial motor nerves (see darker blue in the upper panel of Plate 1-4), sensory ganglia, and associated cranial sensory nerves (lighter pink, Plate 1-4) become clearly visible along the anterior to posterior extent of the midbrain and hindbrain. In parallel, the motor nerves and sensory ganglia and associated sensory nerves of the rest of the body become visible along the anterior to posterior extent of the spinal cord.

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