The midbrain is the smallest of three primary vertebrate brain divisions. Here we use network science tools to reveal the global organizing principles of intramidbrain axonal circuitry before adding extrinsic connections with the remaining nervous system. Curating the experimental neuroanatomical literature yielded 17,248 connection reports for 8,742 possible connections between the 94 gray matter regions forming the right and left midbrain. Evidence for the existence of 1,676 connections suggests a 19.2% connection density for this network, similar to that for the intraforebrain network [L. W.
Swanson et al., Proc. Natl. Acad. Sci. U.S.A. 117, 31470–31481 (2020)]. Multiresolution consensus cluster analysis parceled this network into a hierarchy with 6 top-level and 30 bottom-level subsystems. A structure–function model of the hierarchy identifies midbrain subsystems that play specific functional roles in sensory–motor mechanisms, motivation and reward, regulating complex reproductive and agonistic behaviors, and behavioral state control. The intramidbrain network also contains four bilateral region pairs designated putative hubs. One pair contains the superior colliculi of the tectum, well known for participation in visual sensory–motor mechanisms, and the other three pairs form spatially compact right and left units (the ventral tegmental area, retrorubral area, and midbrain reticular nucleus) in the tegmentum that are implicated in motivation and reward mechanisms. Based on the core hypothesis that subsystems form functionally cohesive units, the results provide a theoretical framework for hypothesis-driven experimental analysis of neural circuit mechanisms underlying behavioral responses mediated in part by the midbrain.According to the classical view, early in vertebrate development the neural plate invaginates to form the neural tube, which immediately displays three sequential swellings that were called the primary forebrain, midbrain (MB), and hindbrain vesicles by von Baer in 1837 (
1) and that are followed by the presumptive spinal cord caudally. Together, these four differentiations or morphogenetic units of the neural tube go on to generate the entire adult central nervous system (
2,
3). As a major part of a systematic research program to analyze the organizing principles of mammalian nervous system macroconnectivity, we recently completed a study of forebrain intrinsic circuitry (
4), and here we present a similar study of MB intrinsic circuitry.Based on developmental and adult topographic features, the MB can be divided into two great parts: tectum (TC) dorsally and tegmentum (TG) ventrally (
5,
6). In mammals, the TC in turn has two parts, the superior and inferior colliculi, which are important nodes in circuitry related to visual and auditory functions, respectively (
3). The TG, in contrast, is much more differentiated structurally and functionally, with a variety of gray matter regions that have been intensively analyzed over the last 75 y. Among the most prominent are three cranial nerve nuclei (oculomotor nucleus, trochlear nucleus, and midbrain nucleus of the trigeminal nerve), as well as the pretectal region, red nucleus, substantia nigra and ventral tegmental area, midbrain raphe nuclei, periaqueductal gray, and midbrain reticular nucleus (
3).This topographic approach to biological structure–function organization is like dividing the body in human anatomy into head, neck, trunk, and upper and lower limbs with hands and feet. Topographic anatomy is particularly useful for describing and mapping structure–function spatial relationships of body parts and for surgical procedures. For example, the hand is an obvious body part with especially important and intricate functions in humans. Systems anatomy, however, is an equally valid and complementary way of describing global principles of body organization. In human biology, the body is conveniently and systematically divided into about a dozen interrelated systems (skeletal, digestive, respiratory, nervous, and so on), and components of each typically play a role in topographic parts such as the hand. The systems approach is particularly useful for organizing vast amounts of data into simplified, readily understandable conceptual frameworks or models of how the body works as a whole.The nervous system can also be treated from the complementary topographic and systems perspectives (
7), and it is the only bodily system remaining without a relatively simple global systems model, largely because its cellular network architecture is much more complex than the other systems. However, general network analysis tools, which can be applied to any complex system, from the internet to social interactions in a human population, offer one promising approach (
8,
9). Basic requirements include a systematic parts list for the network, an understanding of how each part works, and an account of how the parts are connected to form a functional system (
10). Our long-term strategy for the rat nervous system follows the time-honored approach to solving any difficult problem, that is, to proceed from coarser-grained to finer-grained analyses, analogous to the strategy used to sequence the human genome (
11). Thus, using a nested approach, we have started at the coarse-grained macro level of analysis (axonal macroconnections from one gray matter region to another gray matter region), as a prelude and framework for analyses at the finer-grained meso level (connections between neuron types making up each gray matter region), micro level (connections between individual neurons making up each neuron type), and nano level (the set of synapses formed by each neuron) (
12).
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