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The amygdala is a central node in functional networks regulating emotions, social behavior and social cognition. It develops in the telencephalon and includes pallial and subpallial parts, but these are extremely complex with multiple subdivisions, cell types and connections. The homology of the amygdala in non-mammals is highly controversial, especially for the pallial part, and we are still far from understanding general principles on its organization that are common to different groups. Here we review data on the adult functional architecture and developmental genoarchitecture of the amygdala in different amniotes (mammals and sauropsids), which are helping to disentangle and to better understand this complex structure. The use of an evolutionary developmental biology (evodevo) approach has helped to distinguish three major divisions in the amygdala, derived from the pallium, the subpallium and from a newly identified division called telencephalon-opto-hypothalamic domain (TOH). This approach has also helped to identify homologous cell populations with identical embryonic origins and molecular profiles in the amygdala of different amniotes. While subpallial cells produce different subtypes of GABAergic neurons, the pallium and TOH are major sources of glutamatergic cells. Available data point to a development-based molecular code that contributes to shape distinct functional subsystems in the amygdala, and comparative genoarchitecture is helping to delineate the cells involved in same subsystems in non-mammals. Thus, the evodevo approach can provide crucial information to understand common organizing principles of the amygdalar cells and networks that control behavior, emotions and cognition in amniotes.

S. Karger AG, Basel