Neural morphology, circuitry, and activity are all essential in representing behavioral outputs
among animals. Complex behaviors such as sleep and feeding are present in nearly all phyla, yet
the evolution and neural circuitry that underlie these behaviors remains largely unclear. The
Mexican cavefish, Astyanax mexicanus, exists as surface populations that inhabit rivers, and
multiple cave populations with convergent evolution of feeding behaviors and sleep loss. A.
mexicanus, provides a powerful system to investigate behavioral adaptation and whole-brain
evolution. To understand behavioral evolution in context of the neural circuits involved in
generating behaviors, it is necessary to assign imaging of circuitry and neural activity to
anatomical maps of the nervous system. Here, we describe the development of high-resolution
comparative brain atlases of four populations of A. mexicanus. These atlases reveal altered
neural morphological landscapes among cave populations. Further, whole-brain pERK activity
mapping demonstrates significant changes in brain activity patterns. Imaging of hypothalamic
circuits underlying feeding and sleep shows convergent evolution in cave populations. Lastly,
behavioral and pharmacological sleep and feeding assays show distinctly altered brain activity
patterns in populations of cave-adapted animals compared to surface-dwelling populations.
Taken together, these findings establish the first cellular-resolution brain atlases for comparative
evolution in populations of the same species that exhibit vastly different behaviors, allowing for
the direct interrogation of how behaviors and brains evolve.