The origin and early evolution of snakes has long been studied, but little research has focused on soft-tissue organs such as the brain. I report data from dissections and 3D reconstructions of the endocasts of diverse species, including the Cretaceous stem snake Dinilysia patagonica in order to provide a comparative evolutionary framework for the snake brain. Snakes are a special case among reptiles because the braincase almost entirely encloses the whole brain, so endocasts provide realistic representations of brain size and shape. Diversity of brain gross anatomy among snakes is remarkable, encompassing two major cerebrotypes occurring in surface-dwelling and burrowing species. The repeated acquisition of the burrowing cerebrotype in different and phylogenetically distant snake clades suggests that brain gross anatomy is surprisingly evolutionary labile in snakes. Brain gross anatomy and other features such as body size and the absence of any unequivocal osteological feature related to burrowing is interpreted as evidence that D. patagonica was surface-dwelling, and that at least some of the early history of snakes occurred above ground.

Snakes have distinct body plans that can be traced to the origin of the clade. It remains unresolved whether ancestral snakes were adapted to terrestrial environments as burrowers, or to marine environments as swimmers. Recently, new approaches have been used to infer fossorial and aquatic specialists in the early evolution of snakes, using virtual CT models of the ear of fossils. This chapter reviews variation in the osseous part of the ear of major snake lineages. Vestibules are relatively large in fossorial species and small in aquatic snakes. Using quantitative analyses of bony labyrinth geometry, it has been suggested that putative stem snakes, such as Dinilysia patagonica, were fossorial. Improvements to testing correlations between bony labyrinth morphology and ecology can be made in the refinement of quantitative approaches to capturing and analysing shape variations, as well as better classifications of ecology. Using inner and middle ear morphology to improve the accuracy and precision of inferences of the ecology of the ancestral snake will depend also upon robust, well-resolved phylogenies for extinct and extant taxa, and denser taxonomic and ecomorphological sampling.

The distinctiveness of their eyes has played a major role in debates about snake origins and early evolution, having been interpreted as providing evidence for nocturnal and/or fossorial (and to a lesser degree, aquatic) origins. Much of this evidence came from anatomical studies of snake retinas in the 1900s. More recent morphological and molecular studies have provided further evidence for the distinctness of the snake eye that lacks many of the traits present in lizards. Data remain patchy and are particularly sparse for extant lineages (scolecophidians and non-caenophidian alethinophidians) that bear special importance for inferring traits of the ancestral snake. However, evidence is strong for: (1) the ancestral snake having lost multiple anatomical and molecular genetic components present in the eyes of the ancestral squamate and retained by most lizards; (2) the eye of the ancestral snake being adapted for low-light environments and/or activity cycles but being notably less regressed than that of extant scolecophidians; (3) an elaboration and diversification of the eye within endoglyptodont caenophidian snakes.