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Aim Because of their recent evolutionary radiation, capuchin monkeys represent an ideal group with which to investigate ecomorphological adaptations in relation to geography and climate. Our aim was to identify patterns of both skull size and shape variation in capuchins in relation to environmental variables and latitude. Location Tropical and subtropical South America. Methods We performed geometric morphometric analyses of skull shape in 228 capuchin monkey individuals belonging to either the genera Sapajus (seven species) or Cebus (two species), representing 94 localities in South America. Twenty-three homologous landmarks were digitized to describe skull shape. We regressed skull shape against latitude, longitude, skull size and environmental variables, using ordinary and partial least squares regressions. Variation partitioning was used to test for the relative contribution to shape variance by taxonomy, allometry and environment, and their interaction terms. Results We found a significant impact of latitude, climate and size on skull shape. The allometric component of shape variation, although large, is not congruent with shape differences between species, and probably reflects ontogenetic effects. Partial least squares between bioclimatic variables and skull shape explain some 98% of the covariation between environment and shape. Species distributed in drier, more seasonal southern localities exhibit a narrow skull with elongated muzzle and relatively larger teeth. Variation partitioning suggests that the difference in skull shape between species is highly correlated with climatic variation but not with skull size. Main conclusions Skull shape in capuchins is significantly related to both environment and skull size. The former, but not the latter, is significantly associated with shape differences between species. The Sapajus clade originated in the south, and experienced an evolutionary radiation during the Pleistocene. As new Sapajus species moved to the north, they adapted to the local environmental conditions, eventually resembling Cebus in skull shape as they reached the Amazon rain forest, in response to their shared environmental conditions. [ABSTRACT FROM AUTHOR]