Abstract
The Chinchorro culture inhabited the coastal Atacama Desert between 7,500 and 3,500 years BP, maintaining a hunter-gatherer-fisher lifestyle and practicing complex mortuary rituals. With the later adoption of agriculture, shifts in subsistence strategies and burial customs emerged. This study investigated long-term biological variation across three diachronic populations from northern Chile: Archaic-period Chinchorro individuals, pre-Hispanic agriculturalists, and contemporary Chileans. Using computed tomography (CT) and 3D reconstruction techniques, we analyzed intracranial volume (ICV) and estimated stature to assess morphological differences. The results show that both ICV and stature are significantly greater in the present-day Chilean population than in the pre-Hispanic groups. The average ICV was 1,321.26 cc in Chinchorro individuals, 1,336.57 cc in pre-Hispanic agriculturalists, and 1,481.22 cc in modern Chileans—representing a 12.05% increase between the earliest and most recent groups. Males and females exhibited 14.62% and 10.81% increases, respectively. Sexual dimorphism in the ICV was lower among agriculturalists (8.97%) than among Chinchorro (10.84%) and modern individuals (13.68%). Notably, the transition to agriculture did not result in significant changes in either ICV or stature. Instead, the marked increases observed in modern individuals have been associated primarily with improved nutrition, healthcare, and overall living conditions since the 20th century. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-25186-y.