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Desert dunes often exhibit remarkable changes in their morphology over short distances. For example, sediment-rich dunes can break up into smaller, isolated features, and then become stabilized by plants, over distances of kilometres^,,,,,. These pattern transitions often coincide with spatial variations in sediment supply^,,, transport rate^,, hydrology and vegetation^,,, but these factors have not been linked mechanistically. Here we hypothesize that the abrupt increase in roughness at the upwind margins of dune fields triggers the development of an internal boundary layer^,,,,,, that thickens downwind and causes a spatial decrease in the surface wind stress. We demonstrate that this mechanism forces a downwind decline in sand flux at White Sands, New Mexico, using a combination of physical theory^,,,,,, repeated airborne altimetry surveys and field observations. The declining sand flux triggers an abrupt increase in …