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Archaeological evidence shows that populations used to transverse the Sahara Desert throughout the Holocene despite the extreme temperatures and the rough physical terrain. The current paper examines whether the desert inhibited extended gene flow among populations by means of cranial morphology as captured by geometric morphometrics. The examined populations include the Garamantes, a group centered in Southwest Libya and largely controlling trans-Saharan trade, and various Egyptian. Tunisian and Sudanese groups dating to the Middle and Late Holocene. The results showed that most inter-population comparisons were statistically significant and therefore all populations appear more or less distant to each other. The Mahalanobis biodistance measure identified four clusters. The first consists of the Garamantes alone, the second includes the populations from Kerma and Gizeh, the third includes the Badari and Naqada, while the fourth consists of the samples from Algeria, Carthago, Soleb and Alexandria. Moreover, the distance of the Garamantes to their neighbors was significantly high and the population appeared to be an outlier. This is attributed to the location of the Garamantes at the core of the desert, indicating that, despite the archaeological evidence, the Sahara Desert posed important limitations to gene flow between the Garamantes and other North African populations. (C) 2012 Elsevier Inc. All rights reserved.