Transitions from foraging to food-production represent a worldwide turning point in recent human history. In the Middle Nile Valley this cultural shift occurred between the sixth and beginning of the fifth millennium BCE. Significant craniodental morphological differences remain inadequately tested by biometric analyses of ancestry and may reflect population origins or diet change between the last hunter-fisher-gatherers (Mesolithic) and first food-producers (Neolithic). Moreover, with no ancient DNA data for this region and very few morphological studies including large samples of Mesolithic individuals, the late prehistoric population history of the Nile Valley remains unclear. Here, we present enamel-dentine junction (EDJ) morphological analyses (based on X-ray microtomography) and biological affinities for 88 individuals spanning 14,000 y from Sudan and southern Egypt. Significant EDJ morphological differences between the last foragers and first food-producers suggest major biological discontinuity at the Neolithic transition. Nevertheless, the persistence of the earlier forager population in the Sudanese Eastern Sahara indicates settlement and population replacement mainly along the Nile. We also present biological evidence of interaction and mobility between these contemporaneous populations during the middle Holocene in the region. It supports the phylogenetic value of EDJ morphology for investigating population affinities at a microevolutionary scale. These results yield insights into the deep population history of the Nile Valley. They provide firm evidence for population replacement and migration toward the region at the onset of the Neolithic transition, attesting that these key changes were not solely triggered by cultural diffusion and diet change.

Centro Studi Sudanesi e Sub Sahariani Ente Terzo Settore Treviso 31100 Italy

Czech Institute of Egyptology Faculty of Arts Charles University Prague 116 38 Czech Republic

De la Préhistoire à l'Actuel Culture Environnement et Anthropologie Ministère de la Culture UMR 5199 CNRS University of Bordeaux Pessac 33600 France

Department of Anthropology Natural History Museum National Museum Prague 193 00 Czech Republic

Department of Anthropology University of Illinois Urbana IL 61801

Department of Egypt and Sudan The British Museum London WC1B 3DG United Kingdom

Department of Non European Archaeology Institute of Archaeology University of Wrocław Wrocław 50 139 Poland

Institute of Archaeology and Ethnology Polish Academy of Sciences Poznan 61 612 Poland

Institute of Archaeology Czech Academy of Sciences Prague 118 00 Czech Republic

Institute of Archaeology University of Neuchâtel Hauterive 2068 Switzerland

Laboratory of Archaeology of Africa and Anthropology Department of Anthropology University of Geneva Geneva 1205 Switzerland

Research Centre in Evolutionary Anthropology and Paleoecology School of Biological and Environmental Sciences Liverpool John Moores University Liverpool L3 3AF United Kingdom

University Archives University of Wuppertal Wuppertal 42119 Germany

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