Below a nice recap of various archeological studies about the regional continuity of the Nile populations. It was taken from a study posted below.
Main points:The population history of the Nile has been of considerable recent interest and focuses on two competing hypotheses. The first suggests that the Egyptian dynasties developed in situ from the earlier Predynastic and Neolithic populations represented at sites such as el-Badari. The second scenario suggests that migration of people from western Asia led to the development of the Egyptian state (Petrie, 1920, 1939; Kantor, 1965).[b]In general, the archaeological evidence suggests that the Egyptian state had an indigenous origin[/b](Hassan, 1988). Two recent studies provide evidence for population dynamics in the Nile Valley throughout the Holocene. Zakrzewski (2007) demonstrates evidence for broad population continuity through time on the basis of craniometric variation, with some level of population movement . Several recent analyses of dental variation come to essentially the same conclusion (Irish, 2005, 2006; Schillaci et al., 2009). Thus, in the most general terms, there is strong evidence for population continuity along the Nile from the late Palaeolithic through the Egyptian Empire. However, the diffusion of agricultural technologies into the Nile from other regions, and the subsequent trade networks of the Egyptian empire, would have undoubtedly brought with it people and genes from other regions to varying extents through time and space.
1 - In general, the archaeological evidence suggests that the Egyptian state had an indigenous origin
2 - Craniometry (and Dental variation) demonstrate broad population continuity through time on the basis of craniometric variation, with some level of population movement
3 -[b]Strong evidence for population continuity along the Nile from the late Palaeolithic through the Egyptian Empire with some level of population movement[/b]
4 - Trade networks of the Egyptian empire, would have undoubtedly brought with it people and genes from other regions to varying extents through time and space.
So the main point here for us, is the STRONG evidence for population continuity in the Nile region from the late Pleistocene through the Egyptian Empire.
Taken from this study: Body Size, Skeletal Biomechanics, Mobility and Habitual Activity from the Late Palaeolithic to the Mid-Dynastic Nile Valley.
Got it from here: www.pave.bioanth.cam.ac.uk/pdfs/033-Stock (2011HBTA)NileBiomechSize.pdf
The study by itself is also interesting as it analyses the consequences on the body of ancient specimens of the transition in the Nile from different lifestyles (hunting-gathering, pastoral, agriculture, etc).
We can also see it here:
Image from the study: Climate-Controlled Holocene Occupation in the Sahara: Motor of Africa's Evolution
From the image above you can see that the peopling of the Nile was the product of the populations in the A map, from inner Africa, from the South, which expanded in the Sahara and then went back along the Nile to settle down during the desertification of the Sahara (following the Green Sahara period) in search of greener pastures.