Real intruders or outliers in Egypt are from the uppermost portions of the Nile Valley, as opposed to migrants from the Levant and Europe.

Kemetian point of view:

They came from the south

Bio-anthropological perspective:

Indigenous population primarily from a tropical African background, as testified by spread of Afrasan language group and PN2 clade E3b lineages to northwest Africa from East Africa, and into the west Asia via the Nile Valley.

Linguistics:
Afrasan language group: East African origin.

Kemetian point of view:
Southern Egypt: Initiatives of creating the first Nation state took place here, and therefore, lower Egypt was the region that was integrated into that already existing southern Egyptian empire or establishment, to form a bigger Nation state of Egypt.

Pharaonic concept of Dynastic Egypt traces its roots back to the south.

Archeological perspective:
“Archaeological evidence in Lower Egypt consists mainly of settlements, with very simple burials in cemeteries, and suggests a culture different from that of Upper Egypt, where cemeteries with elaborate burials are found. While the rich grave goods in several major cemeteries in Upper Egypt represent the acquired wealth of higher social strata, the economic sources of this wealth cannot be satisfactorily determined because there are so few settlement data, though the larger cemeteries were probably associated with centers of craft production. Trade and exchange of finished goods and luxury materials from the Eastern and Western Deserts and Nubia would also have taken place in such centers. In Lower Egypt, however, settlement data permit a broader reconstruction of the prehistoric economy, which at present does not suggest any great socio-economic complexity.

Differentiation in the Predynastic cemeteries of Upper Egypt (but not Lower Egypt) is symbolic of status display and rivalry (Trigger 1987: 60), which probably represent the earliest processes of competition and the aggrandizement of local polities in Egypt.

Present evidence suggests that the state which emerged by the First Dynasty had its roots in the Nagada culture of Upper Egypt, where grave types, pottery, and artifacts demonstrate an evolution of form from the Predynastic to the First Dynasty.

This cannot be demonstrated in Lower Egypt. Hierarchical society with much social and economic differentiation, as symbolized in the Nagada II cemeteries of Upper Egypt, does not seem to have been present, then, in Lower Egypt, a fact which also supports an Upper Egyptian origin for the unified state. thus archaeological evidence cannot support the earlier theories that the founders of Egyptian civilization were an invading Dynastic race, from the East (Petrie 1920: 49, 1939: 77; Emery 1967: 38), or from the south, in Nubia (Williams 1986: 177).

How this transformation was accomplished and the amount of time involved are points of disagreement…

Given the quality of earlier excavations and publications, and the poor preservation of many settlement data, we still cannot specify how a centralized state emerged in Egypt by 3050 B.C., and explanations for the origin of the early Egyptian state remain hypothetical. Nonetheless, the roots of the major transition from autonomous villages to an early state in Egypt from simple to complex society - are to be found in Upper Egypt at large centers such as Nagada, where Predynastic cemeteries provide the main evidence for this culture.” - Professor Kathryn Bard, Journal of Field Archaeology, Fall 1994.

First posted here

Kemetian point of view:

Clearly distinguished themselves from Asiatics, and are not one and the same, as some like to put forth today.

Anthropological point of view:

Materials Sampled -
Skeletal sampling was mainly restricted to sites from Upper and Middle Egypt, so that individuals would have experienced reasonably similar geographical and climatic conditions. Due to lack of OK postcranial remains from Upper Egypt, one series from Lower Egypt was also analyzed...

The nature of the body plan was also investigated by comparing the intermembral, brachial, and crural indices for these samples with values obtained from the literature. No significant differences were found in either index through time for either sex. The raw values in Table 6 suggest that Egyptians had the “super-Negroid” body plan described by Robins (1983). The values for the brachial and crural indices show that the distal segments of each limb are longer relative to the proximal segments than in many “African” populations (data from Aiello and Dean, 1990). This pattern is supported by Figure 7 (a plot of population mean femoral and tibial lengths; data from Ruff, 1994), which indicates that the Egyptians generally have tropical body plans. Of the Egyptian samples, only the Badarian and Early Dynastic period populations have shorter tibiae than predicted from femoral length. Despite these differences, all samples lie relatively clustered together as compared to the other populations." - Sonia R. Zakrzewski

Historical perspective:
One wonders how on earth that can be the case, when history shows successive waves of intrusions from the Levant and northern Eurasia. The likes of Giza-Rider simply can‘t or refuse to grasp the fact that, “Alterations of original populations” and the “implication that contemporary populations don’t have biological ties to ancient populations” don‘t mean the same.