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Bengston, John D. (ed.), In Hot Pursuit of Language in Prehistory: Essays in the four fields of anthropology. 2008. John Benjamins Publishing: pp. 3-16)

The quotes and pages below are excerpts only, not the full article:

"The dominant pattern in Egypt is M35/M78, an African derived lineage with highest frequencies in Sub-Saharan Africa. The samples from Egypt are almost as diverse as those of the Horn. Some samples have high frequencies of the ancient M60 marker (haplotype B), but the plurality of studies show M35 lineages as predominating. Traces of M2 are found as they are in the Horn. In Egypt the M35 are also primarily M35/M78 with some M35/M81. Egyptian samples show varying frequencies of M89 derivatives and in one sample these actually are the majority; this is not surprising given its locale and the settlement of people from the Near East during the Islamic period..”

It is important to reiterate that the origin of M35 is in East Africa.. The overall pattern is consistent with a model of the first speakers of Afro-Asiatic having emerged in or near the Horn of Africa or in the Nile Valley. . The evidence is also consistent with the biohistorical Africanity of the base populations of the Horn, Maghreb and Nile valley. These genetic data give population profiles that clearly indicate males of African origin, as opposed to being of Asian or European descent. It is important to say that being biogeographical African does not indicate any specific set of skin colors, hair type or facail features; the populations were constantly subject to the forces of microevolutionary mechanisms. The E haplogroup is clearly African in origin as are A and B..

The genetic data do not support a model of demic diffusion by farmers fro the Levant to explain the Neolithic in northern or eastern Africa, or the spread of Afro-Asiatic languages into Africa..

It is of interest that the M35 and M2 lineages are united by a mutation – the PN2 transition. This PN2 clade originated in East Africa, where various populations have a notable frequency of its underived state. This would suggest that an ancient population in east Africa, or more correctly its males, form the basis of the ancestors of all African upper Paleolithic populations, and subsequent descendants in the present day.”

-S. Keita, 2008, “Geography, selected Afro-Asiatic families, and Y chromosome lineage variation.” pg 3-16

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MISC info

Major African haplogroups: [quote]

"Haplogroups A and B are the deepest branches in the phylogeny and are essentially restricted to Africa, bolstering the evidence that modern humans first arose there (14, 15). Haplogroup A is mainly found in the Rift Valley from Ethiopia to Cape Town, mostly but not exclusively in some of the oldest hunter-gatherers who still survive and speak Khoikhoi and San languages, proposed by some to be the oldest languages."

"Haplogroup B is found mainly among African Pygmies, who live in the central African forest and are still predominantly hunters-gatherers but speak Bantu languages borrowed from farmers who arrived in the area between 2,000 and 3,000 years ago."

"The third predominantly African haplogroup, E, diversified some time afterward, probably descending from the East African population that generated the Out of Africa expansion."

--FROM:
Chiaroni, M. et al. (2009). Y chromosome diversity, human expansion, drift, and cultural evolution. ProcNaAcadSci (PNAS) vol. 106 no. 48 20174-20179