Notice that all Y-chromosomes belong to either E-subclades or to J1. I would definitely not equate J1 with the Neolithic in this case; it is more likely to be due to historical movements of Semitic/Arabic populations into Egypt. The complete absence of J2 is noteworthy and resembles Arabian peninsula populations where the J2/J1 ratio reaches its minimum.
American Journal of Physical Anthropology doi:10.1002/ajpa.21078
Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert
Martina Kujanová et al.
The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.