There are lots of replies to this already but I think it's worth simply copying out the relevant parts of the conclusion:

> Although our analyses are limited to a single Egyptian individual who ... may not be representative of the general population, our results revealed ancestry links to earlier North African groups and populations of the eastern Fertile Crescent. ... The genetic links with the eastern Fertile Crescent also mirror previously documented cultural diffusion ... opening up the possibility of some settlement of people in Egypt during one or more of these periods.

This wording is definitely more circumspect than its headline version, "Breakthrough discovery REVEALS Egyptians are in fact MESOPOTAMIANS"