The news article was sourced from this study:
https://www.nature.com/articles/ncomms15694
The authors claim that the mummies from which their samples were taken, were representative of a cross-section of social classes. They were not testing pharaoh's mummies. And although they were definitely able to detect that their samples contained stronger Levantine and European components compared to modern Egyptians, the difference was not as dramatic as one might think from reading the news report. They believe the difference was caused by an admixture of African ancestry, and they report that "Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations". So, a seven to eight percent difference.
