Unfortunately this DNA study doesn’t discriminate between L3 and later non African mutations. However, since M1, U, pre HV and a whole slew of other Eurasian DNA hg’s date to about 35k, then later to 12k in North Africa, this study probably isn’t massively far off the mark for lower Nubia .
mtDNA analysis in ancient Nubians supports the existence of gene flow between sub-Sahara and North Africa in the Nile valley
C. Fox, 1997:
The Hpal (np3,592) mitochondrial DNA marker is a selectively neutral mutation that is very common in sub-Saharan Africa and is almost absent in North African and European populations. It has been screened in a Meroitic sample from ancient Nubia through PCR amplification and posterior enzyme digestion, to evaluate the sub-Saharan genetic influences in this population. From 29 individuals analysed, only 15 yield positive amplifications, four of them (26·7%) displaying the sub-Saharan African marker. Hpa I (np3,592) marker is present in the sub-Saharan populations at a frequency of 68·7 on average. Thus, the frequency of genes from this area in the Merotic Nubian population can be estimated at around 39% (with a confidence interval from 22% to 55%). The frequency obtained fits in a south-north decreasing gradient of Hpa I (np3,592) along the African continent. Results suggest that morphological changes observed historically in the Nubian populations are more likely to be due to the existence of south-north gene flow through the Nile Valley than to in-situ evolution.
Krings et al study, 1999:
A study which included the modern population of both lower and upper Nubia show them to be about 45% maternally Eurasian, and there’s been virtually no immigration into the lower Nubia area from Asia according to the Y chromosome study of the area by Lucotte; which suggests this 60% Eurasian figure in the mummies is probably very roughly correct; (unless you believe there were invading armies of Arab women) particularly since the Dakhleh Oasis ancient and modern mt DNA analysis shows more Sub Saharan mt DNA than the ancient Egyptian samples, which is possibly attributable to the Arab slave trade. The Y chromsome study of lower Nubia here suggests historic male input from non Africans into the area is less than 5%, so it’s hard to argue for the ancient samples being massively different based on the modern DNA of the area.