Being a skeptic of the "Slave theory" of demographic change in established peasant populations at the Malthusian limit (that is excluding frontier situations with a land surplus like those in the New World) I've long suspected that West and East-African-like admixture in North Africans was really about a substrate (semi-)forager/pastoralist Western Green Saharan population and a Neolithic expansion from Egypt. Indeed I think the Tuareg may very well be at least a population with a large component corresponding to this ancient no longer extant in an unadmixed form group of people.
Seeking evidence about Native North Africans I've been thinking about ways to uncover evidence about them indirectly using some supervised mode tricks I've been developing.
First I ran a supervised analysis of Mexicans. I used historically appropriate pole populations: all my 12 Spaniard samples, all 24 Totonac representing Mesoamerican Amerindians, and 68 Yoruba representing the bit of West African present in this population. The Mexican samples were 58. I didn't use recent individual samples in any of the runs since results are highly experimental:
"Spanish" to "Yoruba": 164
"Spanish" to "Totonac24": 170
"Yoruba" to "Totonac24": 258
ADMIXTURE always mixes some bits of components up, it's a statistical tool, so it doesn't matter for this purpose if these are exactly correct or not.
Results are in line with other studies.
It also doesn't matter much how many Totonac samples are used as a pole, since these are close to the actual parent population(s). Here is the same run using only 5 Totonac:
"Spanish" to "Totonac5": 182
"Yoruba" to "Totonac5": 255
Results and fst distances aren't very different. I actually believe these restricted pole results may be closer to the truth since the Amerindian pole is less dominated by the Totonac and more by the Mexican samples' actual Amerindian ancestors.
Now imagine Amerindians were no longer present as unadmixed populations to sample directly. We might know or discover however that this parent population of Mexicans was somewhat similar to the East Asians. So we might try to use say, Beijing-Chinese samples as the proxy for the actual parent population (I used only 24 BJG-Chinese just as Totonac):
"Spanish" to "BJG-Chinese24": 117
"Yoruba" to "BJGChinese24": 210
So, genetic distances and admixture proportions change quite a bit, suggesting as known that BJG-Chinese are not the parent population. The pole was stretched by the 24 Chinese seeding it.
So what would happen by doing the same as in the Totonac runs, restricting the Chinese samples to five?
"Spanish" to "BJG-Chinese5": 113
"Yoruba" to "BJGChinese5": 188
As sometimes happens with inadequate poles, the poles ate up some unrelated segments in this run. But results suddenly became more in line with the Totonac ones. The pole isn't as distorted with 5 as it is with 24 Chinese and it becomes more dominated by the Mexicans East Asian-like ancestors.
Note how genetic distances don't change much with Totonac24 vs Totonac5. They do change a lot with the restriction of the inadequate BJG-Chinese pole. ADMIXTURE is trying to tell us Mexicans aren't really descended from the Chinese.
Now applying these techniques to North African populations. I used all my Basque samples (24), 61 Masai and 24 Yoruba as poles:
Basque to "Yoruba24": 166
Basque to Masai: 98
Masai to "Yoruba24": 35
With only five Yoruba as pole:
Basque to "Yoruba5": 180
Basque to Masai: 112
Masai to "Yoruba5": 53
There is change. The situation is a bit more like Mexicans with BJG-Chinese than with Totonac I think. Basque is now closer to "Yoruba5" just as Masai is more distant. This could be absorption due to the inadequate pole just as in the Chinese5 pole experiment.
So Yoruba are clearly somewhat related but I think also distinct from the Northwest African substract. Perhaps West Africans, East Africans and ancient North Africans are all populations born of a Green Sahara melting pot.
Tomorrow I'll run a control, and do the same using Niger-Congo-speaking Sahel populations. And the same for the Maasai pole. And then it gets even more complicated but hopefully revealing.