Because of the constant kvetching in the comments below about possible affinities between North Africans and Spaniards I was going to do some reanalysis of Botigue et al.’s data set, when this paper came out: A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures. This inference comes from a whole-genome sequence of an ancient DNA sample. Specifically a 7,400 year-old Cardial individual (CB13) from the environs of modern Barcelona. The paper is open access, so read the whole thing yourself, it’s short. But the results are clear above. This individual has affinities with modern Sardinians more than any other modern groups. Second, come the Basques.
The balance of ancient DNA results are suggesting that there was a radical replacement of hunter-gatherers across Europe. These individuals of the early Neolithic seem to derive from the same source group, whether they were Cardial in the Western Mediterranean or LBK in Germany. And, they were admixed by the enigmatic “Basal Eurasians” and a European hunter-gatherer element. Using the CB13 the authors compared shared drift with various European hunter-gatherers. It turns out that CB13 shared the most with Hungarian, not Iberian, hunter-gatherers. The implication is that we’re seeing a common mode of human cultural and genetic change: an initial stage of amalgamation giving way to endogamy. The later resurgence of “hunter-gatherer” ancestry that you see in Spain is probably attributable to the arrival of people from the North, likely Indo-European speakers. Notably, this individual had the derived allele SLC24A5 only
In any case, I also did a little analysis of North Africans, Spaniards, and Orcadians and French as token outgroups. All the plots here.
The Tunisian sample are Berbers. Southern and Northwest Spain are hard to differentiate. I wonder if this is due a lot of gene flow in the kingdom of Castile? I suspect that the gene flow from the Basques to northern Morocco has to do with Moriscos who arrived from Spain. The gene flow into the Spaniards, and Sardinians, is Berber-like, not Middle Eastern.
Note: I forgot to mention, I did a lot of outlier removal of individuals with excess African ancestry.