North African autosomal genetics (again)

Two weeks ago I performed almost the same exercise here at this blog but now a paper with academic seal of proficiency has been published at PLoS Genetics:

Brenna M. Henn et al., Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genetics 2012. Open access.

The basic results are very very similar if not outright identical to what I achieved. And that is because the sampling strategy was also very similar. If anything Henn and colleagues used a broader sample of Tropical African populations.

From Fig. 1 (click to expand)

The choice of North African populations is exactly the same as mine (actually the samples I used are from a previous paper by Brenna Henn, who is making a great job in exploring African genetics, and must be the same as in this paper) exception made that I included 10 HGDP Mozabites also. The choice of West Eurasian populations is different but does not seem to produce any relevant difference in the result. The main differences are in the choice of Tropical African samples, which does produces some differences.

Tunisian Berbers' endogamy

But first of all let's explain what happens with the weird Tunisia sample:

... the Tunisian Berber population displayed an excess of pairs of individuals sharing 200–1200 cM IBD. This bimodal distribution indicates that many 1st and 2nd cousin genetic equivalent pairs were present in this sample, even though donors declared themselves to be unrelated during the sampling process. Analysis of long runs of homozygosity (ROH) indicate that the Tunisian population averaged almost twice as much of their genome is in ROH than other North African populations, 230 Kb versus 120 Kb respectively (Figure S3). The pattern of ROH and pairwise IBD in the Tunisian Berbers is likely the result of endogamy due to geographic isolation or cultural marriage preferences.

That's why they perform so weirdly, relating always to themselves almost before any other affinity. This fact makes them a poor and mostly uninformative population. 

Different sampling strategy, somewhat different results

As I say, the main difference between my sample strategy and Henn's (and the result produced) is in Tropical Africa: I used Ethiopians, Mandenka and Fulani; Henn used also Fulani and then also West and East Africans but different ones. I found apparent Mandinka (West African) admixture in NW Africa (and almost no East African/Ethiopian one), Henn found apparent Luhya (East African) admixture instead (and almost no West African one).

I don't know yet how these two apparent different findings may conciliate but the difference of findings is in itself interesting, outlining the strategy of future research. 

Something that is quite obvious as Henn uses such a broad Tropical African sample is that many of the components discerned are just one for each Tropical African population. This is interesting, underlining the immense genetic diversity of Africa, but not very informative in regard to North Africans. 

That (and the fact that I went down to K=11 - and even K=12 but this one was uninformative) is probably the reason why I, with a smaller peripheral sample, could detect what I believe that is a very old layer of North African specificity. 

So the sampling strategy (both sample choice and number of individuals in each sample), as well as the K-depth reached can affect the results of these analysis of the population genetic structure. There is almost always a different approach that can produce complementary information as result. 

Back to Africa but when?

But overall the results are very similar: the bulk of North African genetic affinity is with West Eurasia and not so much Africa as such. That is the most obvious result and indicates that the Out-of-Africa migration had an important backflow which affected several parts of Africa but very specially the North. 

Nothing unexpected, at least for me. But it really hits a blow to those who, quite lightly, associate Y-DNA and overall ancestry: if there is Y-DNA and mtDNA contradiction, as is the case in North Africa, where most of the patrilineages are African but most of the matrilineages are of Eurasian origin, in most cases the mtDNA is right and the Y-DNA is nothing but a varnish. 

The main exceptions seem to be areas of sustained male inflow across generations, notably some parts of Latin America. But this kind of sustained industrialized migration pattern is unlikely to have ever existed in prehistory or even pre-Modern history anywhere. 

Anyhow, interestingly, the authors make an interesting exercise to find out estimate times of Eurasian arrival. The result is forewarned with reasonable precautions:

Since this model neglects migration, we expect our results to form a lower bound on the population divergence time, as similar levels of population divergence would require a longer separation in the presence of migration.

So at least this old:

Fig. 3 (edited to correct a color typo) - click to expand

Although these divergence time estimates may not be precise, as they do not adequately model ancient migration, they do suggest that the population divergence between the ancestral Maghrebi population and neighboring Mediterranean populations occurred at least 12,000 ya and indeed more likely predated even the Last Glacial Maximum.

It is interesting anyhow that the Fst distance to Europe are lower than to Arabia and that the window for a possible migration from Europe can well fit with the Oranian genesis c. 22,000 years ago, which I am pretty sure that is related with Iberian Gravetto-Solutrean: Oranian was back in the day called Iberomaurusian for a reason and, regardless of revisionisms, the Oranian dates for the West are quite older than those of the East - never mind that at least 25% of North African mtDNA (and maybe 10% of Y-DNA) is of European (and most likely Iberian) derivation and that European affinity remains apparent, distinct and important (specially in Algeria and North Morocco) even after North African specific components have become obvious and dominant.

So the old theory of migration from Iberia c. 22,000 years ago (maybe with some backmigration northwards as well) is not any colonial construct but something most probable, as indicate both archaeological and genetic data very consistently.

Less clear is whether there was a previous West Eurasian flow c. 40,000 years ago with the Dabban industries (so far only known in Libya, although unmistakably "Aurignacoid" in character). Genetically the main support for this first Eurasian backflow is mtDNA U6 (derived from Eurasian U), whose origin is probably in Morocco, where most of the basal diversity accumulates (and then around it, in Canary Islands and Iberia). 

It is not impossible that the lineage might have arrived, still as undefined U*, via Europe, however the structure of the autosomal DNA, as illustrated in this study or in my exercise from December, evidences that the North African specific components (excepted the "Aterian" one) are most akin to West Eurasia (by much). So there was probably a first migration from West Asia c. 40 Ka. ago and then an Iberian layer overlapped. 

This paper also suggests more recent migrations from Tropical Africa, although I am unsure if I can take their timeline conclusions at face value, specially regarding the East African component, that I imagine quite older (they suggest, table 1, just 25 generations ago, what I find most hard to believe for such a notable impact).

I would personally conclude that the North African genetic composition appears to be made up of:

1. A deep, quite diluted, 'Aterian' layer
2. A dominant North African specific layer of mostly West Eurasian roots
3. An Iberian or European layer (Oranian)
4. Maybe an East African (Capsian) layer (needs clarification but agrees with Y-DNA)
5. Maybe a lesser Arab layer and also maybe some recent Tropical African input