Evidence of "recent" Sub-Saharan African admixture in Southern Europeans

I'm really impressed with this Moorjani et al. paper. They've gone out of their way to find and characterize Sub-Saharan African admixture in Southern Europeans, Jews and Middle Easterners. The only problem that I can see is the lack of Sicilian and Greek samples (the latter removed during data prepping).

Abstract: Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.

The article is open access, so anyone can read it, but here are some parts I thought were worth highlighting.

Applying the 4 Population Test to the proposed relationship (YRI,(Papuan,(CEU,X))) where X is a range of West Eurasian populations, we find significant violations for all Southern European, Jewish and Levantine populations but not for Northern Europeans (Table 1). The results remain unchanged even when we use alternate topologies replacing YRI with other African populations (Text S2, Table S4). We further verified these inferences with the 3 Population Test [21], which capitalizes on the insight that for any 3 populations (X; A, B), the product of the allele frequency differences (pX-pA) and (pX-pB) is expected to be negative only if population X descends from a mixture of populations related to populations A and B [21] (Figure S3). We verified that this method is robust to SNP ascertainment bias by carrying out simulations showing that the 3 Population Test detects real admixture even if all SNPs used in the analysis are discovered in population A, population B, or in both populations A and B (Text S3; Table S5; Figure S4). Application of the test to each West Eurasian population (using A = YRI and B = CEU) finds little or no evidence of mixture in North Europeans but highly significant evidence in many Southern European, Levantine and Jewish groups (Table 1).

To estimate the proportion of sub-Saharan African ancestry in the various West Eurasian populations that showed significant evidence of mixture, we used f4 Ancestry Estimation [21], a method which produces accurate estimates of ancestry proportions, even in the absence of data from the true ancestral populations.

...

Application of f4 Ancestry Estimation suggests that the highest proportion of African ancestry in Europe is in Iberia (Portugal 3.2±0.3% and Spain 2.4±0.3%), consistent with inferences based on mitochondrial DNA [6] and Y chromosomes [7] and the observation by Auton et al. [8] that within Europe, the Southwestern Europeans have the highest haplotype-sharing with Africans. The proportion decreases to the north and we find no evidence for mixture in Russia, Sweden and Scotland (Table 2, Figure S5). We also detect about 3-5% sub-African ancestry in all the Jewish populations, a finding that is novel as far as we are aware, and certainly has not been unambiguously demonstrated or quantified.

Here's a map showing regions of Sub-Saharan African admixture in Europe, based on the samples available. Interestingly, even Swiss Italians give a clear signal of this admixture.

Geographic gradient of African ancestry in Europeans. Sub-Saharan African ancestry proportions were estimated using f4 Ancestry Estimation. Populations in grey are estimated to have sub-Saharan African ancestry between 1–4%. The * in Switzerland indicates that the three populations available from this country have variable estimates: Swiss-Germans show no evidence of African mixture, Swiss-French 0.5±0.2% and Swiss-Italians 1.6±0.2%. The ‘+’ sign in Italy indicates that multiple samples were available but all show evidence of African mixture. No data are available from countries filled with diagonal lines.

It seems the table of West African admixture shows something that I picked up myself, and that's the fact that model-based algorithms, like STRUCTURE and ADMIXTURE, tend to underestimate Sub-Saharan African influence in Europeans. See here and here.



Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, et al. (2011) The History of African Gene Flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7(4): e1001373. doi:10.1371/journal.pgen.1001373