Razib Khan

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    • I don’t really see any good evidence of the impact of specifically a German element in this. The Vandals seem to fail the test of long term demographic impact in these samples. To really explore this issue I’d have to look at the ancestry at the chromosomal level, and look for matching haplotypes and segments identical-by-descent. Perhaps I will in the future.

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    As you “move up” the K’s you note that Maghrebi populations “split” from the Near Eastern reference, the Qataris. This is supported by the PCA, which shows that there is a dimension of variation which separates Near Easterners & Europeans from Maghrebis. The authors note that this dimension is orthogonal to the Sub-Saharan African vs. Eurasian component. That suggests that the putative Maghrebi component is likely to be part of the set of “Out of Africa” populations, rather than an African population which simply experienced continuous gene flow with West Eurasians.

    They also estimate a Fst, a statistic which partitions genetic variation within and between groups. The value between Sub-Saharan Africans and Europeans is ~0.15 using HGDP SNP data, and between Europeans and East Asians ~0.10.  Using the Tuscans and Qataris as European and West Asian references against the North African populations along their east-west cline they estimate Fsts from ~0.03 to ~0.06. The higher end values are from populations which are less admixed with Near Eastern elements, and the colored polygons illustrate the domain generated by ADMIXTURE Fsts across inferred ancestral components. You also see in the chart estimated time of divergence. I won’t get into the assumptions in the model, but the authors do note that ~12,000 years B.P. seems to be the low bound estimate for when the Maghbrebis diverged from other West Eurasians. This is important, because it predates agriculture.

    The final set of methods outlined in this paper looked at ancestry on a more fine-grained genomic scale. To the left you see a plot where each horizontal bar represents an individual’s chromosome 1 (among a set of North Africans). Each color in that bar indicates a component of ancestry (except the black, which are centromeres). This sort of information is important, because saying someone is 50% X and 50% Y summarizes information to the point of eliding it. An individual who is a first generation product of a Chinese-European marriage is going to have the same ancestral proportions as someone who is a Uyghur for those respective populations. But a fine-scale mapping of the genomic ancestry would look very different, because the history of the admixture is very different.

    There are many inferences in the paper which I won’t address. Rather, let me focus on this one assertion:

    After accounting for putative recent admixture (Figure 1), the indigenous Maghrebi component (k-based) is estimated to have diverged from Near Eastern/Europeans between 18–38 Kya (Figure 3), under a range of Ne and k values. We hence suggest that the ancestral Maghrebi population separated from Near Eastern/Europeans prior to the Holocene, and that the Maghrebi populations do not represent a large-scale demic diffusion of agropastoralists from the Near East.

    This is not implausible on the face of it. The component of ancestry modal in the Mozabite HGDP sample tends to have a relatively high Fst in relation to other West Eurasian groups. I had wondered if this was due to ancient Sub-Saharan African admixture which had produced a particular stabilized hybrid, but these results indicate that the component is no closer than other West Eurasians. What I’m confused and skeptical about are the range of divergence times which different papers are producing which seem somewhat implausible taken together.

    There are papers which posit that East Asians separated from Europeans ~25,000 years B.P. This is in the same range as the divergence between Maghrebis and West Eurasians, but the Maghrebi genetic distance (Fst) is about 1/2 as great. Also, these sets of results which generate a “bunching” together of the separation of many extant non-African lineages in the 20-40,000 year range imply very rapid differentiation after the “Out of Africa” event, if that event did occur ~50,000 years ago (at least for most Eurasians, even assuming a revised model whereby Australian Aboriginals derive from an earlier wave). One at a time any given divergence estimate may be broadly plausible, but the literature is just not particularly coherent on this matter, and it often seems archaeologically implausible.

    Citation: Henn BM , Botigué LR , Gravel S , Wang W , Brisbin A , et al. 2012 Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397

    Image Credit: Raphaël Labbé

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