Selection for pigmentation in Khoisan?

In the recent paper, Reconstructing Prehistoric African Population Structure, there was a section natural selection. Since my post on the paper was already very long I didn’t address this dynamic.

But now I want to highlight this section:

The functional category that displays the most extreme allele frequency differentiation between present day San and ancient southern Africans is ‘‘response to radiation’’ (Z = 3.3 compared to the genome-wide average). To control for the possibility that genes in this category show an inflated allele frequency differentiation in general, we computed the same statistic for the Mbuti central African rainforest hunter-gatherer group but found no evidence for selection affecting the response to radiation category.

We speculate that the signal for selection in the response to radiation category in the San could be due to exposure to sunlight associated with the life of the Khomani and Juj’hoan North people in the Kalahari Basin, which has become a refuge for hunter-gatherer populations in the last millenia due to encroachment by pastoralist and agriculturalist groups.

I’m a bit puzzled here, because the implication seems to be that the San populations are darker than they were in the past. And yet earlier this summer I saw a talk which strongly suggested that there was a selection in modern Bushman populations for the derived variant of SLC24A5, presumably introduced through admixture from East African populations with Eurasian admixture.

In comparison to their neighbors the San are quite light-skinned, so it’s a reasonable supposition that they have been subject to natural selection recently. The Hadza, in contrast, seem to have the same complexion as their Bantu neighbors.

4 thoughts on “Selection for pigmentation in Khoisan?

  1. Relevant abstract from ASHG 2017:

    https://ep70.eventpilotadmin.com/web/page.php?page=IntHtml&project=ASHG17&id=170122885 – Novel loci associated with skin pigmentation identified in African populations – Further, the alleles associated with skin pigmentation at all loci but SLC24A5 (lighter and darker skin pigmentation associated alleles within Africa are ancient, predating the origin of modern humans. The ancestral alleles at the majority of predicted causal SNPs are associated with light skin, raising the possibility that the ancestors of modern humans could have had relatively light skin color, as is observed in the San population today. This study sheds new light on the evolutionary history of pigmentation in humans.

    It’ll be interesting to see these alleles checked out in the San as well.

    My impressions is that although although East African groups with Holocene West Eurasian ancestry seem to have relatively high frequencies of SLC24A5 derived variant, they actually don’t always look as if they are darker complexioned than West or Central Africans.

    Impressionistically, it seems like San have perceptibly lighter skin than East Africans, with similar / lower frequencies of SLC24A5 derived variant. (For melanin stronk San<Somali<=Yoruba?). I mean, you do not see people who look like (with respect to skin tone) Barkhad Abdi among the San, and the heterogeneity of skin tone among San seems low (not what we'd expect if one large allele of effect of intermediate frequency is the main factor in San skin tone differences against other Africa groups).

    If follow Beleza's model from Cape Verdeans, the variance from even a 50% frequency of SLC24A5 derived variant alone does not seem like it would explain the observed differences – http://journals.plos.org/plosgenetics/article/figure?id=10.1371/journal.pgen.1003372.g007.

    Razib: In comparison to their neighbors the San are quite light-skinned, so it’s a reasonable supposition that they have been subject to natural selection recently. The Hadza, in contrast, seem to have the same complexion as their Bantu neighbors.

    Noteworthy because both groups bear ancestry from the same wave of East African pastoralists (as much as we talk about it less, for various reasons).

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