Skin lightening allele in Khoe-San

[Angela]

See: Meng Lin et al

"[FONT=&quot]Rapid evolution of a skin-lightening allele in southern African KhoeSan[/FONT]

https://www.pnas.org/content/early/2018/12/05/1801948115

It's fast selection on a recent introduction, as I thought, but nice to see it confirmed.

"[FONT=&quot]Skin pigmentation reflects strong local adaptation to latitude after humans migrated around the globe. In the Northern Hemisphere, the gene [/FONT]SLC24A5[FONT=&quot]plays a key role in the genetic basis of light skin pigmentation, where a nonsynonymous mutation in the gene has swept to fixation in contemporary Europeans. Although considered European-specific, we find this mutation at an unexpectedly high frequency in light-skinned KhoeSan from South Africa, far exceeding the European gene flow during colonial migration. Using haplotype analysis and comprehensive demographic modeling including positive selection, we show that this is an example of surprisingly strong adaptation of a recently introduced allele, via back-to-Africa migration, which occurred less than 2,000 y ago.[/FONT][FONT=&quot][h=2]Abstract[/h]Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans."



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[bicicleur 2]

E1b1b1-M293 is the suspect

 

[ThirdTerm]

The Khoisan people are estimated to be 14% European or west Eurasian but the admixture events are dated to be much more ancient than the arrival of European settlers to the Cape Colony. Gene flow from eastern Africa is a plausible source for the west Eurasian ancestry in southern Africa. One admixture event, which introduced ancestry most closely related to European or Middle Eastern populations, is dated to ∼900–1,800 years ago and another admixture event is dated to ∼2,700–3,300 years ago (Pickrell et al. 2014).

The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.