I came across a recent paper published in Science in 2017 by Crawford et al., Loci associated with skin pigmentation identified in African populations, which holds some interesting facts about skin color genetics and when the dark and pale variants arose.
I have posted in the past about light skin pigmentation in Amerindians and Neanderthal skin color, but this post will look into light skin alleles shared by the San people of Africa and modern Europeans.
Skin color genes are ancient
When it comments on how skin pigmentation evolved in modern humans, the paper points out that there is a wide variability within Africa, from the most pale group (the San in southern Africa) to the East African people of the Nilo Saharian region, who aret the darkest. It correctly states that the genes causing both dark and light skin color evolved before our Homo sapiens species appeared around 300,000 years ago (300 ky).
Surprisingly, the paper finds that "the ancestral allele is associated with light pigmentation in about half of the predicted causal SNPs; Neandertal and Denisovan genome sequences, which diverged from modern human sequences 804 ka, contain the ancestral allele at all loci." So, our closest relatives in evolutionary terms carried this ancestral white-skinned allele with them. However, the paper tends to downplay this fact, and it says something which sounds the opposite: "These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years (My) after human ancestors lost most of their protective body hair" and then, like an afterthought mentions the paler tint of Neanderthals and Denisovans: "... although these ancestral hominins may have been moderately, rather than darkly, pigmented. Moreover, it appears that both light and dark pigmentation have continued to evolve over hominid history."
Shared genes between dark pigmented Africans and Australo-Melanesians
It mentions something I hadn't read before (I was always surprised by the similarity in the dark tint of pigmentation in Melanesians, Australian Aboriginal people, Andamenese islanders and Africans): they share a common genetic origin, and could be identical by descent (IBD). The paper says that "Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2, and HERC2 that are identical by descent from Africans. This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution."
It is indeed interesting to note that the bottleneck and founder effects and loss of diversity among the Out of Africa migration population managed to carry, intact, these alleles across Southern Asia, into Australia and Melanesia, while another group managed to carry the white, paler skin alleles.
A light pigmentation variant shared by San and Europeans
There is a variant at SNP rs1800404 within OCA2, that in its ancestral form (with a cytosine base or "C") is found in dark skinned East Asians, most Africans and Australians and Melanesians. The derived variant with a Thymine base or "T", is found in Europeans and the pruportedly most ancestral human beings, the San from southern Afirca! (found among these two groups in frequencies of over 70%). The split is ancient: " Coalescent analysis indicates that the TMRCA of all lineages is 1.7 Ma (95% CI, 1.5 to 2.0 Ma), and the TMRCA of lineages containing the derived (T) allele is 629 ka (95% CI, 426 to 848 ka)"
The tree shown above has two branches with the African one deeper (older) and shorter ones for most modern populations. Note the Oceanians and South Asians are on the African branch.
The allele shared by San and Europeans dates back approximately to the time Neanderthals and Denisovans split from the Modern human lineage.
Another region that acts upon skin color is HERC2, where SNP rs6497271 comes in an ancestral A variant (with an adenine base) providing dark pigmentation to Australo-Melanesians and Africans (identical in both groups, suggesting an identity by descent), and the derived base, (G) or guanine which is linked to lighter skin pigmentation and found in Europeans, and, yes, in the San people. This one is also old, dating back to "921 ka (95% CI, 703 ka to 1.2 Ma)".
If the dark "A" variant is IBD, the pale "G" one should also be IBD, and this one is possibly older than the Denisovan-Neanderthal / Human split as it is 921,000 years old.
The tree (above) show its distribution globally, with two branches the dark skin variant seems to have longer branches making it look more ancestral than the other, pale skin variants. I don't see the link between Africans and Australo-Melanesians in this tree, as mentioned by the authors.
How did Europeans and San people get to share this variant and the other OCA2 variant, while all the Africans living between both groups have the derived dark pigmentation variants? Note that there is 6,600 km (4,100 miles) between the southernmost tip of Europe in Greece and the San homeland in Botswana/Namibia.
We can imagine different alternatives to explain this: (1) A small population of modern humans split, one headed north into Europe, the other was displaced south into the southern tip of Africa. Between them, a mutation appeared, providing dark pigmentation for people living in the tropical regions of Africa, with benefits like UV protection, etc. (the paper hints that dark skin may have positive effects on other bodily functions: "...some of the pigmentation-associated variants identified here may be maintained because of pleiotropic effects on other aspects of human physiology."
Another option (2) is that pale pigmentation was prevalent among the archaic population that evolved into Neanderthal-Denisovan-Humans and moved with them across Eurasia but a later darker variant appeared in Africa and became predominant there, displacing the pale skin to the southern tip of Africa (San), and migrating out of Africa in a sub-population of modern humans that peopled South Asia and Australia-Melanesia (PNG, Aboriginals, Negrito, Andamanese people). Later overlaid by a wave of paler humans in Indonesia, Malaysia, Thailand and North India. Did the Europeans get pale skin from admixing with Neanderthals, and Asians from Denisovans?
(3) Prehaps ancient archaics had the darker pigmentation alleles, and a separate archaic group was lighter colored, the former remained in Africa (H. habilis), the latter moved into Eurasia (H. erectus?). Modern humans evolved in Asia, starting with Neanderthals and Denisovans, and back-migrated into Africa where admixture with archaics in Africa led to a darkening currently observed there. The san, part of the wave of migrants were displaced and isolated, retaining the original alleles. However, the dark skinned south Asians and Melanesians can't be accounted for with this model. Perhaps there was an Out of Africa migration along coastal South Asia into Melanesia? Or an ancient migration of superarchaics into Asia that mingled there with later populations?
In any case, I find it interesting that contemporary Europeans, who are deemed to be very recent, and the San people, supposedly the oldest intact group of humans, that split from the rest of us over 150,000 years ago, share the same light-skin pigmentation alleles. This oddity indicates that there is something amiss with our current idea of human origins and dispersal.
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