Skin color and Neandertals

Qiliang Ding et al., (2014) published a paper (Neanderthal origin of the haplotypes carrying the functional variant Val92Met in the MC1R in modern humans, Molecular biology, DOI:10.1093/molbev/msu180) which looks into the pale skin of Eurasians in general as due to admixture between Homo sapiens and Neandertals.

The color of our skins is due to the combination of two pigments, one red (phaeomelanin) and one black (eumelanin), and the proportion of this color blend is in part defined by the Melanocyte-stymulating hormone or MSH. MSH is encoded by a gene called MC1R.

If the function of this gene is altered by mutations, it impacts on MSH and therefore on skin color.

Five "loss-of-function" variants of MC1R have been discovered to date, and are linked to fair hair (red or blond) and fair skin:

1. Val60Leu (rs1805005*T)
2. Val92Met (rs2228479*A)
3. Arg151Cys (rs1805007*T)
4. Arg160Trp (rs1805008*T)
5. Asp294His (rs1805009*C)

Neanderthals also carried (but we, modern humans don't), another variant of MC1R (Arg307Gly)

Qiliang's team found that "...almost all of the derived alleles at the Val92Met variant of MC1R (rs2228479*A) in the human gene pool are carried by the putative introgressive haplotypes", by "putative introgressive haplotypes" they mean "haplotypes from Neanderthal introgression in modern Eurasians".

It is found at roughly 5% introgression rates in Europeans (not very high), up to 30% in East Asians (Chinese for instance) and at a surprising high introgression rate of 60 to 70% in the Taiwanese aborigine people (the Atayal and the Ami).

They don't know why this cline exists and conjecture: " Therefore, we cannot rule out demographic effects such as population bottleneck as an explanation for the unusually high frequency of rs2228479*A in Atayal and Ami although positive natural selection is also a possibility"

Its origin is linked to the Altai Neanderthal branch and the time line is the following:

"Based on the values, it could be estimated that the putative introgressive haplotypes diverged with the AMH 552.5 ka, then diverged with the Denisovan 159.0 ka, and then diverged with the Altai Neanderthal 103.3 ka (fig. 2). It could be observed that the divergence time between the putative introgressive haplotypes and the Altai Neanderthal (103.3 ka) postdates the reported Neanderthal–AMH divergence time (>270 ka), which indicates the presence of postdivergence introgression"

Altai, Japanese and Africans

The paper reports that "Remarkably, it was observed that all putative introgressive haplotypes carry the derived allele of the Val92Met variant (rs2228479*A), and almost none [except a Japanese subject NA19084_a]... of the nonintrogressive haplotypes carries the rs2228479*A. This suggests that the rs2228479*A carried by the putative introgressive haplotypes might be from archaic hominin lineage. However, rs2228479*A was not found in the Altai Neanderthal genome."

They explain the lack of rs2228479*A in the Altai Neanderthal as follows: " 1) The rs2228479 is polymorphic in Neanderthal populations, and 2) the mutation creating rs2228479*A occurred on the putative introgressive haplotype shortly after it entered modern human gene pool (...) The rs2228479*A was found in one (out of 41) sequencing read of Altai Neanderthal and one (out of 20) sequencing read of Denisovan. All of the relevant sequencing reads and base calls passed quality control filter. Therefore, it could be possible that the Neanderthal and Denisovan are heterozygous at the rs2228479, and some unknown reason caused the imbalanced observation of ancestral and derived alleles of rs2228479 in sequencing reads."

The Japanese subject NA19084-a is among the non-introgresses subjects, so the derived allele at rs2228479 "might be from recurrent mutation, double recombination, or biased gene conversion".

Interestingly they found this allele at rs2228479 in three African subjects: "...among all HapMap African individuals, it was observed that one YRI (Yoruba in Ibadan, Nigeria; NA18852) and two MKK (Massai in Kinyawa, Kenya; NA21339 and NA21574) carry heterozygous alleles at the rs2228479".

They propose three possible explanations for this odd situation:

"Presence of derived alleles at Val92Met (i.e., rs2228479*A) in Africans could be explained by three models: 1) The rs2228479*A existed in the human gene pool before the Neanderthal–AMH divergence and was drifted to very low frequency in modern Africans whereas preserved in the Neanderthals and modern Eurasians (i.e., the “ancestral polymorphism model”), 2) recent gene flow from modern Eurasians to Africans, or 3) independent origin (such as recurrent mutation)."

They reject (1) but consider (2) and (3) as feasible. That is, it originated independently in Africa or there was a recent flow into Africa carrying Neanderthal genes i.e. contemporary Eurasians, which is quite reasonable, nevertheless, I would add, Neanderthals could have entered Africa and mixed there with Massai in Kenya and Yoruba in Nigeria.

Another surprising find was that it appears ata 50% frequency among the Cheyenne people of America. That is high, and rather unique in the New World, where it is hardly found at all.

Below is a map with its global distribution:

It is important to point out that Norton, Werren, and Friedlaender,(2015) found this Val92Met polymorphism in over 600 Melanesians sampled on different islands, reporting that the frequency of the derived allele ranged from 4 to 33% yet it seemed to have no influence whatsoever on the skin or hair color of the individuals. This suggests that it must interact with other genes to define the tone of hair and skin.

The same thing can be seen in East Asians: they have black hair just like Africans - and unlike brown of fair haired Europeans- despite carrying this derived gene that promotes fair hair.

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