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The golden age of pigmentation is yet to come

Skin color is important and interesting. It is important because people think it is important. Humans often classify each other by complexion, and it has a high social importance in many cultures.

This tendency starts at a very young age. When my children are toddlers they’ve all misidentified photographs of black American males with a medium brown complexion as their father (for example, my son recently misidentified a photograph of me that was actually the singer Pharrell). In terms of my background though, I’m 100% Eurasian in ancestry. On a PCA plot, I’m about halfway between Europeans & Near Easterners and East Asians (I have 15% East Asian ancestry so I’m more shifted to East Asians than the typical South Asian).

Skin is the largest human organ, and we are a visual species. It is an incredibly salient canvas. So it’s no surprise that we use complexion as a diagnostic marker for taxonomic purposes. The ancient Greeks correctly observed that the peoples of southern India have dark skin like Sub-Saharan Africans (“Ethiopians”), but that their hair is not woolly. Islamic commenters regularly referred to South Asians as “black crows”, while European observers of the 17th century noted that the ruling class of Indian Muslims tended to be white (i.e., mostly Turkic and Iranian in provenance) while the non-elites were black (descendants of Indian converts).*

Luckily, for a characteristic that we’re fascinated by, pigmentation has been reasonably tractable to genetics. As early as the 1950s human geneticists using classical methods of pedigree analysis predicted that pigmentation was polygenic, but that most of the variation was due to a small number of loci (see The Genetics of Human Populations). In particular, they focused on families of mixed European and African ancestry in British ports with known pedigrees.

When genomic methods came on the scene in the 2000s, pigmentation was one of the first traits that yielded positive GWAS hits as well as population genetic findings related to natural selection. In Mutants, written in the middle aughts, the author observed that there wasn’t much known about the basis of normal human variation in pigmentation. This all changed literally a year after the publication of this book. By the middle of 2006, a review paper came out with the title, A golden age of human pigmentation genetics. The reason this paper was written is that a host of studies on European populations had identified several loci which explained a substantial proportion of the intercontinental difference in pigmentation between Africans and Europeans.

But note the qualification in terms of the populations. As you can see from the figure at the top of this post the vast majority of the study of pigmentation genetics has been performed on Europeans. The figure is from a very comprehensive review, Shades of complexity: New perspectives on the evolution andgenetic architecture of human skin. I recommend all readers of this blog to check it out (the link is not paywalled), because it does a great job of covering all the bases.

First, it turns out that there are probably as many as 50 loci implicated in skin color variation. Focusing on Europeans, and admixtures between Europeans and West Africans, resulted in a major ascertainment bias and a fixation on a few loci and a few variants within these loci. This was probably the reason that the original pedigree analysis inferred such a small number of loci as well.

Second, one of the major issues with pigmentation is that a core set of genes implicated in variation in melanogenesis seem to have been targeted by selection or been subject to drift again and again, but the mutations within those genes may differ. For example, the locus implicated in blue vs. brown eye-color variation in Europeans is also associated with skin color difference in East Asians, but it is at a different SNP.

Third, African variation is a big part of the story, and it looks as if a lot of the variation in pigmentation in modern populations that have been the targets of selection in northern Eurasia may have been segregating in the ancestral African populations. In other words, some African populations may have carried “light” allele variants at low frequencies, and the difference in phenotypes of some Eurasians may simply be the concerted shift in allele frequencies across many loci. Additionally, there is also selection for darker variants in some African groups, such as the Nilotic people, as well as lighter variants in others, such as the indigenous people of southern Africa.

Fourth, there’s still no comprehensive selection story (not much definitive beyond what I reviewed eight years ago). The authors point out that new work shows in India only 12% of the pigmentation variation is due to differences in radiation exposure, but 42% is due to caste. It is suspicious to me that all of these pigmentation loci often show up as positive hits on selection tests…it is hard for me to think that pigmentation is not being targeted. But, it is not implausible that there could be secondary selection targets due to pleiotropy on these genes. The authors point out that there is no evidence for a universal cross-cultural sexual dimorphism, but there is some local evidence. Please note that sexually dimorphic characteristics take about an order of magnitude more time to evolve, because the sexes have to express the trait differentially despite having the same basic genetic character, so the recent selection events are unlikely to be able to drive such a change.

Young boy with typical blond hair of Lajamanu, at the edge of the Tanami.

It’s clear from this review that a lot of the work in the next decade, the real golden age of pigmentation genetics, is going to involve non-European populations. In particular, I have long been fascinated by the fact that among non-Europeans, blondism seems to be a feature of some Oceanian populations. The genetic basis of this trait has already been established in Solomon Islanders, but I am curious if it is the same among the Aboriginal people of Australia. Some of the populations in central Australia have long been well known to exhibit this trait, especially in children and women. If it’s the same mutation and haplotype as in the Solomons, then it is a characteristic ancestral to the original Oceanian meta-population.

The yield of this research is relatively straightforward. In forensics, the methods will continue to get better as we have more results from non-European populations. And the evolutionary patterns yielded by tests for selection will be very informative in understanding the adaptive pressures faced by our ancestors. For whatever reason, pigmentation genes get targeted over and over.

* Immunaeul Kant observed correctly that the Parsis of Bombay were white, not brown, in his attempt at racial anthropology.

9 thoughts on “The golden age of pigmentation is yet to come

  1. At its base it seems to be vitamin D vs skin cancer and folic acid.
    This base can be altered by cultural adaptation in nutrition and clothing for example.
    From this altered or unaltered base there seems to be social and sexual selection in favour of lighter skin tones. So in a lot of cases the natural pressures seem just to prevent or weaken the tendency towards lighter coloration.

    Like always there are different cultural norms for different people and oppsing trends in some cases probably (Nilotes?), but globally and especially in mixed people or even unmixed with obvious variation, the trend is there.

    Apart from that, tribal cultural norms for social and sexual selection might have been very important, favouring once established ideals for physical, even mental traits in given population.
    If someone deviated positively or negatively from the average of the group in this respect, how could this not have an impact on the reproductive success of am individual? Especially in bigger, successful groups with a solid subsistence, not at the verge of extinction.

  2. You mean old I guess. Not sure about skin cancer being completely unimportant. At least a smaller effect should have been there. Even if just your grandparents looking like having leprosy, it wont help your clan.

    Also, strong sun burns and non-lethal unaesthetic skin changes could have been an issue probably. Definitely no advantage under more extreme conditions, but mostly for quite depigmented people probably. So not that important on a global scale.

  3. no, i mean young. selection is strong when people die young and hit reproductive value. that’s why folate+neural tube defects is a big possibility (though not empirically totally validated).

    yes, albinos die young in tropical env. due to skin problems. but they’re mendelian mutations. it’s pretty clear that people didn’t “jump” to being light-skinned. so doubt that skin cancer etc. was major driver after the initial ‘darkening’ after loss of fur.

  4. Thanks for the heads-up on “Of the Different Races of Human Beings” – did not know Kant dabbled in that area. Outmoded race theories are always fun.

    (To his point, a Dutch couple acquainted with my Bombay Parsi friend in Boston misidentified me as her brother.)

  5. “Immunaeul Kant observed correctly that the Parsis of Bombay were white, not brown, in his attempt at racial anthropology.”

    In the recent movie, Bohemian Rhapsody, it was kind of jarring, that Freddy Mercury’s parents were “brown Indians”, although they stated in the movie they were Parisis, and Freddy, being played by the Egyptian Copt actor, Rami Malek, was far lighter than his entire family. Obviously with the genetic diversity in India, it is not exactly strange that a person can be lighter than most of their family members, but in the case of the Parsis, it required a greater suspension of disbelief.

  6. @ Dragon Horse – maybe not an issue for most, but even watching Peyman Moaadi go from ‘white’ Persian in A Separation to ‘brown’ Punjabi/Sindhi in The Night Of required some suspension of belief for me.

  7. Does this suggest that with crispr technology and in vitro fertilization mothers might be able to choose the pigmentation of their babies in the near future?

  8. The Pharrell misidentification is pretty funny! Honestly though he looks a lot more (east) Asian than you do African. He looks kind of San-like so maybe it’s just an ancient phenotype that’s persisted… on the other hand, you don’t see too many African-Americans that look quite so Asian.

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