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.

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Complex evolution of pigmentation in modern humans

Last fall Crawford  et al.Loci associated with skin pigmentation identified in African populations, was published in Science and made a huge splash. As I’ve been saying recently, and most people agree, much of the remaining “low hanging fruit” in human evolutionary genomics, and to some extent, human medical genetics, is going to be in Africa on Africans. From an evolutionary perspective, that’s probably because from a gene-centric viewpoint most of our recent evolutionary history was within Africa. As a friend once told me, “most of the last 200,000 years is about the collapse of ancient population structure.” This goes too far, but at least it gets at something we’ve not been too conscious of.

Top left clockwise: Luo Kenya, Khoisan, South Asian, Arrernte Australia

Crawford  et al. was important because it was a deep dive into a topic which has been understudied, the variation of pigmentation genetics within Africa (also see Martin et al.). The fact that there is variation in pigmentation within Africa should not be surprising, though some people are surprised that there is variation in pigmentation within Sub-Saharan Africa. But anyone who has seen photos of San Bushmen, knows they are very distinct from South Sudanese, who are very distinct from West Africans. As documented by both Crawford  et al. and Martin et al. some of this variation is likely novel.

By this, I mean there has been backflow of the derived Eurasian variant of a mutation on SLC24A5. Arguably the first major human pigmentation locus of the “post-genomic era”, its discovery was enabled by its huge effect in explaining variation among Eurasian populations and their differences from African groups. In Crawford  et al. the author observes within Africans nearly ~30% of the trait variance was due to four loci, with ~13% due to SLC24A5. In earlier work comparing just people of European and African descent, SLC24A5 variance explains closer to 30% of the pigmentation difference. It seems that pigmentation effects genetically exhibit an exponential distribution. A small number of loci have a large effect, and a numerous number of loci have small effects.

Distribution of rs1426654 at SLC24A5

The results from Crawford  et al. and Martin et al., a naive inspection of the modern distribution of the derived rs1426654 allele, and ancient DNA, seem to indicate a mutation associated with lighter skin emerged after 40,000 years ago. After the expansion of non-African humans, and, the divergence between eastern and non-eastern branches of non-Africans. A common haplotype around this mutation suggests that it wasn’t part of the ancestral “standing variation” of the human lineage. Ancient samples from Scandinavia, the Caucasus, and modern samples from Eurasia and from Africa, all exhibit the same pattern, suggesting recent common descent.

And though a mutation on rs1426654 is associated with lighter skin, it does not produce white skin. I have the homozygote derived genotype on rs1426654, as does my whole nearby pedigree. All of us have brown skin, to varying degrees. And interestingly, the locus around rs1426654 seems to be under strong selection in both South Asia and Africa, including East Africa. This makes me somewhat skeptical that there is a simple story to tell on this locus in relation to skin pigmentation being the driver here.

Let me quote from  Crawford  et al.:

Most alleles associated with light and dark pigmentation in our dataset are estimated to have originated prior to the origin of modern humans ~300 ky ago (26). In contrast to the lack of variation at MC1R, which is under purifying selection in Africa (61), our results indicate that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 have been segregating in the hominin lineage for hundreds of thousands of years (Fig. 4). Further, the ancestral allele is associated with light pigmentation in approximately half of the predicted causal SNPs…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 after human ancestors lost most of their protective body hair, though these ancestral hominins may have been moderately, rather than darkly, pigmented (63, 64). Moreover, it appears that both light and dark pigmentation has continued to evolve over hominid history….

For over ten years it has been clear that very light skin in eastern and western Eurasia are due to different mutational events. Crawford  et al. give us results that indicate this pattern of evolutionary complexity is primal and ancient.

But there is often a tacit understanding that the selection process is the same over time and space. Something to do with protection from UV light and also synthesization of vitamin D at higher latitudes. So this paper that just came out definitely piqued my interest, Darwinian Positive Selection on the Pleiotropic Effects of KITLG Explain Skin Pigmentation and Winter Temperature Adaptation in Eurasians. The authors looked at a lot of variants in KITLG with a focus on East Asians. They confirmed that there were at least two selection events, one just around the “Out of Africa” period, and possibly another one later, during a period when West and East Eurasians were genetically distinct.

This section is very intriguing: “Besides pigmentation, KITLG is also involved in mitochondrial function and energy expenditure in brown adipose tissue under cold condition (Nishio et al. 2012; Huang et al. 2014). We demonstrated that winter temperature showed a much stronger correlation than UV for rs4073022.” Earlier the authors review work which suggests that large melanocytes are much more susceptible to damage due to cold than than smaller ones. Dark-skinned individuals tend to have large melanocytes (and more of them!). The KITLG locus does a lot of things; some of you may know its relationship to testicular cancer.

What  Crawford  et al. tells us that there seems to have been recurrent and sometimes balancing selection around loci implicated in pigmentation for hundreds of thousands of years. What ancient DNA is telling us is that the genetic architectures we take for granted as typical across much of Eurasia are relatively novel. But, I think people are perhaps taking the implications of modern genetic architecture too far in predicting the variation of characteristics in the past. Even the best genomic predictors seem to account for only around half the variance in pigmentation. “Ancestry” accounts for the rest, which basically means there are many other loci which are not accounted for. It is not unreasonable to suppose that ancient northern Eurasian populations may have been light-skinned due to genetic variants which we are not aware of.

Of course, there are people at high latitudes who retain darker complexions. From what we know the Aboriginal people of Tasmania were isolated for about 10,000 years at the same latitude as Beijing and Barcelona, and yet their skin color remained dark brown. In contrast, Martin et al. report that Khoisan people who lived 10 degrees further north, in a much sunnier climate, were selected at loci that strongly correlate with lighter skin.

I think it is safe to say that in the near future we will close in on much of the reamining genetic factor accounting for variation in pigmentation in modern populations. It is polygenic, but almost certainly far less polygenic and more tractable than height or intelligence. But the story of why humans have varied so much over time, and why loci implicated in pigmentation are so often targets of selection in some many contexts, remains to be told.

The architecture of skin color variation in Africa

Baby of hunter-gatherers in Southern Africa

Very interesting abstract at the ASHG meeting of a plenary presentation,Novel loci associated with skin pigmentation identified in African populations. This is clearly the work that one of the comments on this weblog alluded to last summer during SMBE. There I was talking about the likely introduction of the derived SLC24A5 variant to the Khoisan peoples and its positive selection in peoples in southern Africa.

Below is the abstract in full. Those who follow the literature on this see the usual suspects in relation to genes, but also new ones:

Despite the wide range of variation in skin pigmentation in Africans, little is known about its genetic basis. To investigate this question we performed a GWAS on pigmentation in 1,593 Africans from populations in Ethiopia, Tanzania, and Botswana. We identify significantly associated loci in or near SLC24A5MFSD12TMEM138…OCA2 and HERC2. Allele frequencies at these loci in global populations are strongly correlated with UV exposure. At SLC24A5 we find that a non-synonymous mutation associated with depigmentation in non-Africans was introduced into East Africa by gene flow, and subsequently rose to high frequency. At MFSD12, we identify novel variants that are strongly correlated with dark pigmentation in populations with Nilo-Saharan ancestry. Functional assays reveal that MFSD12 codes for a lysosomal protein that influences pigmentation in cultured melanocytes, zebrafish and mice. CRISPR knockouts of murine Mfsd12 display reduced pheomelanin pigmentation similar to the grizzled mouse mutant (gr/gr). Exome sequencing of gr/gr mice identified a 9 bp in-frame deletion in exon two of Mfsd12. Thus, using human GWAS data we were able to map a classic mouse pigmentation mutant. At TMEM138…we identify mutations in melanocyte-specific regulatory regions associated with expression of UV response genes. Variants associated with light pigmentation at this locus show evidence of a selective sweep in Eurasians. At OCA2 and HERC2 we identify novel variants associated with pigmentation and at OCA2, the oculocutaneous albinism II gene, we find evidence for balancing selection maintaining alleles associated with both light and dark skin pigmentation. We observe at all loci that variants associated with dark pigmentation in African populations are identical by descent in southern Asian and Australo-Melanesian populations and did not arise due to convergent evolution. Further, the alleles associated with skin pigmentation at all loci but SLC24A5 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.

Much of this is not surprising. Looking at patterns of variation around pigmentation loci researchers suggested years ago that Melanesians and Africans exhibited evidence of similarity and functional constraint. That is, the dark skin alleles date back to Africa and did not deviate from their state due to selection pressures. In contrast, light skin alleles in places like eastern and western Eurasia are quite different.

Nyakim Gatwech

This abstract also confirms something I said in a comment on the same thread, that Nilotic peoples are the ones likely to have been subject to selection for dark skin in the last 10,000 years. You see above that variants on MFSD12 are correlated with dark complexion. In particular, in Nilo-Saharan groups. The model Nyakim Gatwech is of South Sudanese nationality and has a social media account famous for spotlighting her dark skin. In comparison to the Gatwech and the San Bushman child above are so different in color that I think it would be clear these two individuals come from very distinct populations.

The fascinating element of this abstract is the finding that most of the alleles which are correlated with lighter skin are very ancient and that they are the ancestral alleles more often than the derived! We’ll have to wait until the paper comes out. My assumption is that after the presentation Science will put it on their website. But until then here are some comments:

  • There is obviously a bias in the studies of pigmentation toward those which highlight European variability.
  • The theory of balancing selection makes sense to me because ancient DNA is showing OCA2 “blue eye” alleles which are not ancestral in places outside of Western Europe. And in East Asia there their own variants.
  • Lots of variance in pigmentation not accounted for in mixed populations (again, lots of the early genomic studies focused on populations which were highly diverged and had nearly fixed differences). Presumably, African research will pick a lot of this up.
  • This also should make us skeptical of the idea that Western Europeans were necessarily very dark skinned, as now we know that human pigmentation architecture is complex enough that sampling modern populations expand our understanding a great deal.
  • Finally, it’s long been assumed that at some stage early on humans were light skinned on most of their body because we had fur. When we lost our fur is when we would need to have developed dark skin. This abstract is not clear at how far long ago light and dark alleles coalesce to common ancestors.

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.

SLC24A5 is very important, but we don’t know why


The golden of pigmentation genetics started in 2005 with SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Prior to that pigmentation genetics was really to a great extent coat color genetics, done in mice and other organisms which have a lot of pelage variation.

Of course there was work on humans, mostly related to melanocortin 1. But more interesting were classical pedigree studies which indicated that the number of loci controlling variation in pigmentation was not that high. This, it was a mildly polygenic trait insofar as some large effect quantitative trait loci could be discerned in the inheritance patterns.

From The Genetics of Human Populations, written in the 1960s, but still useful today because of its comprehensive survey of the classical period:

Depending on what study samples you use variance on a locus of SLC24A5 explains less than 10% or more than 30% of the total variance. But it is probably the biggest effect locus on the whole in human populations when you pool them altogether (obviously it explains little variance in Africans or eastern non-Africans since it is homozygous ancestral by and large in both groups).

One aspect of the derived SNP in this locus is that it seems to be under strong selection. In a European 1000 Genomes sample there are 1003 SNPs of the derived variant, and 3 of the ancestral. Curiously this allele was absent in Western European Mesolithic European hunter-gatherers, though it was present in hunter-gatherers on the northern and eastern fringes of the continent. It was also present in Caucasian hunter-gatherers and farmers from the Middle East who migrated to Europe. It seems very likely that these sorts of high frequencies are due to selection in Europe.

The variant is also present in appreciably frequencies in many South Asian populations, and there seems to have been in situ selection there too, as well as the Near East. In Ethiopia it also seems to be under selection.

It could be something due to radiation…but the Near East and South Asia are quite high intensity in that regard. As are the highlands of Ethiopia. About seven years ago I suggested that rather that UV radiation as such the depigmentation that has occurred across the Holocene might be due to agriculture and changes in diet.

But a new result from southern Africa presented at the SMBE meeting this year suggests that this can not be a comprehensive answer. Meng Lin in Brenna Henn’s lab uses a broad panel of KhoeSan populations to find that the derived allele on SLC24A5 reaches ~40% frequency. Probably a high fraction of West Eurasian admixture in these groups is around ~10% being generous. Where did this allele come from? The results from Joe Pickrell a few years back are sufficient to explain: there was a movement of pastoralists with distant West Eurasian ancestry who brought cattle to southern Africa, and so resulted in the ethnogenesis of groups such as the Nama people (there is also Y chromosomal work by Henn on this).

Sad human with two derived alleles of SNP of interest

Lin reports that the haplotype around SLC24A5 is the same one as in Western Eurasia. Iain Mathieson (who is now at Penn if anyone is looking for something to do in grad school or a post-doc) has told me that the haplotype in the Motala Mesolithic hunter-gatherers and in the hunter-gatherers from the Caucasus are the same. It seems that this haplotype was widespread early in the Holocene. Curiously, the Motala hunter-gatherers also carry the East Asian haplotype around their derived EDAR variant.

I don’t know what to make of this. My intuition is that if a haplotype like this is so widespread nearly ~10,000 years ago recombination would have broken it apart into smaller pieces so that haplotype structure would be easier to discern. As it is that doesn’t seem to be the case.

And we also don’t know what’s going on withSLC24A5. Obviously it impacts skin color. It has been shown to do so in admixed populations. But it is hard to believe that that is the sole target of natural selection here.