Race is skin deep

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A fascinating paper just came out in Science, SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Heather L. Norton is one of the authors listed, so she knew very well what she was talking about when she suggested that there was far more to skin color variation than MC1R. Here is the eye popper from the text: “Based on the average pigmentation difference between European-Americans and African-Americans of about 30 melanin units (33), our results suggest that SLC24A5 explains between 25 and 38% of the European-African difference in skin melanin index.” I have pointed to models before which suggest ~4-5 loci that control skin color, this work does nothing to falsify that, but, it does show that between populations the variation in coloration in humans might be due to alleles of large effect which are differentially fixed. Evaluated over the whole species it is also certainly true that various alleles account for a different percentages of the genotypic component of variation, with many small effect modifier alleles likely hovering in the background of populations which are fixed for alternative alleles of large effect. Another important point is that the authors point out that both Africans and East Asians exhibit the ancestral allelic state, while Europeans are derived (a mutant descendent form), so the implication is that light skin is generated in East Asians by alternative genetic conformations. I have already pointed out that East Asians seem to be under strong selection, and moving toward fixation for Arg163gln MC1R allele (in contrast, Europeans are highly polymorphic for this locus). This points to the reality that evolution, or precisely, selection, explores a large phenotype & genotype space with multiple fitness peaks, and the expected outcomes might be random in nature when the options are constrained to the various peaks. The title of the post comes from the author’s observation that “This region [of the HapMap -R], which contains several additional SNPs with high-frequency differences between populations, was the largest contiguous autosomal region of low heterozygosity in the European (CEU) population sample…This pattern of variation is consistent with the occurrence of a selective sweep in this genomic region in a population ancestral to Europeans.” The low heterozygosity seems to be due to powerful directional selection which dragged a large number of adjacent SNPs within that haplotype block to fixation.

Finally, I want to add that this is a cool paper partly because of its broad methodological scope. Instead of just scanning the HapMap the authors also confirmed the developmental genetic expression via an animal model, zebrafish, which seems to exhibit the same variation in coloration on this locus as our own species. As they say, nature works with what it’s got, we’ve seen this with Foxp2, which shows up in derived form in humans, birds and whales (highly vocal species).

Anyway, the abstract:

Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.

Here is an easier to digest piece in The Washington Post, Scientist s Find A DNA Change That Accounts For White Skin (the title isn’t true of course, there are East Asians with white skin). And Nick Wade is on it of course. Thanks to Abhi & Theresa for the tip. You can find a PDF of the paper as “whiteskin” in the forums.

Update: NPR has a nice summary. People seem interested in this topic.

Addendum: Check out William Saletan’s idiotic comment:

A single gene makes whites paler than blacks. Until 20,000 to 50,000 years ago, everyone was black; then a mutation in this gene created white people. Reactions: 1) Don’t talk about racial genetics; it encourages racism. 2) If color comes down to one gene, doesn’t that minimize its significance? 3) Did whiteness spread in Europe because it made people healthier, or because it made them more sexually attractive?

Saletan might have been tongue-in-cheek, but if he is he’s only perpetuating public stupidity (something that doesn’t need any reinforcement, thank you very much). First, less than half of the color variation even between Europeans and Africans is accounted for this gene, i.e., it is a necessary condition for “whiteness” (in the European sense), but it is not a sufficient condition. Living in an east coast metro area his model of a black-white dichotomy (i.e., the stories clearly suggest that East Asians lack the derived variant, but they aren’t black to my knowledge) in any conception of race pops up (if ($race != white) { $race = black}). Second, it makes the standard conflation of skin color with populational identity. This map makes it clear that skin color tends to track latitude far more than the combination of latitude & longitude that would imply a tight correlation with geographical populations. If you step outside the black-white world skin color can not predict populational identity very well (except perhaps at the very fair end of the range where Northern Europeans are alone). And as for reaction #2, what idiots actually said anything like this? That is a contention so bizarre that it seems to have been produced by a 3rd grader (I’m expecting to falsified as to the expectation of chronological age). I wouldn’t expect much from Saletan, but he writes the “human nature” column for Slate. How can I get a cushy gig like that???

Addendum II: Check out this post from a few years back on altitude adaptation to see what I mean about stumbling upon different fitness peaks via different strategies. Also, consider that many genes have pleiotropic effects, that is, they are implicated in a multitude of genetic pathways and influence many traits. There are many background assumptions operating when one says that locus x has fitness effect y on population z. Consider that perhaps light skin in the generality is a phenotype that is advantageous at higher latitudes, while dark skin is advantageous at lower latitudes. Since to the first approximation humans are creatures of Africa it makes sense that we would have fixed or constrained toward expression of genes that influence skin color toward a dark optimum. As non-Africans are a subset of Africans it seems plausible that the ancestral dark inducing forms of the genes will be shared. On the other hand, as the constraint for dark skin is released, because selection no longer favors it, the genes will start stumbling randomly in various directions via mutations. In the case of Europeans the MC1R locus seems to have walked in a random fashion and diversified greatly1 (30 alleles of greater than 1% frequency). On the hand, in East Asians the MC1R allele seems to have been selected toward one particular form that differs from the ancestral variant, in other words, constraint that limited the fitness toward those bearing the ancestral dark skin inducing allele(s) was released, but unlike Europeans selection now operated on a different allele and constrained diversification. This new finding makes that more intelligible: Europeans were given license to explore the range of MC1R variants because another locus was sufficient in hastening the induction of a light skin phenotype. Selection operates on genotype via phenotype, so the phenotype is sufficient to allow the individual to be fit and reproduce the genes, it is irrelevant what that particular conformation of genes that results in said phenotype is. An important point I am leaving out of this is that it is likely that MC1R has other fitness effects (recall the finding that redheads might be more sensitive to pain), and it is likely that this new locus is also implicated in other phenotypes, at least indirectly. In other words, loci don’t explore the fitness landscape by their lonesome, but only in the context of changes and conditions on other loci.

1 – Negative frequency dependent sexual selection is another way to generate diversity. Hard to falsify though, and usually neutrality is assumed to be a legitimate null hypothesis.



  1. “I wouldn’t expect much from Saletan, but he writes the “human nature” column for Slate. How can I get a cushy gig like that???” 
    Tell educated people what they want to hear. Usually does the trick.

  2. You’ll notice that all the critics assume that the black Melanesians in “King Kong” are Africans, even though neutral gene analysis suggests they are among the least closely related people on earth. 
    By the way, do we really know that everybody was black originally, instead of brown, or yellow-brown like the Bushmen?

  3. By the way, do we really know that everybody was black originally, instead of brown, or yellow-brown like the Bushmen? 
    [suppression of cynical subtext commentary off] 
    of course steve, everyone knows blackness is the ‘primitive’ (ancestral) state. black africans have been around since the genesis of human kind, everyone else is simply an improvement upon black africans, though europeans are the most improved of all, that’s why they need to carry the white man’s burden of perpetual racism because only they are morally accountable toward the gods of PC. 
    [suppression of cynical subtext commentary on] 
    in all seriousness, the everyone-was-once-black hypothesis is now spun as an affirmation of the unity of our species. but it was once an assumption grounded in the idea that blackness was the primitive ancestral condition which other races, whites (and to a lesser extent east asians), ascended on up from on the great chain of being. the simplistic background assumptions (including other indicators like hypodescent) remain, the values simply differ….

  4. Steve, 
    Depends what you mean by everybody? Are you referring to the Out-of-Africa population, or ones that came before that. 
    From what I gather, most Africans weren’t “Black” even a few thousand years ago, but only after the Bantu expansions did most become black or at least dark brown.

  5. From what I gather, most Africans weren’t “Black” even a few thousand years ago, but only after the Bantu expansions did most become black or at least dark brown. 
    well, it seems that the evidence does point to the reality that the ancestral post-fur condition for humans is some form of dark brown. that being said, there is a problem in that the media elite tends to easily slip between black-as-a-trait and black-as-a-race. this is made all the more confusing by the race-doesn’t-exist-black-skin-is-just-a-feature gibberish.

  6. Likewise it would seem that populations of South East Asia were considerably darker than they are today, only a few thousand years ago – but with the demic diffusion of the Chinese agriculturalists, they have become lighter.

  7. paul, i think the term chinese confuses. the thai speaking population of thailand is obviously related to (and somewhat descended from) the dai speakiing ethnic minority of southern china. if there was a demic diffusion, there was likely one that preceded the rise of the han. the reality is that southern china (south of the yangzi) was only properly sinicized after 300, and only full by around 1500. so speaking of a chinese influx to southeast asia (excluding the overseas chinese, who do have a long term residence) is not accurate.

  8. Yes, you’re right, in that the Han Chinese, pushed the indigenous Southern “Chinese”, into South East Asia, ahead of their advance – I was merely using a geographical shortcut, which probably confuses!

  9. OT question: what ocean is skull island [king kong] supposed to be in?

  10. Speaking of King Kong, why did the natives make the gate so big if they wanted to keep him on the other side?

  11. rikurzhen, chimpansea?

  12. the everyone-was-once-black hypothesis is now spun as an affirmation of the unity of our species. 
    Press Release 
    Museum of the African Diaspora  
    SAN FRANCISCO, November 13, 2005: The Museum of the African Diaspora (MoAD) is dedicated to celebrating the universal connection of all people through our association with Africa?the cradle of humankind. 
    Whether we live in India, Fiji, Germany, France, Spain, Mexico or the United States, everyone is part of the African Diaspora, literally the scattering of people from their homeland ? as Africa is the original birthplace of us all. 
    MoAD will examine our ancient connection to Africa, as well as explore the more recent dispersal of millions from Africa, through the Middle Passage. Art will be used as the catalyst for exploration and discussion of new ideas to help us better understand and appreciate our diversity and the interconnectedness of all humanity. Through programs focused on art, history and culture, MoAD will help to change the way we view the modern world and our global family. 
    MoAD has been in development for ten years and is located at the corner of Mission and Third streets in San Francisco. Opening to the public on December 3, 2005, it is located within the first three floors of the new five-star St. Regis Hotel and Towers, near the San Francisco Museum of Modern Art, the Moscone Convention Center, the Yerba Buena Center for the Arts, the Martin Luther King Memorial, and the California Historical Society. MoAD will be centered in one of America?s busiest cultural crossroads, where millions of people visit each year. ”  

  13. By the way, do we really know that everybody was black originally, instead of brown, or yellow-brown like the Bushmen? 
    This would seem to suggest that the original humans, however defined, were not black: 
    “The intense selective pressure that drove the version to become universal in Europeans may have included sexual selection. [comment: may have? would have to have, right?] 
    In Africa people are much darker than they need to be for UV protection, so to me that screams sexual selection,” Dr. Shriver said. Black skin, in other words, may have been favored by men and women in sexual partners, just as pale skin may have been preferred in sexual partners among Europeans and Asians.
    That’s how I interpret it.

  14. agnostic –  
    The notion that William Saletan tells “educated people what they want to hear” is easily the stupidest thing I’ve read today.  
    Cripes. The man’s whole career is based on telling privileged liberals what they don’t want to hear: that they’re losing the culture wars, that they might actually have to critically re-evaluate their position and take their opponents seriously. 
    Yes, he made a dumb comment in a lightweight column. If you’d seek to do better, though, you may want to read a little before making uninformed comments of your own.

  15. I realize that the same skin color map appears in many physical anthropology textbooks (including Cavalli-Sforza’s). I should point out, however, that this map was originally concocted by the Italian anthropologist Renato Biasutti (Le razze ei popoli della terra) back in 1940. At that time, only a few spectrophotometric studies of skin color had been made (almost all of them were done in North America) and the earlier studies using color tops or color panels were also few in number. Most of the map is simply guesswork and hearsay. This is especially so for North and South America. There is no serious evidence that Amerindian populations differ in skin color.