Gene Expression

Fear of a white planet

i-827d3a15d7fdaef477915d6671a9da45-barackraila.jpgOne of the main facts about American life is hypodescent, “the practice of determining the lineage of a child of mixed-race ancestry by assigning the child the race of his or her more socially subordinate parent.” Barack Obama & the Kenyan politician Raila Odinga (who, probably falsely, claims to be Obama’s first cousin) are both “black,” despite the fact that when compared to each other Obama’s substantial European ancestry is rather clear. I recall years ago watching the Oprah Winfrey television show where they were discussing the issue of self-hatred with a young black woman who was attempting to become impregnated by a white man (any white man) so that her children would “look white” and be beautiful. An adoption counselor rose up and told this young woman that her agency had many biracial children who they were attempting to place, and “none of them look white, they all look black.” The clear and present background axiom here is that the power of black phenotype ensured the futility of this young woman’s “quest.”

In hindsight it seems to me that these perceptions are mostly socially constructed. Years ago I had a friend who was of mixed European and Japanese origin who was raised in Japan. I recall once that someone stated that they were surprised that her father was a white American, as she looked “totally Japanese.” My friend got irritated, and replied that that was rather interesting as growing up in Japan people would tell her how white she looked. Obviously these sorts of gestalt perceptions are scaffolded by social context; in Japan my friend’s white characteristics were very salient, while in the United States her Japanese ones were. The norms of reference were socially conditioned, so the scaling of phenotype did not have a linearly proportional effect on perception in identity. In other words, a rather small absolute physical deviation from the social norm can elicit strong relative perceptions of difference.

All that being said, phenotypes do not emerge just out of our own minds, rather, they often genetically controlled. I have posted a fair amount on skin color because within the last 5 years we’ve really figured out how it shapes the normal range of human variation. In short, about half a dozen loci seem to account for nearly all the between population differences in complexion. But I was talking to a friend today and explained how I realized recently that the nature of the genetic architecture was actually rather counterintuitive from an American perspective. In short, whiteness is dominant!

More precisely, I noticed that two of the loci of largest effect, SLC24A5 and KITLG, manifest a dominance component in terms of lightening skin color. In other words, if you took a West African and a Northern European their offspring would exhibit a lighter complexion than you would expect from simply blending the two phenotypes. Here’s a table to illustrate what I’m talking about:

Genotype M Index decrement
   
SLC24A, rs1426654, GG (homozygous African) 0.0
SLC24A, rs1426654, AG (heterozygote) -7
SLC24A, rs1426654, AA (homozygous European) -9.6
   
KITLG, rs642742, AA (homozygous African) 0.0
KITLG, rs642742, AG (heterozygote) -4.3
KITLG, rs642742, GG (homozygous European) -6.4
   

In the case of SLC24A5 an ancestral guanine base mutated into an adenine at a particular position. For KITLG the reverse occurred. These changes resulted in an operational loss of function in relation to the melanin production for humans so that skin became lighter, and the variant was picked up and driven toward fixation among Europeans by natural selection. The table above illustrates the values of decrease in M index as you substitute an allele on the locus; as you can see, there are diminishing returns. This means that the heterozyogte state is closer to one than the other when taken against a genetic background. Fortunately for us I don’t need to get into statistical assumptions about averaging when comparing Europeans and Africans when it comes to skin color genes; the two populations have very different genetic backgrounds in reference to the variance we’re interested in. For SLC24A5 Europeans and West Africans exhibit disjoint allelic states, almost all Europeans carry the derived variant, while almost all Africans carry the ancestral. For KITLG the numbers are not as extreme, with each population having an 80-95% proportion for the major allele, but the minor allele frequencies are rare enough that its homozygotes are extant on the order of 1%. In other words, if an African and a Northern European produced offspring chances are they would be heterozygotes on these loci.

We know that West Africans average around 60 for their M Index, while Europeans around 30. That’s a 30 unit spectrum. Adding up the unit effects above you see that SLC24A5 and KITLG account for 16 of them, in other words, over half of the between population variation in skin color in regards to West Africans and Europeans can be attributed to differences on these two genes! Let’s assume that additivity and independence apply to the 14 units not accounted for by these two genes. What does the dominance effect manifest on SLC24A5 and KITLG tell us in regards to the expectation for the offspring? I’ll avoid descripition and make recourse to illustration:

i-3efdf8c2c2a7dc0ee076392b652ccb5d-outcomeskin.jpg

This surprised me. The reason is that the emergence of light skin seems to be a case of a loss function mutation. Europeans and East Asians have been subject to sweeps which selected for lighter skin within the last 20,000 years, and these sweeps tend to be independent. This is what you would expect from simple loss of functions which constantly occur in the genetic background of the population, but are normally purified because they are deleterious. In contrast, the genetic architecture for very dark-skinned peoples is very similar; the skin color related genes of Bougainville Islanders show identity by state with those of Africans, though these populations are not closely related (Bougainville Islanders are more closely related to East Asians than the typical African since the former are both descended from a Northeast African ancestral population). It should be noted though that the dominance effect would definitely aid in the spread of these alleles through a population because of their immediate exposure to selection due to their strong expression in heterozygote genotypes.

I think this is all rather interesting because at least judging from emails I receive the general perception is that dark skin is a dominant trait. This is true, if you bin the phenotypes into “dark” and “white,” so that the latter only includes complexions around a narrow range of 30 melanin units. In contrast, when you examine the issue quantitatively it doesn’t turn out that way at all. At a coarse first glance a blending/additive model seems to be appropriate for modeling skin color as a quantitative trait, but upon closer inspection dominance effects need to be noted. Instead of being buried in a rising tide of color, a panmictic world would exhibit a stronger effect of au lait. Next time someone brings up the blondes going extinct meme, you might want to point this out (after explaining the nature of the expression of complex traits in diploid organisms first of course).

Note: The numbers I used for the back-of-the-envelopes here can be found in these papers….

SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

cis-Regulatory Changes in Kit Ligand Expression and Parallel Evolution of Pigmentation in Sticklebacks and Humans

Skin pigmentation, biogeographical ancestry and admixture mapping

Comments

  1. #1 DaleP
    May 21, 2008

    Thanks for this post, (mostly) answering such an important question that has been rattling around my mind for a long while, if not so clearly expressed. I’ve been reading most of your posts on this topic and not being able to understand all of it, but this pulls a lot together.

  2. #2 Lassi Hippeläinen
    May 21, 2008

    The “dominancy” of darkness may be due to visual perception. We humans are better at discerning shades of lightness than darkness. We are no night animals.

  3. #3 razib
    May 21, 2008

    The “dominancy” of darkness may be due to visual perception. We humans are better at discerning shades of lightness than darkness. We are no night animals.

    is this true? my understanding is grayscale perception are due to rods which work in the dark as well as light, not the color perceiving cones which give us our daylight vision.

  4. #4 John Prester
    May 21, 2008

    I recall years ago watching the Oprah Winfrey television show where they were discussing the issue of self-hatred with a young black woman who was attempting to become impregnated by a white man (any white man) so that her children would “look white” and be beautiful.

    Did this episode also have:
    1.) A white guy with dreadlocks who plays in a band and sings anti-racism songs
    2.) An Asian woman who got an operation on her eyes to remove the “epicanthal fold”
    3.) Lawrence Otis Graham – Fair skin black guy who had his nose operated on to narrow it
    4.) A cliched bald “angry black militant” who railed against all of them!

    I might be combining 2 episodes, but I believe this is the same one. I seem to recall the black woman wanting to get pregnant by a white guy, and Oprah brusquely swept her to the side and moved on to another guest.

    This all proves the saying: “Youth is wasted on the young!” If only I was reading books, instead of watching silly shows such as Oprah Winfrey and Morton Downey back in my college years of 1986-1991!

  5. #5 razib
    May 21, 2008

    i remember graham. not the others. i didn’t watch the whole show. i don’t recall ever watching a whole show of oprah….

  6. #6 Luis
    May 21, 2008

    Very interesting and ample meditation. I read it with unusual pleasure (vivid interest).

    Certainly to me Obama doesnt look black, or at least not just black, but I know most US Americans know of no distinctions nor gradations in this aspect.

    It reminds me of my childhood surprise at the use of the term “black” for people who in my eyes looked clearly brown. Most black African people look brown, not even close to real black, there is also a lot of tonal variation among them: near black (some Sudanese), dark brown (most common maybe), middle brown (often reddish) and even quite light pinky brown (just saw it among some Fang women). So my nitty-picky young self was not the least happy about that oversimplification. I also disliked “white”, beige being much more correct in most cases.

    As for the visual perception, I just noticed in the illustration of the white-black strip that I do percieve black color in about 1/4 of it, while white only apears to occupy some 5% (10% being generous). So Lassi’s comment seems to make sense. And maybe that’s a reason why the mixed offspring is technically slanted to the white, while visually not so much.

  7. #7 razib
    May 21, 2008

    re: grading, i didn’t look too closely toward how it was scaled. that might be an issue. but point taken.

  8. #8 Miss Cellania
    May 21, 2008

    I think people rely on other cues more than skin color to identify race. Mixed race children I know (black and white parents) have quite light hair, skin, and eye color but have black features and hair texture. When people in my small town meet my daughter (who is from India) they don’t know how to classify her, since she has very dark hair, skin, and eyes but caucasian features and hair texture.

  9. #9 Kimmie
    May 22, 2008

    This is silly saying that one race is dominant over another. Clearly genes can be stronger in one family than another. For instance, I know a black couple who have two children with sandy brown hair and dark blue eyes. Neither parent has a living relative that recalls having a white family member. I also know a white family who had children who are much darker than they are with thick curly hair. Sometimes genes go back much futher than your oldest living relative can remember, but that doesn’t mean that your kids won’t look like the relatives that you did not know existed. To just assume that white is dominant just because some kids who are born to white and black parents are of a lighter complexion doesn’t mean that white is always dominant. In fact, those children can grow up to have extremely dark children even if they are with two parents who look completely white…it has happened before!

  10. #10 Lassi Hippeläinen
    May 22, 2008

    Razib: “my understanding is grayscale perception are due to rods which work in the dark as well as light, not the color perceiving cones which give us our daylight vision.”

    It’s a bit more complex than that. And I didn’t mean greyness in exact terms, more like a form of lightness. Sorry about that.

    The human eye is fairly good in terms of dynamics. Using photographer’s terms, bright daylight can be at LV16, but thanks to the rods, we can still see in moonlight at about LV-4. That is 20 orders of 2, or about 1:1’000’000. However, the darker it gets, the less is there resolution. The first thing to go is colours.

    Skin colour is meaningful only in daylight. Therefore it is observed with the cones that are good at discerning colours, but not shades of darkness.

  11. #11 Cecilia
    May 29, 2008

    These article and comments are overly simplistic. I have five children. My ancestry is mixed, in that my father’s father was a dark Roman (curly hair, brown skin, dark brown eyes), who could be easily confused with an Arab, about 5’7″, his mother was from the Adriatic coast, and had gold skin, very dark eyes, dark, curly hair, 4′ 10″. My maternal grandmother was “white” (mixed European descent), light hair, green/blue eyes, fair skin with freckles, 5′ 2″, grandfather half “white”, half “dark German” (Jewish descent), and he was olive complected, wiry black hair, dark eyes could easily be confused with an Arab, 6′. I appear to be white, so far as my complection goes, but I have features that are Italianate, I am 5′ tall. My husband is half Spanish, half Apache Indian (the Apaches I know refer to themselves as Indians, hence my use of the term), he has light brown skin, very dark eyes, thick, straight black hair, is 5′ 3″. My mother-in-law was a rich brown color (like milk chocolate with cinnamon), thick, straight black hair, almond shaped black eyes (same color irides as pupil), 4″ 11″, father-in-law appeared to be white (same as me, light eyes, light skin, Mediterranean features), 5″ 5″. Of my children, the eldest is tall, deep golden skin, blue eyes, dark brown hair (was blonde as a child), 5′ 10″, next has Italianate features, is very fair complected, green eyes, brown hair, 5′ 7″, my daughter has nearly black, very thick, slightly wavy hair, medium olive skin, and Mediterranean features, 5′ tall, next son has very light olive skin, with a few freckles on his nose, warm brown almond shaped eyes, straight very dark hair (not thick, just like a typical “white” person, I suppose), 5′ 5″, and the youngest has deep, dark, reddish gold skin, large almond shaped eyes, is 5’3″, has thick, wavy hair, and other features that are obviously taken from his Apache grandmother. 5 children. Same parents. 1 white looking kid, 1 Italian looking kid, 2 Italian/Hispanic looking kids, 1 Apache looking kid. Genetics is an interesting science, but all the color gradiation scales in the world can’t accurately predict what a child will look like. More importantly, they are all incredible people.

    The article was a bit disturbing, as it leads the reader to believe that “when you mix these people, you will get this person”, which is not only untrue, but virtually impossible to accurately predict. There are significant variations, even between full siblings.

    Perhaps the most disturbing thing was the woman who wanted to be “impregnated by any white man” so that her children would be beautiful. All children are beautiful. People who think they must be a certain color to attain beauty are ugly.