Razib Khan One-stop-shopping for all of my content

October 5, 2011

Mixed-race people are mildly complicated

I was pointed today to a piece in the BBC titled What makes a mixed race twin white or black?. The British media seems to revisit this topic repeatedly. There are perhaps three reasons I can offer for this. First, it tends toward sensationalism. Even though the BBC is relatively staid, when it comes to science it converges upon the tabloids. Second, because the number of non-whites in Britain is relatively small, there is a higher proportion of intermarriages between minorities and the white majority (from the perspective of minorities). This is especially true of people of Afro-Caribbean ancestry. So of the proportion of minorities a larger fraction are recently mixed in Britain than in the USA. Finally, the United States has a more complex attitude toward race relations than the United Kingdom, because the former has traditionally had a large non-white minority while the latter has only had so since the years after World War II. I suspect that “black-white twins” stories would seem in bad taste on this side of the pond, and bring up certain memories best forgotten.

Now, there are fallacies, confusions, and misleading shadings, in the BBC piece. I’ll hit those first before reviewing what’s going on here when fraternal twins exhibit totally different complexions.


It starts out somewhat ludicrously: “Her son Leo has black skin and her daughter Hope, has white skin.” This is false in a precise sense. Leo clearly has medium to light brown skin (there are photos in the piece). What’s going on here is that Leo has some African ancestry, and because of the rule of hypodescent all people of African ancestry with a shade of brown skin, from nearly black to light brown are termed “black skinned.” This is not a trivial semantic elision. If Leo truly had black skin, very dark brown, than there’d be a lot of explaining to do, because the genetics would be somewhat mystifying. More on that later.

Second:

She was adopted when she was four years old, and her birth mother is Afro-Caribbean and her British birth father was white. Her DNA tests revealed that, genetically, she was exactly 50% African and 50% European.

This is very unusual, and the results suggested that Shirley’s mother had pure African roots, and that her ancestors must have moved from Africa to the Caribbean quite recently.

Not necessarily. Mixed-race people, especially those with recent admixture, don’t have their different ancestral components distributed equally across their genome. It may be that in the process of sampling chromosomes from this individual’s Afro-Caribbean mother she received almost none of the European quantum, perhaps localized to a few chromosomal segments. This “noise” in the process explains why I seem to carry an elevated proportion of East Asian ancestry in relation to both of my parents. I simply received genetic copies sampled from the more “East Asian” regions of my parents’ genomes.

Next:

“Our skin colour is determined by a number of gene variants – at least 20 variants, I would say, probably quite a few more than that,” says Dr Wilson.

This is complicated, but I’d say that the good doctor is misleading the audience. Skin color seems to be a quantitative trait where you can explain the vast majority of between population variation with only a few genes, at most six. When it comes to European-African difference variants at two loci, SLC24A5 and KITLG can account for well over half of the difference. It is true that there are many, many, genes that effect skin color, but there is a definite distribution where the vast majority of genes tweak the trait only on the margins. In other words, there may be 20 variants (there are more), but for good predictive power at the inter-population level you’re good to go with 4 or 5.

I specify inter-population level, because within populations the gene set which can allow you to predict variation may be slightly different, and you have to take into account sex differences. For hormonal reasons males seem somewhat darker than females in human populations. Additionally, people also are palest in their youth, and become darker as they age. Finally, some of the genes which explain differences between populations are invariant within a population. Therefore the genes which are of lower effect size move up the stack. So when it comes to European-African variation, the largest effect gene, SLC24A5, won’t explain anything within these two populations. That’s because it is fixed for alternative variants (the light vs. dark conferring variants). So the second effect size may move up to first effect size when you evaluate on a smaller grain (but if the second effect size is nearly fixed, then it might drop far down as well).

Now let’s move on to the common idea that darkness dominates over lightness:

As in a painter’s palette, in the skin the presence of pigment dominates the absence of pigment, so the fact that Hope is white is very unusual.

This is hypodescent popping up again. Though in the West we live in an anti-racist age, at least notionally, it is interesting how concepts and models from a white supremacist era remain operative, at least implicitly. The idea that whites are recessive to non-whites makes totally sense if you code anyone with visible non-white ancestry as non-white. Even if they are genetically more white than not. The rationale for this model was the idea that there is a reversion to the more “primitive” type. So a cross between a black and a white produced a black, and a cross between a Nordic and a Mediterranean produced a Mediterranean. Inferiority taints the purity of superiority.

Less ideologically if you classify skin complexion into white and non-white in a dichotomous fashion then you logically consign the non-white trait to dominance. For example, if nearly, but not quite, white skin is “dark,” then you make it very difficult for someone with a substantial number of pigment conferring alleles to produce a child with very light skin.

Finally, now that we have elucidated the genetic architecture of pigmentation to a great extent we can make assessments of dominance and recessiveness on a locus by locus manner. If you plot skin complexion darkness as a function of reflectance you can turn it from a dichotomous or discrete trait to a continuous one. So individuals can have a “melanin index,” an integer value equivalent to their position on a scale of lightness and darkness. Converse to expectations above it turns out that on the two largest effect genes explaining difference between Africans and Europeans the light alleles are more dominant than the dark alleles! In other words, if the two alleles had an equal effect you’d expect a value between the two in their homozygote state. As it is, the values tend toward higher reflectance (light) than dark. I would caution that terms like “dominant” and “recessive” can be highly subjective and dependent on how you code the trait, the nature of the population you sample from in a polygenic character, or even scale the of values. So in this case you notice that switching from a dichotomous code of white vs. non-white to a continuous value corresponding to reflectance flips the model from the light trait being recessive to the dark, to the dark being recessive to the light (albeit, only mildly).

Because pigmentation is controlled by only a few genes the state at these loci are poor proxies for total genome content. In plainer language mixed-race siblings won’t deviate too much in their ancestral quantum, but they can deviate a great deal in their physical appearance. In fact, because of the poor correlation the slightly “blacker” twin in total ancestry may actually look more like a white person, and vice versa.

Now let’s go back to first principles. We’ll make some simplifying assumptions to illustrate what’s going on easily. Take 6 genes which control skin color. Assume equal effect. Each gene comes in two variants. Light and dark. Two copies of light result in a value of 0, while two copies of dark result in 2. A copy of each results in 1. In other words, the alleles are additive across a locus. Also assume that the genes are independent. They’re not linked. So the value at each gene is independent of the other genes. Finally, assume that the genes’ implied values summed together result in a total pigmentation phenotype outcome. So they’re additive across loci.

To make even simpler let’s assume that the parents are F1 African-European hybrids. That means that one of their parents’ was European and the other African. So both share the same ancestry of recent vintage. As it happens Africans and Europeans are very different on pigmentation genes, so we can assume that these parents carry one light copy and one dark copy across the six genes. This means you’d expect them to be brown.

Since they are brown, wouldn’t their children be brown? No. Not necessarily. As per Mendel’s Laws each contributes contributes one gene copy at each locus. So for the 6 loci above each parent contributes one pigmentation gene. What does that mean concretely? I Already simplified things to produce an elegant outcome: the F2 offspring could be all light, all dark, or one copy of both, like their parents, at any given gene. To illustrate what I’m talking about, SLC24A5 is disjoint in frequency across Africans and Europeans. All Europeans have one variant, and all Africans have another. So the offspring of a marriage between an African and a European will be heterozygote on that locus. If they marry another person of similar background, homozygote light and dark genotypes will resegregate out at fractions of 25% each, with half the outcome being heterozygote as in the parental condition. In other words, there are a 25% probability of a F2 child of F1 hybrids being “white” at this locus. There are 6 loci. Assuming independent probabilities, you multiply out 0.256, and get 1 out of ~4,000 that the child will be white like their white grandparents.

I ran this as a binomial 10,000 times, and here’s the distribution I came up with:

The white and black offspring don’t show up because the number of outcomes is so rare in this model, but as you can see the median outcome is brown, like the parents. But the tails are significant. In other words, don’t be surprised if there’s a lot of variation among the siblings. But why should you be? If you know of people from populations where pigmentation alleles are segregating in polymorphic frequencies, such as Latin Americans and South Asians, you are aware that different siblings can look strikingly different when it comes to complexion. Though I guess that’s a new insight for the British….

Mixed-race people are mildly complicated

I was pointed today to a piece in the BBC titled What makes a mixed race twin white or black?. The British media seems to revisit this topic repeatedly. There are perhaps three reasons I can offer for this. First, it tends toward sensationalism. Even though the BBC is relatively staid, when it comes to science it converges upon the tabloids. Second, because the number of non-whites in Britain is relatively small, there is a higher proportion of intermarriages between minorities and the white majority (from the perspective of minorities). This is especially true of people of Afro-Caribbean ancestry. So of the proportion of minorities a larger fraction are recently mixed in Britain than in the USA. Finally, the United States has a more complex attitude toward race relations than the United Kingdom, because the former has traditionally had a large non-white minority while the latter has only had so since the years after World War II. I suspect that “black-white twins” stories would seem in bad taste on this side of the pond, and bring up certain memories best forgotten.

Now, there are fallacies, confusions, and misleading shadings, in the BBC piece. I’ll hit those first before reviewing what’s going on here when fraternal twins exhibit totally different complexions.


It starts out somewhat ludicrously: “Her son Leo has black skin and her daughter Hope, has white skin.” This is false in a precise sense. Leo clearly has medium to light brown skin (there are photos in the piece). What’s going on here is that Leo has some African ancestry, and because of the rule of hypodescent all people of African ancestry with a shade of brown skin, from nearly black to light brown are termed “black skinned.” This is not a trivial semantic elision. If Leo truly had black skin, very dark brown, than there’d be a lot of explaining to do, because the genetics would be somewhat mystifying. More on that later.

Second:

She was adopted when she was four years old, and her birth mother is Afro-Caribbean and her British birth father was white. Her DNA tests revealed that, genetically, she was exactly 50% African and 50% European.

This is very unusual, and the results suggested that Shirley’s mother had pure African roots, and that her ancestors must have moved from Africa to the Caribbean quite recently.

Not necessarily. Mixed-race people, especially those with recent admixture, don’t have their different ancestral components distributed equally across their genome. It may be that in the process of sampling chromosomes from this individual’s Afro-Caribbean mother she received almost none of the European quantum, perhaps localized to a few chromosomal segments. This “noise” in the process explains why I seem to carry an elevated proportion of East Asian ancestry in relation to both of my parents. I simply received genetic copies sampled from the more “East Asian” regions of my parents’ genomes.

Next:

“Our skin colour is determined by a number of gene variants – at least 20 variants, I would say, probably quite a few more than that,” says Dr Wilson.

This is complicated, but I’d say that the good doctor is misleading the audience. Skin color seems to be a quantitative trait where you can explain the vast majority of between population variation with only a few genes, at most six. When it comes to European-African difference variants at two loci, SLC24A5 and KITLG can account for well over half of the difference. It is true that there are many, many, genes that effect skin color, but there is a definite distribution where the vast majority of genes tweak the trait only on the margins. In other words, there may be 20 variants (there are more), but for good predictive power at the inter-population level you’re good to go with 4 or 5.

I specify inter-population level, because within populations the gene set which can allow you to predict variation may be slightly different, and you have to take into account sex differences. For hormonal reasons males seem somewhat darker than females in human populations. Additionally, people also are palest in their youth, and become darker as they age. Finally, some of the genes which explain differences between populations are invariant within a population. Therefore the genes which are of lower effect size move up the stack. So when it comes to European-African variation, the largest effect gene, SLC24A5, won’t explain anything within these two populations. That’s because it is fixed for alternative variants (the light vs. dark conferring variants). So the second effect size may move up to first effect size when you evaluate on a smaller grain (but if the second effect size is nearly fixed, then it might drop far down as well).

Now let’s move on to the common idea that darkness dominates over lightness:

As in a painter’s palette, in the skin the presence of pigment dominates the absence of pigment, so the fact that Hope is white is very unusual.

This is hypodescent popping up again. Though in the West we live in an anti-racist age, at least notionally, it is interesting how concepts and models from a white supremacist era remain operative, at least implicitly. The idea that whites are recessive to non-whites makes totally sense if you code anyone with visible non-white ancestry as non-white. Even if they are genetically more white than not. The rationale for this model was the idea that there is a reversion to the more “primitive” type. So a cross between a black and a white produced a black, and a cross between a Nordic and a Mediterranean produced a Mediterranean. Inferiority taints the purity of superiority.

Less ideologically if you classify skin complexion into white and non-white in a dichotomous fashion then you logically consign the non-white trait to dominance. For example, if nearly, but not quite, white skin is “dark,” then you make it very difficult for someone with a substantial number of pigment conferring alleles to produce a child with very light skin.

Finally, now that we have elucidated the genetic architecture of pigmentation to a great extent we can make assessments of dominance and recessiveness on a locus by locus manner. If you plot skin complexion darkness as a function of reflectance you can turn it from a dichotomous or discrete trait to a continuous one. So individuals can have a “melanin index,” an integer value equivalent to their position on a scale of lightness and darkness. Converse to expectations above it turns out that on the two largest effect genes explaining difference between Africans and Europeans the light alleles are more dominant than the dark alleles! In other words, if the two alleles had an equal effect you’d expect a value between the two in their homozygote state. As it is, the values tend toward higher reflectance (light) than dark. I would caution that terms like “dominant” and “recessive” can be highly subjective and dependent on how you code the trait, the nature of the population you sample from in a polygenic character, or even scale the of values. So in this case you notice that switching from a dichotomous code of white vs. non-white to a continuous value corresponding to reflectance flips the model from the light trait being recessive to the dark, to the dark being recessive to the light (albeit, only mildly).

Because pigmentation is controlled by only a few genes the state at these loci are poor proxies for total genome content. In plainer language mixed-race siblings won’t deviate too much in their ancestral quantum, but they can deviate a great deal in their physical appearance. In fact, because of the poor correlation the slightly “blacker” twin in total ancestry may actually look more like a white person, and vice versa.

Now let’s go back to first principles. We’ll make some simplifying assumptions to illustrate what’s going on easily. Take 6 genes which control skin color. Assume equal effect. Each gene comes in two variants. Light and dark. Two copies of light result in a value of 0, while two copies of dark result in 2. A copy of each results in 1. In other words, the alleles are additive across a locus. Also assume that the genes are independent. They’re not linked. So the value at each gene is independent of the other genes. Finally, assume that the genes’ implied values summed together result in a total pigmentation phenotype outcome. So they’re additive across loci.

To make even simpler let’s assume that the parents are F1 African-European hybrids. That means that one of their parents’ was European and the other African. So both share the same ancestry of recent vintage. As it happens Africans and Europeans are very different on pigmentation genes, so we can assume that these parents carry one light copy and one dark copy across the six genes. This means you’d expect them to be brown.

Since they are brown, wouldn’t their children be brown? No. Not necessarily. As per Mendel’s Laws each contributes contributes one gene copy at each locus. So for the 6 loci above each parent contributes one pigmentation gene. What does that mean concretely? I Already simplified things to produce an elegant outcome: the F2 offspring could be all light, all dark, or one copy of both, like their parents, at any given gene. To illustrate what I’m talking about, SLC24A5 is disjoint in frequency across Africans and Europeans. All Europeans have one variant, and all Africans have another. So the offspring of a marriage between an African and a European will be heterozygote on that locus. If they marry another person of similar background, homozygote light and dark genotypes will resegregate out at fractions of 25% each, with half the outcome being heterozygote as in the parental condition. In other words, there are a 25% probability of a F2 child of F1 hybrids being “white” at this locus. There are 6 loci. Assuming independent probabilities, you multiply out 0.256, and get 1 out of ~4,000 that the child will be white like their white grandparents.

I ran this as a binomial 10,000 times, and here’s the distribution I came up with:

The white and black offspring don’t show up because the number of outcomes is so rare in this model, but as you can see the median outcome is brown, like the parents. But the tails are significant. In other words, don’t be surprised if there’s a lot of variation among the siblings. But why should you be? If you know of people from populations where pigmentation alleles are segregating in polymorphic frequencies, such as Latin Americans and South Asians, you are aware that different siblings can look strikingly different when it comes to complexion. Though I guess that’s a new insight for the British….

June 18, 2011

Of literality and metaphor in the war between Arya and Dasa

Filed under: Admixture,Aryans,Dasas,History,Skin Color — Razib Khan @ 12:27 pm

Over at Brown Pundits Zach Latif brings up the point that the Indian bias for light skin may date back to the Aryans. And it does seem that such a bias manifests in the earliest texts. But as someone not able to read the original languages I can ascertain the arguments as the import of these passages only at a remove, second and third hand. Some scholars have suggested that the racialized interpretations of the treatments of the interactions between the Aryans and the natives of India are just a look at the past through the lens of the present. They are argue that color terms in the Vedas are metaphors. In contrast, there are others who seem to be arguing for a more straightforward and "literal" reading of the source text. As a non-philologist there's little I can add. But I didn't dismiss those who argued for a metaphorical reading because I know from the literature in the area of Biblical scholarship that straightforward and "literal" readings are quite often deceptive and require their own interpretation (it is difficult to transfer idioms and metaphors properly across languages, and the translators are tempted to render them in the most congenial manner to their own broader theses).

To be frank the information being uncovered by Zack and others makes me think that there was a racial aspect to these conflicts; that the literal reading has some truth. The tribal folk of India are genetically distinct from the caste populations, especially the higher castes. Though all South Asians are a mix to varying degrees of an exogenous West Eurasian element and a South Eurasian indigenous component, the non-Austro-Asiatic tribal populations seem to be a relatively simple combination. The genetic complexity of the structure of other groups suggests to me that there were several later West Eurasian intrusions after the arrival of the "Ancestral North Indians" (ANI), and their hybridization event with the "Ancestral South Indians" (ASI). Racialized language in the older Hindu scriptures may then be conceived of as a conflict between the latest arrivals and the older long established groups which were a stabilized ANI-ASI compound.

One can imagine that this process recapitulated itself in the late medieval and early modern period with the arrival of the Muslims. The ruling Islamic elites who were of Persian and Turk stock viewed the native Hindus through a racialized lens, and were at pains (and to some extent still are!) to distinguish between Muslims of foreign provenance who were "white" and converts from the native populations who were "black." The physical differences are evident when you compare the Emperor Akbar with his grandson Shah Jahan, whose other three grandparents were Rajputs.

May 21, 2011

Skin color, “if you’re white you’re alright!”

Filed under: Culture,Skin Color — Razib Khan @ 10:32 am

This is a brown blog, so it must be mooted. Peter Frost has some good ethnographic data in Fair Women, Dark Men: The Forgotten Roots of Color Prejudice, but I think there’s also a pretty easy explanation for a lot of the cross-cultural preference for fair skin: social stratification. This is straightforward when light skinned Muslims arrive from Iran, Turan, and further parts west, or when Spaniards conquer Mesoamerica, but it applies within societies. The peasant in traditionally stratified societies is blacker than the noble. The “field negro” is darker than the “house negro.” The inversion that we see in Western cultures actually probably has the same dynamic: as elites were the ones who had leisure to visit tropical climes and engage in rugged outdoor activities a “healthy tan” became a sign of “vigor.” In contrast, the proletariat worked in factories or were unable to afford vacations to the Caribbean. The paleness which had been a sign of privilege became pallidness.

This modern Western sensibility is actually prefigured in some pre-modern archetypes. In particular, I am thinking of Herakles, who was a powerful beast of a man who is sometimes depicted as sun-blacked through his naked exertions. Color, as extensively documented by Peter Frost, does have some gendered connotations. In Chinese society vigorous exertion was not seen as a manly pursuit, so the preference for fair skin among men has long been more stark than in the West, where the martial nobility engaged in healthy outdoor pursuits even when not in a state of war.

September 28, 2010

To gain pallor is easier than losing it

journal.pbio.0000027.g002

John Hawks illustrates what can be gained at the intersection of old data and analysis and new knowledge, Quote: Boyd on New World pigmentation clines:

I’m using some statistics out of William Boyd’s 1956 printing of Genetics and the Races of Man[1]. It gives a good accounting of blood group data known more than fifty years ago, which I’m using to illustrate my intro lectures. Meanwhile, there are some interesting passages, from the standpoint of today’s knowledge of the human genome and its variation.

On skin pigmentation – this is the earliest statement I’ve run across of the argument that the New World pigmentation cline is shallower than the Old World cline because of the relative recency of occupation….

Looking at what was said about pigmentation generations ago is of interest because it’s a trait which in many ways we have pegged. See Molecular genetics of human pigmentation diversity. Why humans vary in pigmentation in a deep ultimate sense is still an issue of some contention, but how they do so, and when the differences came about, are questions which are now modestly well understood. We know most of the genetic variants which produce between population variation. We also know that East and West Eurasians seem to have been subject to independent depigmentation events. We also know that some of the depigmentation was relatively recent, probably after the Last Glacial Maximum, and possibly as late as the advent of agriculture.

On the New World cline, which is clearly shallower than that of the Old World. The chart below from Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms is useful:


skinvarianceWhat you’re seeing here are patterns of relationships by population when it comes to the select subset of genes which we know are implicated in between population variation in pigmentation. The peoples of Melanesia are arguably the darkest skinned peoples outside of Africa (and perhaps India), and interestingly they are closer to Africans than any other non-African population. But in total genome content they’re more distant from Africans than other non-African populations, excluding the peoples of the New World.

This disjunction between phylogenetic relationships when looking at broad swaths of the genome, as opposed to constraining the analysis to the half a dozen or so genes which specifically encode between population differences on a specific trait, is indicative of selection. In this case, probably functional constraint on the genetic architecture. From the reading I’ve done on skin pigmentation genetics there is an ancestral “consensus sequence” on these genes which result in dark complexions. In contrast, as has been extensively documented over the last few years there are different ways to be light skinned. In fact, the Neandertals which have been sequenced at those loci of interest also turn out to have a different genetic variant than modern humans.

How to explain this? I think here we can go back to our first course in genetics in undergrad: it is easier to lose function than gain function. The best current estimate is that on the order of one million years ago our species lost its fur, and developed dark skin. And it doesn’t look like we’ve reinvented the wheel since that time. All of the peoples termed “black” across the world, from India, to Australasia, to Africa, are dark because of that ancestral genetic innovation. In contrast, deleterious mutations which “break” the function of the genes which gave some of us an ebony complexion occur relatively frequently, and seem to have resulted in lighter skinned groups in more northerly climes. It turns out that some of the pigmentation genes which are implicated in between population variance in complexion were actually originally discovered because of their role in albinism.

So how does this relate to the New World? I think the difficulty in gaining function once it has been lost explains why the people of Peru or the Amazon are not as dark skinned as those of Africa, Melanesia, or South Asia. They haven’t had enough time to regain function which they lost as H. sapiens traversed northern Eurasia. So there you have it. A nice little illustration of how the genetics taught to 18 year olds can be leveraged by the insights of modern genomics and biological anthropology! In the end, nature is one.

Image Credit: Dennis O’Neil

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