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Credit: Graham Crumb

Credit: Graham Crumb

If population genetics is “study of the distributions and changes of allele frequency in a population,” then the understanding of the maintenance of variation (or lack thereof) is one of the major topics of focus. In the first half of the 20th century when there was a lot more theory than data there were arguments about whether polymoprhism (in this era they’re talking about classical markers) was maintained through balancing selection or whether it was just a transient phenomena, and that at any given moment you’re just getting a snapshot of alleles sweeping up to fixation, or being purged out of the gene pool. In the second half of the 20th century it was all about neutral theory, and its discontents. Then the post-genomic era showed up, and geneticists had access to a lot of data and computational power to analyze it. Rather than relying on older molecular tests which were geared toward detecting inter-specific selection events population geneticists began scouring haplotype structure.

But even now there’s a lot of mystery. First, you might be able to adduce that selection is highly likely in a given region, but you may have no clue what that region does functionally (in some cases the region may not even be genic, in which case it has be a mysterious regulatory element). There are some good case studies where the mystery has cleared. Lactase persistence. The ways you can fight malaria. But over the past day I’ve been having to admit that it sure looks like the regions of the genome around pigmentation function are the targets of selection. But we don’t really know what selection is selecting for. And this is actually a set of selection events that I can imagine some day reaching a resolution into their probable cause. But we’re far from that.

A few years ago Eimear Kenney and company solved the mystery of why some Melanesian populations had very dark skins but blonde hair. I blogged about it, but didn’t read the paper too closely. Looking at the publication date, May 2012, I realize I was busy studying for some really big end of first year exams at that time, so that explains my lack of attention. In any case they found that a mutation, rs13289810 in TYRP1, results in blonde hair when it’s a homozygote. They didn’t find strong evidence for recent selection. That is there wasn’t a long haplotype block indicating a sweep in the past 10,000 years. The allele frequency difference across populations as well as long range linkage disequilibrium was suggestive of past selection.

map2 This was in the Solomon Islands. Today I decided to see if there was any follow up on this work. Well, Heather Norton’s group published a paper, Distribution of an allele associated with blond hair color across Northern Island Melanesia. It’s on a different set of islands, but the same results pretty much hold. The allele has a recessive effect on hair color, not much on skin color (there was a small effect in the original paper, so it seems it’s not wholly tissue specific in expression). But I just kept staring at this map and the frequencies. Look at the derived proportions…they don’t get above 0.50. But in most of the populations they’re around in appreciable proportions. I had a hard time not thinking there wasn’t balancing selection going on here. That this was something old that was persisting, but not fixing.

I asked Carlos Bustamante, and he got back me on Twitter:

I also had an exchange with the first author, and she pointed out in the supplements that the frequencies in the Solomons were quite curious too:

Region Genotype counts Frequency of 93C
Central 126 80 22 0.27
Choiseul 17 2 0 0.05
Guadalcanal 33 33 13 0.37
Isabel 23 17 7 0.33
Makira 13 11 3 0.31
Malaita 98 185 92 0.49
40 11 0 0.11
Temotu 13 11 3 0.31
Western 40 22 2 0.2
Total 405 374 142 0.36


When they looked in the HGDP data set it’s ancestral everywhere else. The derived variant isn’t floating around at low frequencies. One might naively think that it’s overdominance, but I suspect we’re looking at some negative frequency dependent selection. In the 2014 paper by Norton et al. it’s pretty clear that this is distributed across rather disparate populations. It is unlikely in my opinion to be purely due to population structure, as diverse islands have been sampled. It looks to be an old variant that’s persisted, so it dates to the Pleistocene settlement of Near Oceania. It’s also found in Australia, though we don’t know the genetic basis.

Ten years ago I would have been super excited to know the genetic basis of an interesting trait like this. But now I’m left with why? Why? We’ll be grappling with a lot of why’s in the next few decades.

• Category: Science • Tags: Blondism, Selection 
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As a small child perusing old physical anthropology books I would occasionally stumble upon images of people of Oceanian stock with light hair color. I would wonder: is this a biological or cultural feature? In other words, were people bleaching their hair? If it was biological, was it heritable, or was it simply malnutrition? Another aspect of the phenotype was also straightforward: it did not seem that light hair color resulted in any concomitant lightening of the skin. Granting that this was a heritable biological trait, the questions then were simple: was this trait an independent occurrence of de-pigmentation in Oceania, or was it due to introgression of European alleles?

First, one must note that this is not an isolated feature in Oceania. Rather, blondism crops up in the Solomon Islands, in New Guinea, as well as among some Australian desert groups. This in itself should make us skeptical of the model of European admixture. Additionally, blue eyes, which exhibits a higher frequency in Europeans than blonde hair, is not similarly common in these populations. But all this speculation is now a historical curiosity. The results are widely known from conference presentations that have been reported , but finally the paper is out in Science which solves the “riddle” of hair color in Oceania at the level of genetic causation.

Melanesian Blond Hair Is Caused by an Amino Acid Change in TYRP1:

Naturally blond hair is rare in humans and found almost exclusively in Europe and Oceania. Here, we identify an arginine-to-cysteine change at a highly conserved residue in tyrosinase-related protein 1 (TYRP1) as a major determinant of blond hair in Solomon Islanders. This missense mutation is predicted to affect catalytic activity of TYRP1 and causes blond hair through a recessive mode of inheritance. The mutation is at a frequency of 26% in the Solomon Islands, is absent outside of Oceania, represents a strong common genetic effect on a complex human phenotype, and highlights the importance of examining genetic associations worldwide.

The study was a classic cases vs. controls GWAS. They looked at variants in a lot of people with the trait, vs. those without the trait. Additionally, if you check the supplements and read the text it’s obvious there is no population straification. That is, having blonde hair is not correlated with a different ancestry in these Melanesian populations. Rather, this is a relatively robust recessively expressed trait that seems to have been segregating within these groups before contact. Those individuals who are homozygotes tend to have blond hair, while those who are not tend not to have blonde hair. TYRP1 is a pigmentation related locus, so it isn’t surprising that the mutation was around that region of the genome. The key though is to note that the specific mutation is not found in Europeans. Rather, it is limited to Oceanians. The extremely close correspondence between the genotype and the trait, and the lack of similarity in the variants between Europeans and Oceanians, ends debate on questions of the heritability and possible exotic origin of the trait in Oceanians. Now it is known, and the debate shall end.

So how did the Oceanians come to have such a high frequency of this trait? Here’s a comment from one of the preeminent biological anthropologists of Melanesia:

The mutation, which has no obvious advantages, likely arose by chance in one individual and drifted to a high frequency in the Solomon Islands because the original population was small, says Jonathan Friedlaender, an anthropologist emeritus at Temple University in Philadelphia, Pennsylvania, who was not involved in the study. “This whole area seems to have been populated by very small groups of people making it across these stepping-stone islands, so you do have very dramatic effects in fluctuations of gene frequency.”

It is absolutely correct that Oceanian populations exhibit a lot of evidence of small effective population, and so are subject to random genetic drift. In this model the frequency of ~0.25 for the allele which results in bondlism in the homozygote in the Solomon islands is high as it is due to a drift event up in frequency from an initial variant mutation. But there are reasons I am skeptical of this. The first is a somewhat technical one: if the high frequency in the Solomons is due to rapid rise in frequency due to large generation-to-generation fluctuations, you’d expect to see some linkage disequilibrium in the region of TYRP1. That’s because presumably the blonde allele comes from a common ancestor, which just happened to be over-sampled in a high drift regime. Even if it wasn’t a selective sweep, flanking SNPs would still be transmitted at high frequency with the causal variant through drift. If the drift event occurred in the past, the allele should be fixed, or, it should be extinct. If you imagine that it was fixed in some populations, and then admixture resulted in the allele segregation, then there should be LD around the SNP too.

It is noted in the text that the authors did not find evidenc of high LD in their tests for natural selection, XP-EHH or iHS. These tests are cued to pick up relatively recent selective events, on the order of ~10,000 years or so. They’re geared toward detection of correlations of variation across regions of the genome generated by positive selection (though as I suggest above, they can also yield false positives due to stochastic events, especially iHS). Additionally, using Fst, a between population genetic variation measure, the authors note that the SNP in question has a high Fst when comparing Solomon Islanders with non-Oceanians, but nearby SNPs to it do not.

But there’s a very good reason I never expected there to be recent selection driving this anyhow: Australian Aboriginals sometimes manifest blonde hair, and the best genetic data suggests separation from Melanesians of at least 10,000 years. Additionally, the Solomon Islands were not part of Sahul, so that’s a conservative estimate. We don’t know if the Aboriginals have the same TRYP1 mutation, but there’s the same tendency toward dark skin and light hair amongst them. It also seems rather suspicious to me that the highest frequency of blonde hair outside of West Eurasia is all amongst Oceanian populations, who are phylogenetically a distinct clade.

What I am suggesting then is that this pigmentation mutation is an old feature of the Oceanian populations, on the order of tens of thousands of years. That is why there isn’t LD around this region; any LD which existed was long ago eliminated by recombination. But why is it still around at minor allele level frequencies? When all other explanations are found wanting, you go where you have to, so therefore I suggest some form of balancing selection. One could posit overdominance on a trait other than pigmentation, with the hair color being simply a correlated response.

Finally, I want to note that this really does confirm that as an overall trait controlled by a relatively small number of genes pigmentation in the lightening direction has a huge mutational target on it. Remember that East and West Eurasians are light skinned for different reasons. And in regards to skin color, an interesting point is that Melanesians, in particular Solomon Islanders, are amongst the most genetically similar to Africans when it comes to variation on these loci. TYRP1 is quite the exception.

Citation: DOI:10.1126/science.1217849

Citation: DOI:10.1111/j.1469-1809.2006.00341.x

Image credit: Graham Crumb

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I have posted on the existence of blonde hair amongst some Melanesians before. There are natural chemical treatments as well as extreme malnutrition which can result in blonde hair in dark skinned people. The latter seems unlikely from the photos I’ve seen (the lightening of hair due to lack of food has been reported in African refugee camps). In regards to the former I’m confused as to why chemical treatments would be common among Oceanian people as disparate as Solomon Islanders and central desert Australian Aborigines, and yet not among many other east Eurasian populations.

In any case, in response to this comment below on Negrito appearance, I started using google images, and I stumbled upon something strange. In my Malaysian Negrito sample there’s a division between two ethnic groups, Kensiu and Jehai. The Kensiu have hardly any Austro-Asiatic or Austronesian admixture compared to the Jehai. When I looked for images of the Kensiu I came upon on this page, which seems to relate an experience of an aid worker in an isolated Malaysian village. The inhabitants were ethnically diverse, some Malays, but indigenous Negritos a well. Well, it turns out that some of the Negrito children don’t have black hair.

I have no explanation for this phenomenon. The Pan-Asian SNP data set is rather thin on markers, so looking for functional variants isn’t usually fruitful. At least not manually.

Below are some blonde Solomon Islander children singing about Jesus…. ((via Western Confucian)

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Populations_first_wawe_migrRecently I was looking for images of the alpine biomes of the New Guinea highlands* and stumbled onto some intriguing, though not entirely surprising, set of photographs of individuals from Papua New Guinea. They were noteworthy because they manifested the conventional Melanesian physical type, but their hair had a blonde cast to it. For example, here is a charming blonde boy. The photographer has several other striking portraits of Melanesians with lighter hair at his website. In regards to the peculiar hair color of these people he says: “When you ask the people why there are so many blonde people on the islands, they answer 3 things: they have white ancestors, they receive too much sun, or they do not eat enough vitamins! – Langania village, New Ireland, Papua New Guinea.” There is more discussion in the comments about this issue, some claiming that likely it is the sea water and sun which is producing bleaching naturally. If you look around you will see references to bleaching of hair among some of these people as a cultural trait, though the references tend not to be concrete (many clearly assume they’re bleaching their hair, rather than reporting bleaching). The blonde being at the tips from what I can tell in some cases I certainly don’t reject the explanation that bleaching is a cultural practice among these peoples, albeit for children and women only.

But the peculiar hair color of these populations is noted in the scientific literature as if it is a biological characteristic of these groups, not a cultural artifact. From Molecular genetic evidence for the human settlement of the Pacifc: analysis of mitochondrial DNA, Y chromosome and HLA markers: “The Tolais of New Britain are phenotypically ‘Melanesian’, with fairly dark skin and frizzy hair, some-times almost blonde as in some highland Papuan groups.” Enter Tolai ‘New Britain’ into Google Images and the first few pages have several instances of blonde children, including this cute triplet.

Before we go any further, I want to express my skepticism at the idea that this is European admixture. The loci associated with higher odds of having blonde hair in Europeans, OCA2, KITLG, etc., also result in light skin, and secondarily blue eyes. In other words in Europeans blonde hair is to a large extent one effect of generalized depigmentation. There is no magic “blonde gene” which operates independently from the variants which produce lighter skin, or lighter eyes. Though the outcome is not deterministic, the probabilities make it so that someone who has naturally blonde hair is very unlikely to have dark brown skin, at least in any genetic architecture we’re familiar with in Europeans (e.g., African Americans with light eyes and/or hair, also tend to be light skinned).

But if you want more than my logic above, here’s a STRUCTURE plot from The Genetic Structure of Pacific Islanders:


I reedited for clarity. Remember that K = putative ancestral populations. So you’re looking for population substructure, and inferred admixture. I’ve compared the Oceanian groups to French from the HGDP sample. The Polynesians in the sample have clear European admixture, but the Melanesians generally do not. The aforementioned Tolai are one of the groups analyzed in this paper, and contrary to one of their explanations for their high frequency of blondness they do not some to have any European ancestry.

What about bleaching? I will be interested to hear what readers have seen, but to my limited knowledge dark skinned populations in other oceanic environments do not seem to have such bleached hair. But, relatively simple forms of hair bleaching do exist which would be possible for a less affluent population to practice as a rite of some sort, or perhaps for simple aesthetic reasons. I put a modest probability on this being the full explanation for this phenotype, and a high probability for it being some of the explanation.

So let’s move to the most novel explanation: that the populations of Oceania have an independent genetic architecture for the emergence of lighter hair color. For me the biggest factor to weight in this hypothesis’ favor is that to my knowledge there are only two population groups in the world which have an appreciable frequency of lighter hair which are not of West Eurasian origin, and they are the indigenous peoples of Melanesia and the Australian desert (this trait seems to be relatively common in the children of the Warlpiri people for example). As we noted last week these two populations form a natural phylogenetic clade, so it seems highly coincidental to me that both exhibit the unique phenotype of relatively dark general pigmentation, but lightness of hair. Additionally, like Europeans lighter hair color seems to be concentrated among children and women in both these groups, aligning with what we know are the correlations of pigmentation and hormones (males and adults are darker).

One obvious model for the blondeness of central desert Australian Aboriginals is European admixture. But the same problems emerge as in the case of the Melanesians: of presumed European traits only the blonde hair expresses, which is a highly peculiar phenomenon. Additionally, we have a relatively recent report from a scientific perspective on the genetics of this trait among these populations, Joseph Birdsell’s Microevolutionary Patterns in Aboriginal Australia: A Gradient Analysis of Clines. The book is from 1993, and no doubt most of the research was done earlier, so the techniques and analyses may seem a bit crude to us. Birdsell observed that the inheritance pattern of blonde hair among the desert Aboriginals exhibited “incomplete dominance.” He recorded that the frequency of the trait was rather high within these tribes, at least for children and women. Additionally, he observes that people with an eastern Aboriginal parent and European parent usually had brown hair of various shades. But among individuals who had one blonde (at least as a child) desert Aboriginal parent and a European parent the offspring tended to be disproportionately blonde, even if the European parent was a brunette! Finally, he observed that aside from head hair, only the body hair of the forearm was blonde. The rest was dark in these Aboriginals.

From what I can tell Birdsell’s monograph is the only recent scientific exploration of this particular topic of blondism among the peoples of Oceania. Many physical anthropologists record the observation of non-black hair among these peoples, but for most their interest did not go beyond cataloging the fact, or it was an incidental result in a bigger project. There’s still a lot about human variation we don’t know. In regards to human pigmentation most of the puzzle has been completed. This is one piece which remains to be found.

Addendum: Some work on the pigmentation genetics of Melanesian populations has been done. They resemble Africans more than any other non-African group in their genetic architecture of loci implicated in the variation of pigmentation. That would basically eliminate the European admixture model to my mind to explain light hair, and increase the probability of bleaching and/or a different and unknown locus.

Note: Blondism among North African, Middle Eastern, Central and South Asian populations is I believe either simply part of the natural continuum of West Eurasians, or, admixture from Europeans or other blonder groups. I believe that this is even the source of blondism among groups like the Hmong, who have a legend of migration from deeper in Asia, where they may have mixed with West Eurasian populations on the fringes of China proper.

Related: Blondism in Melanesia.

* The highest peak in New Guinea is ~14,000 feet above sea level, and in the higher reaches of the uplands it snows periodically.

Image Credit: Wikimedia

Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"