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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
CC CT TT
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
Polynesian
Outliers
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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  1. Several minor stray points for RK:

    The allele frequency difference across populations as well as long range LD was suggestive of past selection. Perhaps it is too early in the morning, but I cannot figure out what LD means.

    I had a hard time not thinking there wasn’t balancing selection going on here.
    Do you mean this double negative here?

    But we don’t really know what selection is selecting for. Fitness? 😉

  2. Eight thousand years of natural selection in Europe, line 75

    The derived allele of rs12913832 at the HERC2/OCA2 locus is the primary determinant of blue eyes in Europeans, and may also contribute to light skin and hair pigmentation Our analysis detects a genome-wide signal of selection at this locus, but instead of the signal being one of positive selection with a coefficient of 0.036 as in a previous study of ancient DNA in the eastern Europe steppe, our signal is of weakly negative selection One possible explanation is local adaptation: that the allele is advantageous in the north and disadvantageous in the south of Europe. [!] This hypothesis is supported by the fact that our data shows that an extreme north-south gradient in allele frequencies has been maintained in Europe for the last 8,000 years (Figure 2C, Extended data Figure 3).

    • Replies: @Rick
    Yes. But before the Neolithic farmers moved in, the local Hunter-Gatherers of southern Europe also had blue eyes (at least in Spain). And southern Europe still has a bit more Neolithic farmer ancestry.

    Also, the more north-eastern "Eastern Hunter-Gatherers" did not have so much of the blue eye genes.

    I think it is all a bit more complicated than just a north vs south selection with eye color.

    Nonetheless, there has definitely been some extreme selection. I think modern Estonians are >99% blue eyed. It's as if brown eyed babies were just thrown out!
  3. @Sean
    Eight thousand years of natural selection in Europe, line 75

    The derived allele of rs12913832 at the HERC2/OCA2 locus is the primary determinant of blue eyes in Europeans, and may also contribute to light skin and hair pigmentation Our analysis detects a genome-wide signal of selection at this locus, but instead of the signal being one of positive selection with a coefficient of 0.036 as in a previous study of ancient DNA in the eastern Europe steppe, our signal is of weakly negative selection One possible explanation is local adaptation: that the allele is advantageous in the north and disadvantageous in the south of Europe. [!] This hypothesis is supported by the fact that our data shows that an extreme north-south gradient in allele frequencies has been maintained in Europe for the last 8,000 years (Figure 2C, Extended data Figure 3).
     

    Yes. But before the Neolithic farmers moved in, the local Hunter-Gatherers of southern Europe also had blue eyes (at least in Spain). And southern Europe still has a bit more Neolithic farmer ancestry.

    Also, the more north-eastern “Eastern Hunter-Gatherers” did not have so much of the blue eye genes.

    I think it is all a bit more complicated than just a north vs south selection with eye color.

    Nonetheless, there has definitely been some extreme selection. I think modern Estonians are >99% blue eyed. It’s as if brown eyed babies were just thrown out!

    • Replies: @Sean
    No those hunter gathers did not have actual blue eyes, it was just journalist's shorthand for 'not standard dark brown'. I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea. It seems unlikely as many north Europeans live in countries far more sunny than southern Europe.

    Razib mentions Frequency-dependent selection (ie term given to an evolutionary process where the fitness of a phenotype depends on its frequency relative to other phenotypes in a given population). That was what I was getting at. But I think you make a good point. If 99% of a population have the same colour eyes, or hair, then selection was probably not for rare colours.

  4. LD = Linkage Disequilibrium

  5. @Rick
    Yes. But before the Neolithic farmers moved in, the local Hunter-Gatherers of southern Europe also had blue eyes (at least in Spain). And southern Europe still has a bit more Neolithic farmer ancestry.

    Also, the more north-eastern "Eastern Hunter-Gatherers" did not have so much of the blue eye genes.

    I think it is all a bit more complicated than just a north vs south selection with eye color.

    Nonetheless, there has definitely been some extreme selection. I think modern Estonians are >99% blue eyed. It's as if brown eyed babies were just thrown out!

    No those hunter gathers did not have actual blue eyes, it was just journalist’s shorthand for ‘not standard dark brown’. I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea. It seems unlikely as many north Europeans live in countries far more sunny than southern Europe.

    Razib mentions Frequency-dependent selection (ie term given to an evolutionary process where the fitness of a phenotype depends on its frequency relative to other phenotypes in a given population). That was what I was getting at. But I think you make a good point. If 99% of a population have the same colour eyes, or hair, then selection was probably not for rare colours.

    • Replies: @Tobus
    many north Europeans live in countries far more sunny than southern Europe.

    I call "bullshit" - do you have solid data to back up this claim?
    , @CupOfCanada

    I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea.
     
    I wouldn't scoff at some selection there. I know doctors have told me the pigmentation of my eyes puts me a much greater risk for sun related damage to them.
  6. @Sean
    No those hunter gathers did not have actual blue eyes, it was just journalist's shorthand for 'not standard dark brown'. I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea. It seems unlikely as many north Europeans live in countries far more sunny than southern Europe.

    Razib mentions Frequency-dependent selection (ie term given to an evolutionary process where the fitness of a phenotype depends on its frequency relative to other phenotypes in a given population). That was what I was getting at. But I think you make a good point. If 99% of a population have the same colour eyes, or hair, then selection was probably not for rare colours.

    many north Europeans live in countries far more sunny than southern Europe.

    I call “bullshit” – do you have solid data to back up this claim?

    • Replies: @Razib Khan
    https://www.google.com/search?q=sunlight+per+year+map+world&num=20&es_sm=122&source=lnms&tbm=isch&sa=X&ved=0CAcQ_AUoAWoVChMI0rXcpIO0xwIVFVqICh1rdABu#imgrc=29jK3qdDl1AgFM%3A
    , @Sean
    You look at people who work outside in the far north they look as if they have had a lot of sun. Averaged over a year UV is indeed less in the north, because there are months vompleatle without strong enough UVb to move vit D. But vitamin D can be stored. Read my links.

    More UV and UVb hits the earth in the north during a full summer day's sun in Sweden than in equatorial Africa. A key point is vitamin D synthesis switches off in 20 minutes or so in direct European summer sun. If it didn't we would get vitamin D poisoning.

    European are not selected to maximise vitamin D from UV . They are selected to go a few months without UVb.
  7. @Sean
    No those hunter gathers did not have actual blue eyes, it was just journalist's shorthand for 'not standard dark brown'. I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea. It seems unlikely as many north Europeans live in countries far more sunny than southern Europe.

    Razib mentions Frequency-dependent selection (ie term given to an evolutionary process where the fitness of a phenotype depends on its frequency relative to other phenotypes in a given population). That was what I was getting at. But I think you make a good point. If 99% of a population have the same colour eyes, or hair, then selection was probably not for rare colours.

    I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea.

    I wouldn’t scoff at some selection there. I know doctors have told me the pigmentation of my eyes puts me a much greater risk for sun related damage to them.

    • Replies: @Sean
    Snow blindness? Yes melanin protects against noise induced deafness too. Red hair is a total pain in the sun. But the UVb in summer in the north is much greater than Jablonski's data suggest. So why would natural selection make whites sooo pale?
  8. @Tobus
    many north Europeans live in countries far more sunny than southern Europe.

    I call "bullshit" - do you have solid data to back up this claim?
  9. Blondism among Melanesian children is way more common than among Middle Eastern children. Not even Southern European children have the same high rate of blondism as Melanesian children.

    The Melanesian children are a lot blonder than the Italian children you see in the Connie’s wedding scene in The Godfather.

    Only Northern European children and Slavic children can compete with Melanesian children in the childhood blondism department.

  10. @CupOfCanada

    I was not suggesting a a north vs south selection with eye color, I was scoffing at the idea.
     
    I wouldn't scoff at some selection there. I know doctors have told me the pigmentation of my eyes puts me a much greater risk for sun related damage to them.

    Snow blindness? Yes melanin protects against noise induced deafness too. Red hair is a total pain in the sun. But the UVb in summer in the north is much greater than Jablonski’s data suggest. So why would natural selection make whites sooo pale?

  11. @Tobus
    many north Europeans live in countries far more sunny than southern Europe.

    I call "bullshit" - do you have solid data to back up this claim?

    You look at people who work outside in the far north they look as if they have had a lot of sun. Averaged over a year UV is indeed less in the north, because there are months vompleatle without strong enough UVb to move vit D. But vitamin D can be stored. Read my links.

    More UV and UVb hits the earth in the north during a full summer day’s sun in Sweden than in equatorial Africa. A key point is vitamin D synthesis switches off in 20 minutes or so in direct European summer sun. If it didn’t we would get vitamin D poisoning.

    European are not selected to maximise vitamin D from UV . They are selected to go a few months without UVb.

    • Replies: @Tobus
    You look at people who work outside in the far north they look as if they have had a lot of sun.

    This is what we call anecdotal evidence, I asked for "solid data" like the map that Razib linked to. Like every other piece of empirical evidence available, this map show a general cline of solar radiation from the South to the North. Here's one zoomed in on Europe: http://meteonorm.com/images/uploads/demo_uploads/ghi_europe_mn71.png - as you can see, your claim that "many north Europeans live in countries far more sunny than southern Europe" is not supported by empirical evidence... in other words, it's "bullshit".

    More UV and UVb hits the earth in the north during a full summer day’s sun in Sweden than in equatorial Africa.

    ... very disappointing Sean, not only did you fail to provide evidence for your original claim, but you actually went on to make another equally unlikely claim, again with no evidence to back it up. So again, I call bullshit - can you please provide solid data that backs up this claim.

    I'll draw your attention to the EuroSun project, in particular this page: http://www.eurosun-project.org/UV-Maps/Maps.html, which shows monthly maps of UV over all of Europe, and this one: http://www.eurosun-project.org/UV-Maps/Results.html which shows month-by-month UV levels at the 40th, 50th and 60th parallels north. You can see that there is indeed a summer increase in UV in Scandinavia (see the June map for instance), but you can also see that it is limited and doesn't reach the levels recorded in southern Spain, Italy and North Africa for example. Given that the summer UV at the 60th parallel fails to exceed that of the 40th parallel, I find it very hard to believe it exceeds the level at the equator.. so please, solid data if you have it, stop saying it if you don't.

    European are not selected to maximise vitamin D from UV.

    Please note I am not arguing for or against a vitamin D hypotheses for depigmentation, I am just pointing out that your statements about higher UV in the north than the south are categorically false. Given the general link between latitude and pigmentation, Vitamin D synthesis is the obvious go-to theory and Jablonski et. al. can be excused for jumping to that conclusion when originally making the connection. Subsequent data however has been ambivalent and there are many reasons today to doubt Vitamin D as the primary driver of pigmentation selection. So feel free to critique the Vitamin D theory of depigmentation, but please do so on it's actual defects and stop with the nonsense about UV being higher in the north than the south - it's just not true.
  12. @Sean
    You look at people who work outside in the far north they look as if they have had a lot of sun. Averaged over a year UV is indeed less in the north, because there are months vompleatle without strong enough UVb to move vit D. But vitamin D can be stored. Read my links.

    More UV and UVb hits the earth in the north during a full summer day's sun in Sweden than in equatorial Africa. A key point is vitamin D synthesis switches off in 20 minutes or so in direct European summer sun. If it didn't we would get vitamin D poisoning.

    European are not selected to maximise vitamin D from UV . They are selected to go a few months without UVb.

    You look at people who work outside in the far north they look as if they have had a lot of sun.

    This is what we call anecdotal evidence, I asked for “solid data” like the map that Razib linked to. Like every other piece of empirical evidence available, this map show a general cline of solar radiation from the South to the North. Here’s one zoomed in on Europe: http://meteonorm.com/images/uploads/demo_uploads/ghi_europe_mn71.png – as you can see, your claim that “many north Europeans live in countries far more sunny than southern Europe” is not supported by empirical evidence… in other words, it’s “bullshit”.

    More UV and UVb hits the earth in the north during a full summer day’s sun in Sweden than in equatorial Africa.

    … very disappointing Sean, not only did you fail to provide evidence for your original claim, but you actually went on to make another equally unlikely claim, again with no evidence to back it up. So again, I call bullshit – can you please provide solid data that backs up this claim.

    I’ll draw your attention to the EuroSun project, in particular this page: http://www.eurosun-project.org/UV-Maps/Maps.html, which shows monthly maps of UV over all of Europe, and this one: http://www.eurosun-project.org/UV-Maps/Results.html which shows month-by-month UV levels at the 40th, 50th and 60th parallels north. You can see that there is indeed a summer increase in UV in Scandinavia (see the June map for instance), but you can also see that it is limited and doesn’t reach the levels recorded in southern Spain, Italy and North Africa for example. Given that the summer UV at the 60th parallel fails to exceed that of the 40th parallel, I find it very hard to believe it exceeds the level at the equator.. so please, solid data if you have it, stop saying it if you don’t.

    European are not selected to maximise vitamin D from UV.

    Please note I am not arguing for or against a vitamin D hypotheses for depigmentation, I am just pointing out that your statements about higher UV in the north than the south are categorically false. Given the general link between latitude and pigmentation, Vitamin D synthesis is the obvious go-to theory and Jablonski et. al. can be excused for jumping to that conclusion when originally making the connection. Subsequent data however has been ambivalent and there are many reasons today to doubt Vitamin D as the primary driver of pigmentation selection. So feel free to critique the Vitamin D theory of depigmentation, but please do so on it’s actual defects and stop with the nonsense about UV being higher in the north than the south – it’s just not true.

    • Replies: @Sean
    Thank you for taking the trouble to respond to my comments. I do not intend to engage in another protracted correspondence on the issues raised because they are graphically set out in the link

    https://www.unz.com/gnxp/the-genetic-architecture-natural-history-of-pigmentation/#comment-1070347
  13. @Tobus
    You look at people who work outside in the far north they look as if they have had a lot of sun.

    This is what we call anecdotal evidence, I asked for "solid data" like the map that Razib linked to. Like every other piece of empirical evidence available, this map show a general cline of solar radiation from the South to the North. Here's one zoomed in on Europe: http://meteonorm.com/images/uploads/demo_uploads/ghi_europe_mn71.png - as you can see, your claim that "many north Europeans live in countries far more sunny than southern Europe" is not supported by empirical evidence... in other words, it's "bullshit".

    More UV and UVb hits the earth in the north during a full summer day’s sun in Sweden than in equatorial Africa.

    ... very disappointing Sean, not only did you fail to provide evidence for your original claim, but you actually went on to make another equally unlikely claim, again with no evidence to back it up. So again, I call bullshit - can you please provide solid data that backs up this claim.

    I'll draw your attention to the EuroSun project, in particular this page: http://www.eurosun-project.org/UV-Maps/Maps.html, which shows monthly maps of UV over all of Europe, and this one: http://www.eurosun-project.org/UV-Maps/Results.html which shows month-by-month UV levels at the 40th, 50th and 60th parallels north. You can see that there is indeed a summer increase in UV in Scandinavia (see the June map for instance), but you can also see that it is limited and doesn't reach the levels recorded in southern Spain, Italy and North Africa for example. Given that the summer UV at the 60th parallel fails to exceed that of the 40th parallel, I find it very hard to believe it exceeds the level at the equator.. so please, solid data if you have it, stop saying it if you don't.

    European are not selected to maximise vitamin D from UV.

    Please note I am not arguing for or against a vitamin D hypotheses for depigmentation, I am just pointing out that your statements about higher UV in the north than the south are categorically false. Given the general link between latitude and pigmentation, Vitamin D synthesis is the obvious go-to theory and Jablonski et. al. can be excused for jumping to that conclusion when originally making the connection. Subsequent data however has been ambivalent and there are many reasons today to doubt Vitamin D as the primary driver of pigmentation selection. So feel free to critique the Vitamin D theory of depigmentation, but please do so on it's actual defects and stop with the nonsense about UV being higher in the north than the south - it's just not true.

    Thank you for taking the trouble to respond to my comments. I do not intend to engage in another protracted correspondence on the issues raised because they are graphically set out in the link

    https://www.unz.com/gnxp/the-genetic-architecture-natural-history-of-pigmentation/#comment-1070347

    • Replies: @Tobus
    No worries Sean, but please do look at the EuroSun data - it's solid empirical evidence you can use to assess the validity and/or relevance of the more sensationalist claims you hear.
  14. @Sean
    Thank you for taking the trouble to respond to my comments. I do not intend to engage in another protracted correspondence on the issues raised because they are graphically set out in the link

    https://www.unz.com/gnxp/the-genetic-architecture-natural-history-of-pigmentation/#comment-1070347

    No worries Sean, but please do look at the EuroSun data – it’s solid empirical evidence you can use to assess the validity and/or relevance of the more sensationalist claims you hear.

    • Replies: @Sean
    Does the Eurosun data explain why Melanotan II (a non-selective agonist of the melanocortin receptors) acts like an overdose of viagra. Or why a number of studies have found black men are evaluated as more physically attractive by women of all races?
  15. @Tobus
    No worries Sean, but please do look at the EuroSun data - it's solid empirical evidence you can use to assess the validity and/or relevance of the more sensationalist claims you hear.

    Does the Eurosun data explain why Melanotan II (a non-selective agonist of the melanocortin receptors) acts like an overdose of viagra. Or why a number of studies have found black men are evaluated as more physically attractive by women of all races?

    • Replies: @Razib Khan
    Or why a number of studies have found black men are evaluated as more physically attractive by women of all races?

    these sorts of studies are not robust whenever i look into them. i wouldn't cite them this way if you want people to take you seriously ;-)

  16. @Sean
    Does the Eurosun data explain why Melanotan II (a non-selective agonist of the melanocortin receptors) acts like an overdose of viagra. Or why a number of studies have found black men are evaluated as more physically attractive by women of all races?

    Or why a number of studies have found black men are evaluated as more physically attractive by women of all races?

    these sorts of studies are not robust whenever i look into them. i wouldn’t cite them this way if you want people to take you seriously 😉

  17. Can’t what is popular be in play? Human appetites for what is the current style isn’t new.

    • Replies: @Sean
    Yes, but you have to know something is fashionable to think it looks good (like women wearing ponchos a few years ago). Humans seem to have innately similar ideas about what goes to make an attractive individual of either sex. Charles Darwin's informants in recently contacted parts of Africa reported that they and the African men thought the same African women were attractive and agreed about which European women were best looking too. More interestingly the Africans admired beards, although they could hardly grow one. The adaptationist view of human geographical variation can't really explain that.
  18. @PaulS
    Can't what is popular be in play? Human appetites for what is the current style isn't new.

    Yes, but you have to know something is fashionable to think it looks good (like women wearing ponchos a few years ago). Humans seem to have innately similar ideas about what goes to make an attractive individual of either sex. Charles Darwin’s informants in recently contacted parts of Africa reported that they and the African men thought the same African women were attractive and agreed about which European women were best looking too. More interestingly the Africans admired beards, although they could hardly grow one. The adaptationist view of human geographical variation can’t really explain that.

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