The Unz Review: An Alternative Media Selection
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
 TeasersGene Expression Blog
Different Ways to Color a Cat
🔊 Listen RSS
Email This Page to Someone

 Remember My Information



=>

Bookmark Toggle AllToCAdd to LibraryRemove from Library • BShow CommentNext New CommentNext New ReplyRead More
ReplyAgree/Disagree/Etc. More... This Commenter This Thread Hide Thread Display All Comments
AgreeDisagreeLOLTroll
These buttons register your public Agreement, Disagreement, Troll, or LOL with the selected comment. They are ONLY available to recent, frequent commenters who have saved their Name+Email using the 'Remember My Information' checkbox, and may also ONLY be used once per hour.
Ignore Commenter Follow Commenter
Search Text Case Sensitive  Exact Words  Include Comments
List of Bookmarks

Credit: CISC

Credit: CISC

Early last year an ancient genomics paper came out with the title Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. The point here is that light pigmentation associated alleles common in Europeans seem to be relatively new derived mutations from the ancestral state, associated with Africans. An Ewen Callaway write up highlighted the fact that one of the inferences made from these genomes is that these hunter-gatherers had light eyes (blue) and dark(er) skin. At the time I pointed out to Callaway on Twitter that we need to be careful here, as ancient Europeans may have had different variants, and these traits are not monogenic but exhibit dependencies on multiple loci. In light of my post below Graham Coop suggested a similar issue, that there could have been convergence. In other words, just because modern Europeans have particular derived alleles which confer a particular trait, it does not entail that ancient peoples who lived in Europe had to have the same alleles to confer the same phenotype. Alicia Martin observed that OCA2 is a locus where fast evolution occurred in both East Asians and West Eurasians (especially Europeans), but at different SNPs. In other words, the same gene is modified, but the mutational event is distinct.

Pigmentation in humans seems to be a trait we have a pretty good grasp of. Because most of the genetic variation between populations seems to be localized at relatively large effect loci GWAS has been good at picking up the signals. Tests of selection which look at haplotype structure also detect these loci because many of them seem to have swept up in frequency relatively recently. This is consonant with what ancient DNA is telling us, as a substantial proportion of modern European ancestry does derive from peoples who have been resident at high latitudes for tens of thousands of years, but new variants, possibly from the Middle East or elsewhere, have increased in frequency within this admixed populations (in South Asia the same pattern is evident, as the Ancestral North Indians likely introduced West Eurasian variants into the hybrid daughter populations).

But let’s think through some of the implications of the alternative scenarios. One model is implicitly the dominant one, that the modern skin lightening alleles which are derived in contemporary populations are due to new pressures for de-pigmentation. Though some de-pigmentation likely occurred early on, perhaps even in Neandertals, the full suite is recent. Another model is that there were other variants segregating in the older populations, and that new populations brought new variants which swept to fixation. My question is simple: if the indigenous populations of Europe were already relatively light skinned whey did the new alleles rise in frequency so rapidly?

Let’s unpack what I’m getting at. OCA2 and SLC24A5 are two loci implicated in de-pigmentation in Europeans. The regions around the selective events are highly homogenized so that there’s a long haplotype around them. This means that the causal variant was targeted by such strong selection that the flanking regions of the genome were swept upward in frequency faster than recombination could break apart the association. SLC24A5 in particular seems to have been under very strong selection, to the point where almost all variation has been purged from European populations at this locus. In India SLC24A5 is also at a higher frequency than might be predicted by simple contribution of ANI ancestry. The issue that I’m getting at, assuming that modern continental populations such as Europeans are admixed, is why these skin lightening alleles swept to frequency so rapidly and in the case of SLC24A5 nearly to fixation. It’s framed by the analysis presented by this paper, Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?:

Models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci. These mutations can each quickly reach intermediate frequency, preventing any single one from rapidly sweeping to fixation globally, leading to a “soft” sweep in the population. Here we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure. The slow geographic spread of a selected allele due to limited dispersal can allow other selected alleles to arise and start to spread elsewhere in the species range. When these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation. This spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population. We show that the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization, which we extend. We find that the probability of parallel mutation and the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele. This characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection. While our knowledge of these parameters is poor, we argue that even in widely dispersing species, such parallel geographic sweeps may be surprisingly common. Thus, we predict that as more data become available, many more examples of intraspecies parallel adaptation will be uncovered.

Basically, if the ancient North Eurasian populations had lighter skin due to their own alleles, why are the new light skin alleles sweeping up in frequency so strongly after admixture? (for Europeans, I’m thinking SLC45A2 and SLC24A5 in particular). Perhaps the selective sweeps were not driven by light skin at all? Or, perhaps the ancient North Eurasians didn’t have their own variants.

Addendum: The 2007 Neandertal red hair paper offers up a possible solution toward phenotype reconstruction: test the ancient genetic variants in cell lines to check for expression.

 
• Category: Science • Tags: Selection 
Hide 18 CommentsLeave a Comment
Commenters to Ignore...to FollowEndorsed Only
Trim Comments?
  1. “Though some de-pigmentation likely occurred early on, perhaps even in Neandertals”

    They had no tailored clothing and finger bone adaptations for clinging on to mothers coat– like chimps’. So Neanderthals were prolly light skinned–under their fur. And that would explain why red hair goes with such pale skin, and skin cancer.
    ——

    ” In India SLC24A5 is also at a higher frequency than might be predicted by simple contribution of ANI ancestry.”

    I think the simplest explanation for that requires an open mind about what effect white skin can have on reproductive fitness per mate selection, especially when men are taking their pick from an excess of prospective wives. Fair Women, Dark Men and all that

    Colour is quite a marker for social status even now (Rajiv Gandhi may have been the lightest skinned adult Indian male in the country he led) I have seen a documentary about people trying to arrange marriages among some south asian community and the skin colour was asked about by the prospect male over the phone, it was a deal breaker in one case they showed, because the girl was a dark skinned girl. Back in pre modern times a light skinned girl could likely marry up, up out of her caste even. that would have been selection.
    ——-

    “why are the new light skin alleles sweeping up in frequency so strongly after admixture? (for Europeans, I’m thinking SLC45A2 and SLC24A5 in particular). Perhaps the selective sweeps were not driven by light skin at all? ”

    Well the current evidence is pointing to Jablonski and the agriculture vitamin D synthesis theories being wrong so that leaves sexual selection. Given that outsiders with less sexual selection would find the indigenous European women desirable the Indo Europeans invaders of Europe (for example) may have took surviving indigenous farmer women as wives and the the lightest skinned women among the conquered found it easier to marry up and reproduce that would be a possible explanation that tallied with what is now looks increasingly like what white skin (or at least the hair and eyes that go with it) is actually quite good for .
    ——

    ” flanking regions of the genome were swept upward in frequency faster than recombination could break apart the association. …why are the new light skin alleles sweeping up in frequency so strongly after admixture? ”

    I’m a bit out of my depth here but maybe the strertches of the genome with the skin lightening genes made indigenous whites a lot better at surviving, and the dark interlopers’ pigmentation geneses got edged out in the mix by those stretches of indigenous white Europeans genes, even thought he european white skin genes had not all that much of an advantage in and of themselves, by that time.

  2. (Rajiv Gandhi may have been the lightest skinned adult Indian male in the country he led)

    that’s retarded. there are plenty of sardars in particular that are as fair or fairer. keep this a retard light zone and police your own thoughts.

    I’m a bit out of my depth here but maybe the strertches of the genome with the skin lightening genes made indigenous whites a lot better at surviving, and the dark interlopers’ pigmentation geneses got edged out in the mix by those stretches of indigenous white Europeans genes, even thought he european white skin genes had not all that much of an advantage in and of themselves, by that time.

    i don’t really know what you are saying here. say differently.

    • Replies: @Tim
    I think he is just trying to say that he doesn't really understand how genetics and selection work.

    Also, why is the high latitude/vitamin D/agriculture hypothesis being discarded? It seems like it still makes sense. Only when agriculture reached high latitudes did the light skin alleles sweep to rapid fixation, and this happened independently in the farmer populations of both Europe and Asia. As for blue eyes, I guess the selective force isn't yet clear.
  3. Not literally . But his skin made him stand out in a crowd.

    Just what I took it you said: more recently flanking regions of the genome were swept upward in frequency faster than recombination could break apart the association and light skin got carried along.

    But, be that as it may, white skin back in the stone age was spread by sexual selection of women

  4. But, be that as it may, white skin back in the stone age was spread by sexual selection of women

    you don’t know that, so don’t assume it’s a fact. i know more evolution and genetics than you, so don’t speak ex cathedra, it annoys me.

    there’s actually an interesting way that peter’s thesis might be tested, and that’s looking at reproductive skew in sexes. i happen to know researchers working in this area, so the hypothesis of sexual selection might be testable in that way if we get precise enough ratios. should be doable.

    since i’m trying to work on my research i don’t have time to test other peoples’ shit. but someone should at least simulate sexual selection in R instead of just talking about it. i’m mildly skeptical that the selection coefficients are going to work out, but you’ll never know until you test.

    • Replies: @iffen
    If the light skinned groups killed off the darker-skinned groups and assimilated the lighter-skinned groups, would that satisfy the genetics?
  5. @Razib Khan
    But, be that as it may, white skin back in the stone age was spread by sexual selection of women


    you don't know that, so don't assume it's a fact. i know more evolution and genetics than you, so don't speak ex cathedra, it annoys me.

    there's actually an interesting way that peter's thesis might be tested, and that's looking at reproductive skew in sexes. i happen to know researchers working in this area, so the hypothesis of sexual selection might be testable in that way if we get precise enough ratios. should be doable.

    since i'm trying to work on my research i don't have time to test other peoples' shit. but someone should at least simulate sexual selection in R instead of just talking about it. i'm mildly skeptical that the selection coefficients are going to work out, but you'll never know until you test.

    If the light skinned groups killed off the darker-skinned groups and assimilated the lighter-skinned groups, would that satisfy the genetics?

  6. #5, i have no idea what you are talking about. but i don’t think what i think you might be saying works.

  7. @Razib Khan
    (Rajiv Gandhi may have been the lightest skinned adult Indian male in the country he led)

    that's retarded. there are plenty of sardars in particular that are as fair or fairer. keep this a retard light zone and police your own thoughts.

    I’m a bit out of my depth here but maybe the strertches of the genome with the skin lightening genes made indigenous whites a lot better at surviving, and the dark interlopers’ pigmentation geneses got edged out in the mix by those stretches of indigenous white Europeans genes, even thought he european white skin genes had not all that much of an advantage in and of themselves, by that time.


    i don't really know what you are saying here. say differently.

    I think he is just trying to say that he doesn’t really understand how genetics and selection work.

    Also, why is the high latitude/vitamin D/agriculture hypothesis being discarded? It seems like it still makes sense. Only when agriculture reached high latitudes did the light skin alleles sweep to rapid fixation, and this happened independently in the farmer populations of both Europe and Asia. As for blue eyes, I guess the selective force isn’t yet clear.

  8. “reproductive skew in sexes”

    In various posts Peter has asserted that ” Blond hair darkens with age more slowly in women than in men … blue-eyed men seem to have a more feminine face shape … girls tend to have lighter coloured hair.

    About eye and hair colours, I think there is no way they can not be from sexual selection, which is the last explanation standing. Academic comment in media about old blue eyes above mentioned sexual selection (previously avoided as the most controversial hypothesis) might be the explanation. Finding that some Mesolithic men had blue eyes with dark skin, made it it forcefully apparent that eye colour is most certainly not a side effect of skin lightening.

    Back to white skin, women who are trying to look sexually appealing to men (ie female porn performers) typically have their hair bleached, breasts enhanced, and their skin tanned. So light skin is not for eliciting lust, which means it is not sexual selection in the strict sense.

    My bet is white skin is a female adaptation that functions to elicit care and provisioning of the woman by her husband, maybe it helps to get a husband in a monogamous mating system.

  9. In various posts Peter has asserted that

    i’ve read peter’s book and his work. it’s certainly interesting, but please do understand that it’s not the last word on everything.

    Academic comment in media about old blue eyes above mentioned sexual selection (previously avoided as the most controversial hypothesis) might be the explanation.

    it didn’t previous avoid it. it’s a deus ex machina which shows up regularly when there isn’t another option. don’t characterize the academic opinion when you don’t know it.

    Finding that some Mesolithic men had blue eyes with dark skin, made it it forcefully apparent that eye colour is most certainly not a side effect of skin lightening.

    again, you’re sounding like a retarded teenager pretending to be a lawyer. stop this now. 1) we don’t know that the MHG had blue eyes and dark skin, though it’s a plausible conjecture (THIS POST EXPLAINS WHY!) 2) we don’t know that it’s not a side effect of skin lightening even if they had blue eyes, because OCA2-HERC2 has been known to have an independent effect on skin lightening (this is referenced in this very post). if you did not know this YOU SHOULD STOP COMMENTING ON THE TOPIC.

    Back to white skin, women who are trying to look sexually appealing to men (ie female porn performers) typically have their hair bleached, breasts enhanced, and their skin tanned. So light skin is not for eliciting lust, which means it is not sexual selection in the strict sense.

    until after world war 2 the fashion was for light skin, not tanning.

    maybe it helps to get a husband in a monogamous mating system.

    i already explained how you could test this. you don’t need to repeat peter’s conjecture. we need to test it.

  10. Only when agriculture reached high latitudes did the light skin alleles sweep to rapid fixation, and this happened independently in the farmer populations of both Europe and Asia

    yes, but we don’t know if the sweep was due to that. remember that slc24a5 looks to be under selection even in south asia.

  11. I happen to think I know enough about vitamin D and how its synthesis is controlled in the body and the binding proteins that moderate its transport ect ect in whites and blacks to conclude that the theories which postulate a connection between vitamin D synthesis and white skin are basically wrong. And the worlds premier medical authority, the Institute of Medicine, in its large US government commissioned report on D found none of the claims for low D levels stood up.

    —–
    Sexual selection was was described as a controversial theory by a science journalist in an article dedicated to the origin of white skin colour.

    “Where does white skin come from? 19 August 2009 by Anil Ananthaswamy
    Juzeniene and her colleagues recently reviewed alternate hypotheses for why humans might have evolved lighter skin (Journal of Photochemistry and Photobiology B: Biology, vol 96, p 93). One highly controversial idea involves sexual selection: once sensitive light skin was no longer hazardous, as in Africa, it was selected for sexual attractiveness. The other idea is that dark skin was more prone to frostbite in higher latitudes, and hence would have come under negative selection pressure, a claim that comes from studies of soldiers during the Korean war, when black soldiers suffered far more frostbite than white soldiers. Juzeniene is not convinced by these alternatives. “The vitamin D hypothesis is the most likely hypothesis although there is still no consensus about it,” she says. Robins, on the other hand, is keen on the frostbite theory for the evolution of lighter skin. “If darker skin people are going to have frostbite, and babies and mothers’ nipples are going to be frostbitten, then like sunburn, this is going to be a potent selective force,” he says.”

    I suppose that controversial means that scientists are less likely to be bringing it up . When scientist are quoted bringing sexual selection up as a possibly explanation (as one was about old blue eyes above) it is reasonable to say that the balance of opinion is beginning to shift away from the idea that sexual selection is a controversial and rather fringe theory
    —–

    “OCA2-HERC2 has been known to have an independent effect on skin lightening (this is referenced in this very post). ”

    The hair and eye genes are not noticeably affecting skin colour, you can have olive skin and blue eyes.
    Now doesn’t that seem the long way round for evolution to have simple loss of skin pigment? Nothing to do with vitamin D.

  12. Sexual selection was was described as a controversial theory by a science journalist in an article dedicated to the origin of white skin colour.

    FUCK YOU! don’t quote a science journalist you just googled asshole. i keep telling you not to pull that shit and think you can get away with it, and you just keep doing it. i actually read the science literature and it’s in there.

    The hair and eye genes are not noticeably affecting skin colour, you can have olive skin and blue eyes.

    there’s been research on this dumbfuck. i can point you to it but there’s no way you’re going to read it.

    banned.

  13. My question was if the people with the light-skinned genes preferred other light skinned people and de-selected darker skinned people wouldn’t we end up with lighter skinned populations.

    yes. it’s a tautology.

  14. Were the Aryan invaders in India light-skinned? Makes sense then, the preference for light skin there. Preference for light skin is probably universal, according to Judith R. Harris.

  15. Were the Aryan invaders in India light-skinned?

    yes, but, 1) i suspect there were pre-aryan ppl from west asia 2) later invaders also were lighter skinned. the color terms in north india actually derive from the muslim period, when ‘white muslims’ (from persia and central asia) were keen to distinguish themselves from ‘black’ converts.

    Preference for light skin is probably universal, according to Judith R. Harris.

    peter frost is a better authority on this sort of thing. and the preference seems to show up stratified societies. like a lot of evolutionary psychological inferences i’m now starting to wonder whether it is universal, or whether it emerges specifically in particular social contexts as part of evoked culture (e.g., the waist-hip ratio preferred by males in developed societies may be a function of those societies!)

  16. The most basic thing to take into account when thinking about strong selection is that for an allele to spread, it must lead to more viable offspring who also reproduce.

    This is a real problem with the sexual selection hypothesis of light skin. What about the darker skinned people? By what mechanism would they reproduce any less? By not being able to find a mate at all?

    In the case of height, people might try to find a taller mate, but generally shorter people still end up having children with other shorter people anyway. In the case of lactose tolerance, there are clearly nutritional advantages. Lactose tolerant people don’t avoid certain partners, yet the genes have spread rapidly because of an invisible advantage to thw offspring.

    How many people would actually not have sex with someone because their skin was just as dark as their own skin? That would require an extremely strong cultural influence, and it is hard to see how that could be maintained across an entire continent long enough for total fixation of these genes. If the selection was purely for “looking like a real farmer” and then being allowed to get the calorie benefits and community support of a farmer, then why did the blue eye allele also increase so quickly?

    Were light skinned babies given more food, or a spot closer to the fire over hundreds or even thousands of years? It is very hard to imagine that purely visual selection would drive such a fast gene fixation.

    I am sure that this kind of sexual selection could happen (otherwise we wouldn’t have peacocks and such) but it just seems like too much of a coincidence that it spread with a new dramatic change in diet.

  17. degeneration into an incoherent bull session. closing.

  18. […] Different Ways to Color a Cat – from razib. – h/t billare! who tweeted: “Progenitors of modern Europeans were fairly light-skinned–why did a 2nd bout of selection leave its tell-tale marks?” […]

Comments are closed.

Subscribe to All Razib Khan Comments via RSS