SLC24A5, yet again

Posted on July 10, 2017 by gcochran9

It’s under selection all over the place: Europe, Ethiopia, and now among the Bushmen. The advantage can’t be more vitamin D, nor is it associated with agriculture. It does have other effects. Next, the haplotype is very long, yet has been around a long time. Shouldn’t be like that. I was talking with Razib Khan about this a while back: could be that there is more than one active site on the haplotype? Epistatic? That you need at least two changes to get the positive effect, whatever it is? So recombined haplotypes that don’t hold both sites are not favored?

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10 Responses to SLC24A5, yet again

epoch2013 says:

July 10, 2017 at 12:11 pm

“The advantage can’t be more vitamin D, nor is it associated with agriculture.”

But the Koreans, North-Chinese and Japanese have different haplogroups causing skin lightening which are similar to Europeans. They are on similar geographical latitudes and have roughly similar neolitizationed diets. There might have been selection elsewhere but no as strong as in Europe: Nobody is as white as Europeans or the aforementioned Asians.

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- epoch2013 says:
  
  July 10, 2017 at 12:12 pm
  
  “have different haplogroups causing skin lightening which are similar to Europeans.”
  
  The resulting lightness of skin being similar, not the haplogroups. I must learn to reread responses before hitting the Post button.
  
  Reply
- Karl Zimmerman says:
  
  July 11, 2017 at 8:21 am
  
  The more important thing to note, as I said last year in a similar thread, is that populations which are mixed between East and West Eurasian, like the Uighurs, do not show any evidence of elevated frequency.
  
  This suggests that not only did East Asians have an SNP which provided a parallel method of doing…whatever it does…but also that the selective advantage is not additive – that either SLC24A5 or its East Eurasian analogue alone will do you just fine.
  
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  - Uighur Question says:
    
    July 11, 2017 at 2:01 pm
    
    You may need to look at the frequency of the whole haplotype, per Greg’s comments.
    
    Though it’s hard to see how exactly what you suggest would work, exactly. Uighurs are not a population who are uniformly heterozygote for one copy of derived SLC24A5 and one copy of some East Eurasian variant somewhere else.
    
    Another note – Uighurs are probably recently admixed with recent Mongolian ancestry, so may not be much time for selection to operate. May be more interesting to look at ancient Scythians and Siberians and any direct descendant populations who exist – e.g. https://www.nature.com/articles/ncomms14615. All East Scythians have a derived European SNP at SLC24A5, despite East Eurasian ancestry 30-60%. Sample size only 4 sites though.
    
    Reply
epoch2013 says:

July 10, 2017 at 12:59 pm

Another thing that is so interesting is that blond hair, blue eyes and light skin is so tightly connected nowadays, but originated independently. Could that mean that a least in Europe there was sexual preference selection?

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- Razib says:
  
  July 10, 2017 at 2:30 pm
  
  no, because that happened in the high latitude tundra-steppe in the late pleistocene 😉 j/k
  
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  - epoch2013 says:
    
    July 11, 2017 at 12:16 pm
    
    Absolutely, I see it now. Same adaptation as the snow leopard and snow fox. (kidding back)
    
    Reply
  - epoch2013 says:
    
    July 17, 2017 at 4:01 pm
    
    Damn.. Turns out you were no kidding at all..
    
    Click to access 164400-2.pdf
    
    “However, for all three well-characterized skin and eye-color associated SNPs, the SHGs display a frequency that is greater for the light-skin variants and the blue-eye variant than can be expected from a mixture of WHGs and EHGs. This observation indicates that the frequencies may have increased due to continued adaptation to a low light conditions.”
    
    Reply
sammy says:

July 14, 2017 at 12:35 pm

SLC24A5 became popular in a lot of places because of migration not selection. In became popular in Europe because of Anatolian migration. Migration might also be able to explain SLC24A5 in India and Ethiopia.

I’m not saying it hasn’t been selected for in many places, I’m just saying migration plays a role.

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caethan says:

July 17, 2017 at 12:10 pm

Well, if there really is epistasis in an old and conserved haplotype, it should be fairly easy to identify where at least two of the putative epistatic sites are: at the ends of the conserved regions.

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