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Some European Hunter-Gatherers Were Brown
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San_tribesman A phenotypic takeaway from the ancient European DNA preprint has been that the hunter-gatherer from Luxembourg was light eyed and darker skinned (and dark haired), while the early farmer from Germany was lighter skinned and darker eyed (and dark haired). In yesterday’s post a reader pointed out that I misinterpreted the genotypes of these two individuals at a very important pigmentation locus: I thought that it was homozygous for the lighter skin conferring allele which is at very high frequency in modern Europeans. I was wrong. A SNP at this locus, SLC45A2, correlated with darker complexion and eyes, is present at ~3% in Europeans (as opposed to ~100% in East Asia and Sub-Saharan Africa). In a European American sample the genotypes are as follows:

15, CC
321, CG
3964, GG

Both the hunter-gather and the farmer are CC. Combined with the hunter-gatherer being GG (which is nearly absent in modern Europeans) at SLC24A5 it does seem that as the authors of the preprint were right, the hunter-gatherer had darker skin. The twist is that the region of the genome, OCA2/HERC2, that seems to explain most of the blue vs. non-blue eye color difference in Europe, is homozygous for the blue variant in the hunter-gatherer. I would say that if I had just the pigmentation loci I would think that the hunter-gatherer in this study was from a population mixed between Europeans and non-Europeans. For example, inhabitants of Cape Verde.

The hunter-gatherer individual sequenced from Loschbour rock shelter may be an anomaly. But you wouldn’t find this sort of individual among modern Europeans without recent non-European ancestry, even as an anomaly. So there’s something to explain.

• Category: Science • Tags: Pigmentation 
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  1. There’s also the AMY1 result for Loschbour, which is much closer to post-Neolithic people than the Motala people. That also seems worthy of explanation.

  2. Here’s a Kenyan child with the blue eye gene. I doubt it’s the same variant as the one in Europeans because the child appears to be non-admixed. May just be a local, random mutation. Any thoughts?

  3. many of the loci implicated in normal variation in pigmentation were discovered through pathologies of albinism. so isn’t surprising that the same genes get knocked out over and over. though something like albinism is often a byproduct of inbreeding (a high proportion of albinos are offspring of cousins).

  4. For Insightful; it is a case of Waardenburg syndrome

  5. It’s interesting that on some of the newer admix analyses I show some NE African – which is usually Egypt, Negev and nearby areas. Of course this would potentially point to the Natufian Culture…

    Also, FWIW, my father is Native Irish, has blue eyes, black hair and tans readily – which is the actual stereotypical Irish look – think Irish actor, Gabriel Byrne – despite most Americans thinking Irish have red hair.

    Though all of us are rs16891982=GG

  6. There was an indian tribe called Mandan in the North East of the USA that were renowned for their blue and grey eyes.

    Since genetic links between Europeans and Indians seem to have been found in the Mal’ta boy maybe members this tribe would illustrate the finds?

  7. 1) admixture happened likely earlier than ‘traditoinal’ european coloring evolved

    2) ma’lta boy was dark

  8. “The twist is that the region of the genome, OCA2/HERC2, that seems to explain most of the blue vs. non-blue eye color difference in Europe, is homozygous for the blue variant in the hunter-gatherer.”

    Well, it causes blue eyes in modern Europeans who have “light” alleles at other loci. But what does it do in people who have “dark” alleles at other loci? Does it affect pigmentation as well?

    One possible interpretation would be that the (presumably local European) hunter-gatherers and the (presumably Near-Eastern) farmers evolved different ways to look pale, and when they mixed, modern Europeans kept both “pale” variants due to intense selection for paleness. Blue eyes being a nice epistatic side benefit.

    (This post served to you by Wilde X. Trapolation, press-release-science consultant)

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