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European Hunter-Gatherers, Blue Eyes and Dark Skin?
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Citation: Nature (2014) doi:10.1038/nature12960

Citation: Nature (2014) doi:10.1038/nature12960

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European:

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe…The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

The headlines about this individual having dark skin are well founded, like the Luxembourg hunter-gatherer the sample has ancestral “non-European” copies of most of the major loci which are known to have large effect sizes (SLC24A5, which is now fixed in Europeans, SLC45A2, which is present at frequencies north of 80% in most of Europe, and KITLG, a lower frequency variant known to have a major impact on skin and hair). Additionally, this individual is related to the Ma’lta individual, just like the Swedish hunter-gatherers, but unlike the Luxembourg male (which did predate the Spanish samples by 1,000 years). Lots of functional stuff is in this paper too. Seems like immune adaptations aren’t just a function of agriculture.

One thing I want to note is that I’m not sure how much of the shift toward Finns of the Swedish and Spanish hunter-gatherers is due to Paleolithic European ancestry, vs. admixture with “eastern” elements. Since the Finns seem to have more recent East Asian ancestry excess paleo-Siberian in the Mesolithic samples may shift them in the same direction. The eastward since of the La Brana individuals is really obvious in the world wide PCA, they are farther toward East Asians than any other modern Europeans.

• Category: Science • Tags: Ancient DNA 
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  1. OK, I’ll ask again:

    Do we know whether the so-called “blue eyes” alleles also cause blue eyes when the genetic background at other loci is distinctly “dark-skin”?

    Is there a possibility that it’s just another light-skin allele, that only turns eyes blue in conjunction with light alleles at other loci?

  2. @toto: There are literally thousands of examples of this “blue eyes/dark skin” phenotype in mixed-races people today (search google images for “Blue eyes dark skin” for examples)… so no, I don’t think it’s possible that it’s a light skin gene that also turns eyes blue – plus the many GWASs would have detected this already if it were true. It’s certainly possible that there are other pigmentation alleles that haven’t been discovered that would paint a different picture, but given the knowledge that we have at this point in time the phenotype presented is correct. It’s only our prior assumptions that make us question it’s accuracy – if the DNA were retrieved this morning from a murder scene in NY, the police would definitely be on the lookout for a black man with blue eyes, no question.

  3. there is evidence that the blue eye gene has an effect on skin color. but it’s relatively minor compared to the SLCs

  4. Freckles?

    I’m thinking why would the red hair allele have spread and one possibility – if there is a latitude advantage at play – is a quick and dirty quasi-albinism without some of the negative consequences of full albinism. If so might not IRF4 be similar but dark hair, light eyes and freckles instead of red hair, light eyes and freckles? If you take the near eastern skin lightening alleles out of Irish people would they get darker all over or would a mass of freckles appear?

  5. It’s a huge logical fallacy to correlate SLC24A5 with light skin color in Europeans. I repeat from elsewhere:

    “Yes, of course – as I have mentioned in the past, this is a necessity since the Neolithic/ SE European/ West Asian variants don’t really code for particularly light skin at all in the European context. And as you state, this causes a huge problem: if we don’t know what those mutations/ locations are, we really have no clue what skin (or even hair) color Mesolithic Europeans had – but most likely it was not very dark or brown, at all.”

    “We should also keep in mind that this single mutation [SLC24A5] does not make the skin particularly fair, on its own (it occurs at a significant fraction of people who have Mediterranean, dark Mediterranean, dark W Asian, or even dark S Asian/ African skin color). As I have mentioned before, one also needs to distinguish between static skin color and adaptable (over the seasons), and perhaps take into account subtle photochemistry effects on the molecular level that don’t express themselves that simply and naively as “skin tone.”

  6. if we don’t know what those mutations/ locations are, we really have no clue what skin (or even hair) color Mesolithic Europeans had – but most likely it was not very dark or brown, at all.”

    if we have no clue how can you hazard to guess about likelihoods? 🙂

    anyway, we do have a clue. i turns out that pigmentation is a pretty well characterized pathway. though different populations have different variants, it seems that the same finite number of genes are targeted over and over across metazoans. so you'd just want to look for high coverage whole genome differences.

    We should also keep in mind that this single mutation [SLC24A5] does not make the skin particularly fair

    i’m a homozygote for the derived variant, so obviously i know that. but, presence of the *ancestral* variant seems to make west eurasians rather dark (east eurasians different story). in fact, even one copy of the ancestral variant of slc45a2 tends to give europeans an olive tone.

    you are correct that this population might have had a different genetic architecture toward light skin. but you shouldn’t pretend as if pigmentation pathways are a system we don’t know much about. we have some reasonable prior hunches, albeit uncertain.

    p.s. and chill out on the tone of certainty, since you yourself are admitting that we need to be more skeptical

  7. “chill out on the tone of certainty, since you yourself are admitting that we need to be more skeptical”

    Fair enough, although I only tried to be a bit certain about both our general uncertainty concerning the effect of single mutations, and the main driver, which appears to prefer lighter skin with fewer sunshine hours, like in the special NW subcontinent region island, much of Europe, and especially NW Europe.l

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