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250px-Indig1 One of the most interesting results in the preprint on ancient European genetics (or more accurately, the ethnogenesis of Europeans in a genetic sense) is the fact that the ~8,000 year old hunter-gatherer sample from Luxembourg had a GG genotype on the SLC24A5 locus. Actually, interesting isn’t the right word, shock, and frankly a little skepticism is more precise. The reason for my reflexive incredulity is that the GG genotype is very much the minor variant in Western Eurasia, and extremely rare among unadmixed Europeans. Europeans have such a high fraction of the A allele that some population genetic statistics to test for selection at a locus are not viable, because there’s not enough variation segregating in that region. This allele also is present outside of Europe, with the A allele being the major variant in South Asians, albeit at a lower fraction, verging on ~50% or less in some South Indian groups. Yet it is not entirely implausible that this allele only swept to fixation over the past 8,000 years in Europe looking at the genomic features* of the region in which it is embedded.

I want to make more concrete why this result is a pretty big deal. If you look at the 1000 Genomes data you have results for British, Finnish, Tuscan, and Spanish individuals, as well as a well characterized sample of white Utahans of Northwest European heritage. There is also a less well characterized pooled data set of “European Americans.” Here are the genotype counts by population:

Population AA AG GG
Utah white 85 0 0
British 89 0 0
Finnish 91 2 0
Tuscan 97 1 0
Spanish 14 0 0
European American 4256 40 1

Yesterday on Twitter I suggested that I’d want at least 10,000 individuals of unadmixed Northern European ancestry before I might take a bet that I’d find someone with a GG genotype. I don’t think I was exaggerating. The sample size might be one, but the fact that the individual was homozygous for GG implies to me that the G allele was present at a far higher fraction in Northern Europe 8,000 years ago than today. In contrast the LBK farmer individual was AA on SLC24A5. Why this matters functionally is that no matter how you look at it, when comparing Europeans and dark skinned populations (e.g., Africans, South Indians, and Australasians) this locus is the one that explains the highest proportion of the variation on pigmentation of any gene. Comparing simply people of African ancestry and Europeans the variation at this gene accounts for on the order of ~1/3 of the difference.** I myself have the “European” AA genotype, with most of my other large effect loci being of the “dark” correlated alleles. The pigmentation difference between a Sub-Saharan African and myself is probably accounted for just by this locus alone. But a twist on this story is that the hunter-gatherer also exhibited the genotype associated with blue eyes in Europeans. In contrast, the farmer genotype was the one not correlated with blue eyes. On another locus which is not quite fixed for a derived light encoding variant, but very close in Europeans (and found in much lower proportions in other West Eurasians), SLC45A2, it looks as if both the hunter-gatherer and the farmer carry the modal European form.

220px-Lucy_Merriam Rather that squeezing too much more out of a few samples, I want to posit that these results increase the plausibility that the suite of genetic variants across many loci which are often diagnostic of the complexion of Northern Europeans are a function of a combination of admixture and then selection within the resultant Northwest European lineages. It seems plausible that independent selection events were occurring across these groups, and with admixture more novel variants were present in the combined population which allowed for a skew even further along the phenotypic continuum, toward the physiological limit (at least for non-albinos). Though it looks like the majority of the ancestry of Northern Europeans, especially populations around the coastal East Baltic region, derive from hunter-gatherer groups indigenous to the continent (i.e., pre-Holocene), if they were not fixed for the derived variant on SLC24A5 it seems implausible that these ur-Europeans were defined by the rosy complexions which are archetypical for Northern Europeans . This is part of the broader picture whereby the phenotypically salient population clusters we see around us today, as if they are Platonic ideals of underlying racial forms, may themselves be phenomena distinctive to the Holocene .

* A large correlated block of markers which seem to have risen in frequency recently and rapidly within the population.

** Northeast Asians have their own distinct mutations which confer light skin.

• Category: Science • Tags: Pigmentation, Population Structure, Race 
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  1. Maju says: • Website

    SLC24A5, TYR, and SLC45A2, the three genes found to affect skin color in South Asians (Stokowski 2007) only explain some 25% of skin color variation in Cape Verdeans (Baleza 2003). Together with APBA2 (OCA2), they explain about 50% of inheritance in this trait (the rest remains unexplained so far) and about 40% of the actual phenotype variance (20% is not heritable).

    Another study in Europeans (Candille 2012) attributed most of the skin color variation to SLC45A2, founding TYR variance as only related to freckles and not skin color as such within Europe. SLC24A5 could not be discerned in this study because of its near-fixation status in Europe.

    So we are before one out of three relevant SNPs in a gene that, as a whole, only seems to weight around 15% on skin color phenotype (Baleza). With some uncertainty I would think that this site alone only weights around 5% on skin color, so rushing to conclusions regarding Lochsbour’s phenotype on this aspect seem to me rather unjustified. Furthermore: the Lochsbour genome is extremely good quality, why aren’t people discussing all the other pigmentation related sites? I’m guessing that they have not been published and the study as such does not discuss them, you tell me.

    Anyhow, as I have mentioned elsewhere, judging from the PCA (and also he unusual archaism of the skull), I have the most serious reservations about Lochsbour being a good representative for the WHG ancient population and modern genetic component.

    [PS- how can one subscribe to the discussion?]

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  2. So we are before one out of three relevant SNPs in a gene that, as a whole, only seems to weight around 15% on skin color phenotype (Baleza)

    i’m very familiar with the baleza paper and this literature. you can’t just arbitrarily say “let’s pick baleza, because….” the variations effect depends on the nature of the variation segregating in the population. e.g. in populations where a SNP is fixed for ancestral or derived it’s not going to explain much of the variation. having some difficulties with understanding other aspects of your comment probably due to some language confusion.

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  3. Tobus says:

    SLC45A2, it looks as if both the hunter-gatherer and the farmer carry the modal European form

    Unless I’m reading it wrong, both have the ancestral African form, from Table 7 of the SI:
    rs16891982 SLC45A2 C/C C/C

    From NCBI (C/C, C/G, G/G):
    HapMap-CEU (0), 0.034, 0.966
    HapMap-YRI 1, (0), (0)

    By my reading Loschbour has none of the 3 known European “white” skin genes, Stuttgart has 1 and half (heterozygous for TYR).

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  4. yeah, i think i misread this. if this is right this is an even bigger deal. dark skinned hunter-gatherers with bright blue eyes?

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  5. “unusual archaism of the skull” – I have been wondering why no one seems to have mentioned the brow ridges apparent on the Loschbour skull.

    And I’m being completely objective because my mtDNA is U5a :)

    Yes, I know it’s only a little bit. But it’s mine!

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  6. While I am at it, does anyone happen to know the variant that causes freckling in northern Chinese? Is it the same as in Europeans? It’s a tough one because it’s not very common, but certainly not unknown. My Chinese mother-in-law had freckles, and not from any cryptic European ancestry, because my daughter’s results show her to be 50% East Asian, i.e. from her mother.

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  7. dixie says:

    “freckling in northern Chinese”
    Both freckle and red hair are caused by the MC1R gene. While the red hair effect is recessive, not sure about freckle.

    Historically the third Chinese dynasty Zhou (from about 1100 BCE) was formed from the alliance of the Ji and Jiang tribes.
    The Zhou dynasty lasted more than 700 years and about half of the Chinese surnames derived from these two tribes. So they are the mainstream ‘Chinese’.
    Out of the over 30 Kings of Zhou, 14 of them had senior wives from the Jiang tribe.

    The chinese word Jiang is also used to describe people with red hair. The Jiang tribe was descended from the ‘Flame Emperor’ and they were named after the Jiang river at NW China close to Altai and Lake Baikal.
    Prior to the alliance out of the 10 Jiang tribal leaders four of them had senior wives from the area close to Altai (Guifang in Chinese
    Some of the Ji tribe leaders also had senior wives from there also.

    After the formation of the Zhou dynasty, the Jiang tribe was given the duchy called Qi, with capital called Linzi. The ancient DNA from Linzi was analysed by Wang, Oota et al,

    For the DNA data from 500 BCE the closest modern population to them were from Iceland, the decendents of the Viking (with many red hairs). The Linzi data from 0 CE (there was a change of dynasty and ruling house) was closest to the modern Uigher. The DNA drift is apparent.

    The re-analysis from Bennett re-affirmed the general result from Wang and Oota.

    If these are true then 50% the descendents from the Jiang tribe (roughly 8% of Chinese) will have at least one red hair gene. There will be some from the descendents of the Ji tribe but the percentage will be hard to estimate.
    The son-in-law of certain Australian politician whose surname is from the Jiang lineage and his daughter has red hair (for privacy reason not naming her directly but photos are readily available on internet). Note it takes a pair of red hair genes one from each parents to produce a red head, and red hair gene is recessive and black hair gene is dominant.

    What is the surname of your Chinese mother-in-law?

    Interestingly, from Shetland Island UK,

    “Due to patronymics, the surnames of his surviving descendants in the male line today are either is with
    the matches Altai people of Central Asia. The only exact matches in about 100,000 samples are found in Altai people of Central
    Asia. The only exact matches in about 100,000 samples are found in Nepal, and is with the Western Norway, as well as Shetland”

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  8. Wang. She was from a long line in the area that was the state of Qi.

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  9. dixie says:

    Re: “freckling in northern Chinese”

    The Wang is the most complex Chinese linage. Originally derived from the Ji tribe. A Zhou royal prince had disagreement with the emperor and self exiled to north east China, changed the surname to Wang, meaning descendent of King.
    However since then any descendants of the sinicised tribal chieftains of Mongol, Jurchen, Xianbe, etc adopted that surname.

    The important Wang lineage from the area of Qi is the Langye Wang from progenitor Wang Dao,

    “Wang’s line, during the subsequent Southern Dynasties, was known as one of the two most honored lines of nobles—the other being Xie An’s line—and in the people’s minds no less honored than imperial households.”

    The Xie linage is descended from the Jiang tribe and the two linages inter-married for more than thoudsand years since pre-history times.

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  10. Thank you. And thanks for the references in your previous comment.

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