Light skin allele of SLC24A5 gene was spread by the Indo-Europeans (R1a + R1b)

[Maciamo]

A new paper published by V. Canfield and his colleagues looked into the allele distribution of the SLC24A5 gene, whose A111T (rs1426654) mutation is linked with light skin pigmentation in European, Middle Eastern and Central/South Asian populations. The paper comes just two months after a similar study by Mallick et al., which already suggested an Indo-European diffusion of the A111T allele.

A quick glance at the distribution maps of the A111T allele from both studies immediately shows the very strong association with the spread Indo-European languages and paternal lineages (R1a and R1b). The map by Canfield et al. (in brown) displays a particularly strong correlation with Y-haplogroup R1b, showing peaks in the A111T frequencies in Northwest and Central Europe, the Danube basin, the Caucasus, Anatolia, Iran and Turkmenistan.







Where did the light skin allele first appear ?

Mallick et al. estimated the coalescence time of the rs1426654 mutation at 28,100 years, although with a very wide confidence interval (95% CI - 4,900 to 58,400 years), which doesn't help at all determining its place or population of origin.

Canfield et al. narrow this down to 12.4 years ago, with a 95% confidence interval for the range 7.6−19.2 kya. This would correspond to the terminal Upper Paleolithic to the Middle Neolithic period, in other words exactly the period during which I have estimated R1b people to have settled down around modern Kurdistan, domesticated cattle, then migrated to the Pontic Steppe.

It is not certain that the SLC24A5 mutation conferring fair skin arose within haplogroup R. The Mal'ta boy (Y-DNA R*) didn't have it 24,000 years ago. Considering the very dark skin of R2 populations in Southeast India and Southeast Asia, it surely wasn't present among the original R2* lineages either. Based on its equally strong association with modern R1a and R1b populations, it is far more likely to have arisen among R1 carriers. Nonetheless it could just as well have been picked up in another population and been transmitted to R1a and R1b men through the maternal side.

The question is where and when exactly did this mutation occur ? It could have been in Anatolia, Kurdistan or around the Caucasus, but then how comes it doesn't peak in the Middle East today, and is even more common in places like eastern Spain and northern Pakistan at equal latitude ? It could have first appeared among some European tribes during the Late Palaeolithic. However even Mesolithic European samples from Western and Northern Europe had apparently darker skin than Neolithic farmers. Yet it surely wasn't spread by Neolithic farmers, otherwise the Sardinians would be a hotspot of fair skin in Europe, which isn't the case. Greece and western Anatolia also have lower frequencies.

What seems undeniable is that there is a connection to R1a and R1b. My guess is that the A111T mutation arose shortly before the end of the last glaciation (perhaps 18 to 12 kya) among mtDNA U5 lineages of R1 people in Eastern Europe (southern Russia ?).

UPDATE

It's also interesting that the Sahel region of sub-Saharan Africa, where R1b-V88 is found at relatively high frequency in numerous ethnic groups (Fulani, Kirdi, Hausa), falls in the range 15 to 30% for the A111T mutation. This clearly confirms that R1b people already had this mutation before the split between V88 and P297 (M269+M73), which I estimate to have taken place just after the domestication of cattle in northern Mesopotamia 10,500 years ago. The A111T allele frequency also happens to match pretty well the percentage of Eurasian autosomal DNA found in northern Africa (much better than the frequency of R1b, which is more liable to drift).

The very high frequency of A111T alleles along the Mediterranean coast of Africa confirms that the mutation was spread by a variety of historical people from the Middle East (Phoenicians, Arabs) who contributed to the gene pool in the region.

In both maps the gradient over the Sahara is unreliable though, as there are no sampled population between northern Algeria and the southern Sahel (Canfield) or even farther south in Central Africa (Mallick).

[Nobody1]

Maybe its a combo of Neolithic and Indo-European (at least in Euroland);

Neolithic Ötzi already had the rs1426654 mutation (light skin) at ~3300 BC + earlier;

''A111T set by the finding that the Alpine “iceman” dated to 5.3 kya was homozygous for this variant''
Keller et al 2012 - p.4
http://www.nature.com/ncomms/journal...ncomms1701.pdf

But since a frequency is attached to it (the higher the lighter) maybe the Neolithic amount was lower than the Indo-Europeans;
Because the distribution of A111T (rs1426654) clearly mirrors the Indo-European range; No doubt about that;

And Loschbour (hunter-gatherer) was darker (skin pig) than Stuttgart (farmers-chick) i.e. Neolithic farmers and than the Indo-Europeans;

[Maciamo]

Maybe its a combo of Neolithic and Indo-European (at least in Euroland);

Neolithic Ötzi already had the rs1426654 mutation (light skin) at ~3300 BC + earlier;

''A111T set by the finding that the Alpine “iceman” dated to 5.3 kya was homozygous for this variant''
Keller et al 2012 - p.4
http://www.nature.com/ncomms/journal...ncomms1701.pdf

But since a frequency is attached to it (the higher the lighter) maybe the Neolithic amount was lower than the Indo-Europeans;
Because the distribution of A111T (rs1426654) clearly mirrors the Indo-European range; No doubt about that;

And Loschbour (hunter-gatherer) was darker (skin pig) than Stuttgart (farmers-chick) i.e. Neolithic farmers and than the Indo-Europeans;

Neolithic farmers obviously caried the A111T allele as you pointed out with Ötzi and the LBK sample from Stuttgart, although not at a nearly 100% frequency like the Indo-Europeans. The way I see it is that the A111T mutation did not originate with Neolithic farmers, but they were somehow blended with a population that had it. If R1b did indeed come from eastern Anatolia/Caucasus during the Neolithic (as cattle herders) before moving to the steppes, as I have suggested, then R1b populations could easily have contributed to the A111T among their Near Eastern neighbours (E1b1b, G2a) on their way from the Levant to the Balkans. Actually, if R1b-V88 arrived in the Levant around 8000-7500 BCE as I have estimated, then R1b-V88 herders could have intermarried with G2a and E1b1b farmers before they even reached Anatolia.

Since over 95% of people in core European R1a and R1b populations today have the A111T mutation, chances are that the Indo-European R1a and R1b had a frequency close to 100%, since they managed to keep high frequencies even after mixing with other populations. Of course natural selection due to environmental factors (UV rays) might have played a role too, but not that much considering that other mutations can also influence skin pigmentation. It is obvious that Iraqi or Pakistani are darker skinned than the Finns or Northeast Asians, but someone with no knowledge of modern phenotypes could not guess from the map of A111T.

[Alan]

The epicenter looks more like to be between West Asia (minus Arabia) and Western part of South_Central Asia (minus India).

It reminds very well to the distribution of Caucasus-Gesdrosia even in Europe.

[bicicleur]

UPDATE

It's also interesting that the Sahel region of sub-Saharan Africa, where R1b-V88 is found at relatively high frequency in numerous ethnic groups (Fulani, Kirdi, Hausa), falls in the range 15 to 30% for the A111T mutation.

It would be interesting to know whether R1b-V88 have more A111T than others in this region.

[bicicleur]

It seems to me Frenchmen and Brits have more light skin allele than Scandinavians, alltough Scandinavians seem to have lighter skin.
Is this due to more exposure to sunshine in France and on the British Isles?

[Alan]

It seems to me Frenchmen and Brits have more light skin allele than Scandinavians, alltough Scandinavians seem to have lighter skin.
Is this due to more exposure to sunshine in France and on the British Isles?

I always had this impression that Scandinavians and East Europeans do not have pale skin per se but a yellowish tone into it. While real rosy-pale skin is more common in NW Europe. Scandinavians on average have lighter hair and eye color.

Also this map just shows the regional frequency of this mutation. And between Scandinavia (95%) and West Europe (100%) isn't much difference at all.

And as you said UV rays probably play a role too.

[Maciamo]

It seems to me Frenchmen and Brits have more light skin allele than Scandinavians, alltough Scandinavians seem to have lighter skin.
Is this due to more exposure to sunshine in France and on the British Isles?

SLC24A5 is not the only allele involved in skin pigmentation. For instance there is also MC1R, which is associated with extremely white skin, freckles and red hair (several mutations). East and North Asians, as well as some Russians, Finns and Scandinavians also have mutations on the OCA2 gene.

[Maciamo]

The epicenter looks more like to be between West Asia (minus Arabia) and Western part of South_Central Asia (minus India).

It reminds very well to the distribution of Caucasus-Gesdrosia even in Europe.

One problem is that neither map has any sample for Syria or Iraq, nor for eastern Anatolia or the Caucasus. The Canfield map also lacks samples for Iran. That leaves a big question mark over most of West Asia. Looks like there isn't any for Scandinavia, Central Europe and the Benelux either. I wonder why they bothered getting so many samples for East Asia and Native Americans and so few in Europe and West Asia. Only the Levant, Ethiopia, Central Africa and South Asia are well sampled.

[Maciamo]

It would be interesting to know whether R1b-V88 have more A111T than others in this region.

According to the ALlele FREquency Database, the Hausa have 10.5% of A111T mutations, which is the highest for Central Africa. The Fulani and Kirdi are not tested. The Mandenka of West Africa (around Gambia and Senegal) have 15% and have about 5% of E-M81.

They even have a map too.




This data also shows that the Kuwaiti and Levantine Bedouins possess respectively 96% and 93% of this light skin allele.

[Alan]

One problem is that neither map has any sample for Syria or Iraq, nor for eastern Anatolia or the Caucasus. The Canfield map also lacks samples for Iran. That leaves a big question mark over most of West Asia. Looks like there isn't any for Scandinavia, Central Europe and the Benelux either. I wonder why they bothered getting so many samples for East Asia and Native Americans and so few in Europe and West Asia. Only the Levant, Ethiopia, Central Africa and South Asia are well sampled.

Since they have tested Turkey and Balochistan if I am not mistaken, I assume they thought it would be logical that Caucasus, Kurdistan and Iran can't be very different. But indeed it would have been interesting to have data from this region.

Also the two major parts of Indo European dna must have been Caucasus-Iranian-Gedrosia and North European (+some additional EEF). Since we know that North European like H&G had dark skin, and EEF like populations of Europe and the Middle East do not fit the distribution this Allels, it looks like Caucasus-Iranian-Gedrosia is the best fit.

[Maciamo]

Since they have tested Turkey and Balochistan if I am not mistaken, I assume they thought it would be logical that Caucasus, Kurdistan and Iran can't be very different. But indeed it would have been interesting to have data from this region.

It's a dangerous assumption since the Turks have considerable levels of European admixture (up to 25%) and the Pakistani and Balochi have more European admixture than the Iranians. The Iraqi and Syrians have close to no European admixture. Syrian and Iraqi data on A111T could have helped us determine if that mutation arose among R1 people or among other Middle Eastern people.

[Aberdeen]

If most British have the allele for light skin, how do we explain the fact that some of them seem to be quite dark when compared to other Europeans, such as Germans? Some Brits are very light skinned but others are not - just look at some British celebrities, such as John Lennon, Lilly Allen and Russel Brand, and you'll see what I mean. Of course, those three examples, although considered English, are actually recently descended from folks from Ireland and Wales, which are the areas with the highest levels of R1b, and where there are a fair number of white folks who aren't that pale, alone with many who are. So I'm not sure about R1b being associated with the light skin allele. R1a and I1 seem like better candidates for that, IMO. Maybe the R1b folk were more mixed between white and beige.

[nordicwarrior]

If most British have the allele for light skin, how do we explain the fact that some of them seem to be quite dark when compared to other Europeans, such as Germans? Some Brits are very light skinned but others are not - just look at some British celebrities, such as John Lennon, Lilly Allen and Russel Brand, and you'll see what I mean. Of course, those three examples, although considered English, are actually recently descended from folks from Ireland and Wales, which are the areas with the highest levels of R1b, and where there are a fair number of white folks who aren't that pale, alone with many who are. So I'm not sure about R1b being associated with the light skin allele. R1a and I1 seem like better candidates for that, IMO. Maybe the R1b folk were more mixed between white and beige.

Aberdeen, we must not look at modern distributions and their obvious phenotypes to understand the genetic history of Europe. Like Maciamo says... R1b and the great Indo-Europeans brought light skin to the European theater. Of course they also brought blue eyes, blond hair, pixie dust, fluffed pillows, the martini glass, and flushing toilets.

Please don't question these facts by looking at current populations. This will only confuse you.

P.S. Before settling on the Russian Steppes, the R1b/R1a/R* clans first travelled through all of Europe, sailed around the British Isles, and mounted every peak of Norway planting bright red flags the entire way... so as you can see these lands have been initially discovered if not settled by the R family as well.

[Alan]

It's a dangerous assumption since the Turks have considerable levels of European admixture (up to 25%) and the Pakistani and Balochi have more European admixture than the Iranians. The Iraqi and Syrians have close to no European admixture. Syrian and Iraqi data on A111T could have helped us determine if that mutation arose among R1 people or among other Middle Eastern people.

Turks and Balochis have on average 2-3% more North European this is far to noisy to have any significant effect. And The Balochi have also ASI admixture which causes in India darker skin color, similar case with Turks and their East Asian. The other "European" among Turks is connected to their East Mediterranean admixture but since we know that this allele has no connection with farmer isolate population, it mus be Caucasus_Perso_Gedrosia.


But I agree with you that this component must have been brought to Europe, together with North Euro, by Indo Europeans.

[Aberdeen]

Aberdeen, we must not look at modern distributions and their obvious phenotypes to understand the genetic history of Europe. Like Maciamo says... R1b and the great Indo-Europeans brought light skin to the European theater. Of course they also brought blue eyes, blond hair, pixie dust, fluffed pillows, the martini glass, and flushing toliets.

Please don't question these facts by looking at current populations. This will only confuse you.

P.S. Before settling on the Russian Steppes, the R1b/R1a/R* clans first travelled through all of Europe, sailed around the British Isles, and mounted the peaks of Norway planting white flags the entire way... so of course these lands have been initially settled by the R family as well.

I don't think Maciamo's comments deserve that kind of comment - he is, after all, providing a map based on solid research. But I do see what looks to me to be a bit of an anomaly and I wanted to discuss it, not snark about what someone else said. I do think there's a bit of a problem with equating R1b with the light skinned allele. And Norway does fit into that question, since it's higher in R1b than Sweden and Denmark and there are those dark skinned Norse who look so different from other Norse folk. It would probably be quite impossible at this point to equate R1b and autosomal DNA for individuals, in order to find out if R1b folk originally had darker complexions. At this point, such a relationship wouldn't necessarily exist anymore, because of intermarriage in recent centuries. But I personally wouldn't necessarily equate R1b with the pale skin that you see on some British and Norwegian folk.

[nordicwarrior]

I don't think Maciamo's comments deserve that kind of comment - he is, after all, providing a map based on solid research. But I do see what looks to me to be a bit of an anomaly and I wanted to discuss it, not snark about what someone else said. I do think there's a bit of a problem with equating R1b with the light skinned allele. And Norway does fit into that question, since it's higher in R1b than Sweden and Denmark and there are those dark skinned Norse who look so different from other Norse folk. It would probably be quite impossible at this point to equate R1b and autosomal DNA for individuals, in order to find out if R1b folk originally had darker complexions. At this point, such a relationship wouldn't necessarily exist anymore, because of intermarriage in recent centuries. But I personally wouldn't necessarily equate R1b with the pale skin that you see on some British and Norwegian folk.

Fair enough. When taken singularly this thread seems harmless enough.

However, stick around awhile and see if you don't pick up on a bias.

[Maciamo]

If most British have the allele for light skin, how do we explain the fact that some of them seem to be quite dark when compared to other Europeans, such as Germans? Some Brits are very light skinned but others are not - just look at some British celebrities, such as John Lennon, Lilly Allen and Russel Brand, and you'll see what I mean. Of course, those three examples, although considered English, are actually recently descended from folks from Ireland and Wales, which are the areas with the highest levels of R1b, and where there are a fair number of white folks who aren't that pale, alone with many who are. So I'm not sure about R1b being associated with the light skin allele. R1a and I1 seem like better candidates for that, IMO. Maybe the R1b folk were more mixed between white and beige.

See my reply to bicicleur above.

[nordicwarrior]

SLC24A5 is not the only allele involved in skin pigmentation. For instance there is also MC1R, which is associated with extremely white skin, freckles and red hair (several mutations). East and North Asians, as well as some Russians, Finns and Scandinavians also have mutations on the OCA2 gene.

I feel a tad guilty for using such heavy-handed sarcasm. In a hurry, I skipped over this explanation the first time reading through the comments.

However that being said, I do detect an ongoing Indo-European/R1b favoritism on Eupedia, so I'm not going to retract fully.

It's understandable though, if this was my site I'm sure my own spin would show through-- even if I was trying to be completely neutral. Human nature.

[MOESAN]

It seems to me Frenchmen and Brits have more light skin allele than Scandinavians, alltough Scandinavians seem to have lighter skin.
Is this due to more exposure to sunshine in France and on the British Isles?

more than a locus plays a role in skin pigmentation - so even if the mutation in discussion seems having an heavy role, we cannot conclude that a population having a bit less % of this mutation would be by force darker skinned as a mean - Scandinavians HAVE LIGHT SKINS - but do not confuse basic skin colour with capacity to tan - yes Scandinavians tan easily enough spite they do not reach the dark complexion of dark skinned europeans (who become as Indids under sun) -
the fact that more than a locus is concerned (or that more than a mutation is?) stays in the gradual scale of skin colours, even among Europeans even living in the same region the same way of life ... surely not a biallelic system only (look at the crossings balck-white) - by yhe way, Frenchies have more often "dark" skins than Scandinavians - and as a whole Scandinavian pigmentation differs from the Finns and Estonians and Balts one - more pinky skins among germanic Scandinavians, more greyish yellowish white among the others, roughly -

[Angela]

According to the ALlele FREquency Database, the Hausa have 10.5% of A111T mutations, which is the highest for Central Africa. The Fulani and Kirdi are not tested. The Mandenka of West Africa (around Gambia and Senegal) have 15% and have about 5% of E-M81.

They even have a map too.




This data also shows that the Kuwaiti and Levantine Bedouins possess respectively 96% and 93% of this light skin allele.

I suppose everything is in the eye of the beholder. Looking at this map, the most striking thing to me is that while the epicenter seems to be the Middle East, the spread is to the southeast, down into India, west along the coast of north Africa, and then north and north east

Usually, I think you're supposed to look for the most parsimonious explanation, and that seems to me to be the fact that this is tracking the movement of agriculture, or perhaps specifically animal husbandry? I would think multiple yDNA and mtDNA lineages would have been involved in its spread. I doubt that scientists would be able to track the actual occurrence to one specific group with one specific y lineage, but it's possible I suppose. Subsequent migrations would affect the results as well. For example, it's interesting that Orcadians show a bit of yellow...perhaps that's a Siberian segment from the east? There's one in southern Spain as well...perhaps the Moorish invasions? You would think in that case the Sicilians would show a slice of yellow, but perhaps they weren't tested.

The allele, once present in an expanding population such as one that has adapted agriculture could spread very quickly. We only have to look at G2a Oetzi in 3300 BC who was already homozygous for it, as Nobody 1 mentioned up thread.

One thing that I don't think it means, however, is that even being homozygous for it means that people would have been fair in the way that people in this thread seem to be imagining. I believe that Razib Khan mentioned in one of his posts on this subject that he is homozygous for it as well.

Then, the mere presence of these alleles doesn't mean that they were always expressed in the same way. Gene expression is a very complicated and not very well understood phenomenon. So, just as selection or deselection for the alleles could occur based on a combination of climate and perhaps diet, these things could also affect the expression of the alleles in certain conditions. Someone living in cloudy Britain could express the alleles differently than someone baking by the sea in Crete.

Then, there's the other more European specific allele for skin pigmentation, 374f.

That has also been studied: You can find the list of values for European cities in this Lucotte et al paper. Unlike the prior snp, it has not quite reached fixation in Europe, which to me indicates it may be younger than the prior snp. To me, it looks like a more straight north south cline, with the Scandinavian countries having the highest values, although France presents a more complicated picture.

Does anyone remember if this is the snp for which Oetzi was heterozygous? Anyway, here's the paper:

http://www.academicjournals.org/arti...uasa%20pdf.pdf

[Nobody1]

Does anyone remember if this is the snp for which Oetzi was heterozygous?

Rememberence according to what study?

[epoch]

First this: The fact that Chinese, Koreans and Japanese developed lighter skin with different genes involved than Europeans basically points to evolutionary pressure. So what would that be? Most probably vitamin D. Apart from Rachitis a number of diseases seem to be affected by vitamin D deficiency:

http://anthrogenetics.wordpress.com/...athyway-genes/

The list has a number of interesting health issues. Lower fertility, higher mortality, infectious diseases. Now, as far as I understand the part of mankind that departed Africa carried for a large part a number of genes that give lighter skin. This feature is shared with East-asians , Indian and Amerindians. Apparently this is enough "lightening" of the skin for hunter gatherers as American Indians basically carry these. Off course, hunter gatherers eat basically game and fish, which is relatively rich in vitamin D. Especially if you'd eat fish liver. So, we have a number light skinned genes that allow for more sunlight to reach the skin to make vitamin D, but not yet the light skin of European. Remember that the Loschbourg mesolthic hunter-gatherer does not share any of these specifically European light skin genes with us, even if he possibly had blue eyes.

Now the neolithic revolution kicks in. The amount of available food is high but it's mostly cereals. So far less vitamin D enters the body via food. Since farming is considered to be related to the emerging of a number infectious diseases the notion that vitamin D is highly involved in immune system evolutionary pressure for more light skin is quite relevant. It is also noteworthy that in similar environment both Europeans and East-Asians, heavy cereal using agricultural cultural conglomerates, develop genes for lighter skin independently, whereas the mostly hunter-gatherer American Indians do not. That may serve as evidence for neolithic selective pressure.

So, whatever the scenario that brought in the mentioned mutations, I am beginning to get the idea that evolutionary selective pressure assured the ascendancy to 100% of the current genetic make up.

[LeBrok]

First this: The fact that Chinese, Koreans and Japanese developed lighter skin with different genes involved than Europeans basically point to evolutionary pressure. So what would that be? Most probably vitamin D. Apart from Rachitis a number of diseases seem to be affected by vitamin D deficiency:

http://anthrogenetics.wordpress.com/...athyway-genes/

The list has a number of interesting health issues. Lower fertility, higher mortality, infectious diseases. Now, as far as I understand the part of mankind that departed Africa carried for a large part a number of genes that give lighter skin. This feature is shared with East-asians , Indian and Amerindians. Apparently this is enough "lightening" of the skin for hunter gatherers as American Indians basically carry these. Off course, hunter gatherers eat basically game and fish, which is relatively rich in vitamin D. Especially if you'd eat fish liver. So, we have a number light skinned genes that allow for more sunlight to reach the skin to make vitamin D, but not yet the light skin of European. Remember that the Loschbourg mesolthic hunter-gatherer does not share any of these specifically European light skin genes with us, even if he possibly had blue eyes.

Now the neolithic revolution kicks in. The amount of available food is high but it's mostly cereals. So far less vitamin D enters the body via food. Since farming is considered to be related to the emerging of a number infectious diseases the notion that vitamin D is highly involved in immune system evolutionary pressure for more light skin is quite relevant. It is also noteworthy that in similar environment both Europeans and East-Asians, heavy cereal using agricultural cultural conglomerates, develop genes for lighter skin independently, whereas the mostly hunter-gatherer American Indians do not. That may serve as evidence for neolithic selective pressure.

So, whatever the scenario that brought in the mentioned mutations, I am beginning to get the idea that evolutionary selective pressure assured the ascendancy to 100% of the current genetic make up.

I think this is a brilliant observation and conclusion.:69:
The farmers needed to be whiter than WHG to live up North, because they were more deficient in D3.

[kamani]

If the farmers were whiter than WHG, then Southern-Europeans are darker than North-Europeans because of natural selection and adaptation to sunlight, not because of Near-Eastern admixture. I guess I can buy that.