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Tomenable
05-07-16, 01:05
Light skin in Western Eurasians s caused by many genes, but two most important ones (probably lightening skin more than other genes) seem to be SLC45A2 and SLC24A5. Below I quote data from ED Table 5. in "Genetic History of Ice Age Europe" (2016):

https://www.researchgate.net/profile/Johannes_Krause2/publication/301742169_The_genetic_history_of_Ice_Age_Europe/links/5727c8ca08aee491cb414d0e.pdf?origin=publication_de tail

As we can see, Karelian EHG from Red Deer Island were the only population which had SLC45A2 mutation. On the other hand, the other mutation - SLC24A5 - was present among CHG from Caucasus (Georgia) and unmixed WHG hunters from Hungary:

https://s32.postimg.org/t2tko9xx1/Light_skin.png

https://s32.postimg.org/t2tko9xx1/Light_skin.png

Tomenable
05-07-16, 01:16
So it seems that SLC45A2 derived allele has EHG origin, and SLC24A5 derived allele has CHG origin.

But it turns out, after all, that some WHG - namely those from Hungary (KO1) - also had SLC24A5.

But I wonder how should we interpret Kostenki14 - 17% of derived allele frequency.

Is it enough to assume that he really did carry the SLC24A5 mutation ???

Fire Haired14
05-07-16, 08:55
Levant Neolithic had both as well.

Tomenable
05-07-16, 10:23
But Levant Neolithic:

1) Was younger than these samples (so presence of these mutations in European/Caucasus HG is older)

2) Did have some European HG admixture (= most likely these mutations spread from Europe to Levant)

=======================

As for EHG in Russia, they also had both types of light skin mutations:

https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1800275085

https://s32.postimg.org/ewm8lloyt/Russia.png

Tomenable
05-07-16, 10:23
In Lazaridis 2016 paper, only the Natufians did not have any European admixture.

Other samples did have at least some Euro admixture. Including Levant_Neolithic.

Even in the "Abstract", they write that Euro HG admixture entered the Near East.

berun
05-07-16, 12:52
Even in the "Abstract", they write that Euro HG admixture entered the Near East.

Realy? And how it is that Yamnayists are not saying that this is proof of IE languages and Yamnayan genes entering Palestine around 8000 BC?
:)

Sorry for the off topic irony, I was not able to resist it...

Greying Wanderer
05-07-16, 20:25
SLC24A5 is the one that is very widespread - even pushing into India and Africa - so presumably it has a beneficial effect in addition to the high latitude benefit (whatever it is)

https://westhunt.files.wordpress.com/2014/01/slc24a5.jpg

whereas SLC45A2 is more restricted and therefore maybe only has the high latitude benefit.

My guess is there is an iodine desert (relatively speaking) behind the Himalayas and SLC24A5 has some effect on brain development through more efficient use of iodine on top of the high latitude benefit and this is why it spread into areas where light skin is not an advantage.

Hence the CHG drift into the middle east and beyond because they carried it.

(If this is correct then EDAR would produce the same effect east of the Himalayas and both together aren't additive.)

ThirdTerm
05-07-16, 23:13
https://s32.postimg.org/t2tko9xx1/Light_skin.png

Kostenski14 had the SLC24A5 mutation at 17% and it belonged to mtDNA haplogroup U2, while the allele frequency of SLC24A5 was only 2% for Ust'Ishim in western Siberia. Ust'Ishim man belonged to mtDNA haplogroup R* and mtDNA haplogroup U is its descendant haplogroup and light skin mutations may have originated in this genetic lineage. Ust'Ishim man lived in the immediate aftermath of the genetic interchange between Neanderthals and modern humans and the Neanderthal DNA in Ust'Ishim man occurs in clusters as a result. The initial introduction of the SLC24A5 gene to human lineages could be associated with Neanderthal admixture.

https://s31.postimg.org/qanh596sb/figure3.png

Eiberg et al. (2008) previously reported that a mutation in the HERC2 gene causes blue eyes. HERC2/OCA2 (rs12913832) was found at 100% frequency in the European hunter-gatherers analysed by Mathieson et al. (2015) and Villabruna man is the oldest human specimen with this blue eye mutation at HERC2/OCA2 (100%). The OP's table further shows that Villabruna man did not possess the light skin mutations (SLC45A2, SLC24A5) and he was probably a dark-skinned and blue-eyed individual.



The second strongest signal in our analysis is at the derived allele of rs16891982 in SLC45A2, which contributes to light skin pigmentation and is almost fixed in present-day Europeans but occurred at much lower frequency in ancient populations. In contrast, the derived allele of SLC24A5 that is the other major determinant of light skin pigmentation in modern Europe (and that is not significant in the genome-wide scan for selection) appears fixed in the Anatolian Neolithic, suggesting that its rapid increase in frequency to around 0.9 in Early Neolithic Europe was mostly due to migration (Extended Data Fig. 4). Another pigmentation signal is at GRM5, where SNPs are associated with pigmentation possibly through a regulatory effect on nearby TYR27. We also find evidence of selection for the derived allele of rs12913832 at HERC2/OCA2, which is at 100% frequency in the European hunter-gatherers we analysed, and is the primary determinant of light eye colour in present-day Europeans28,29. In contrast to the other loci, the range of frequencies in modern populations is within that of ancient populations (Fig. 3). The frequency increases with higher latitude, suggesting a complex pattern of environmental selection.

Fire Haired14
06-07-16, 04:29
@Tomenable,

No one has ever claimed Levant_Neolithic had European ancestry. We don't have enough ancient DNA data to know if they had ancestry from Europe or not. They had lots of ancestry similar to Paleo Europeans, that's all we know. Their Paleo-Euro like ancestors could have lived in the Middle East. There's definitely nothing strongly suggesting they had EHG ancestry. At this point we can't conclusively say they did or not. It's definitely possible CHG and Iran_Neo had EHG ancestry though.

This is all we know so far.
Paleolithic and Mesolithic Western Europeans lacked Light skin mutations.
Paleo North Asia(ANE) lacked both or had a low frequency.
Paleo Caucasus and Iran had SLC24A5 but no or a low frequency of SLC45A2.
Levant and Anatolia Neolithic had SLC24A5 at a very high frequency, and a somewhat high frequency of SLC45A2.
Mesolithic Sweden and Russia had a high frequency of both SLC24A5 and SLC45A2.

We can't conclude much about the distant origins of those two mutations with this data. Frequencies of SLC24A5 and SLC45A2 drastically changed in some populations. Most Mesolithic Swedes had both even though they were ~50% WHG who had 0% for both. Most EHG had both even though they were ~50% WHG and ~50% ANE, and none of our WHG or ANE genomes have either mutation. Mesolithic Swedish results make no sense. Maybe there was a Near Eastern population 10,000 years ago who also mostly had both mutations. Anything is possible now.

Sile
06-07-16, 06:04
Below is what Genetiker states for light skin pigmentation from Laz latest paper

SLC24A5, rs1426654, Caucasoid light skin

Sample Region Culture Date D/T
I1633 Armenia Kura-Araxes 2619–2410 BC 1/1
I1290 Iran Neolithic 8179–7613 BC 3/3
I1661 Iran Copper Age 4696–4491 BC 1/1
I1955 Iran Recent 1430–1485 AD 1/1
I1072 Levant Natufian 11840–9760 BC 0/1
I1707 Levant PPNB 7722–7541 BC 0/1
I0867 Levant PPNB 7300–6750 BC 3/3
I1706 Levant Early Bronze Age 2490–2300 BC 4/4
I1730 Levant Early Bronze Age 2489–2299 BC 3/3



SLC45A2, rs16891982, Caucasoid light skin

Sample Region Culture Date D/T
I1407 Armenia Copper Age 4350–3700 BC 11/11
I1634 Armenia Copper Age 4330–4060 BC 3/4
I1631 Armenia Copper Age 4250–4050 BC 14/23
I1632 Armenia Copper Age 4230–4000 BC 19/19
I1658 Armenia Kura-Araxes 3347–3092 BC 0/21
I1633 Armenia Kura-Araxes 2619–2410 BC 8/20
I1635 Armenia Kura-Araxes 2619–2465 BC 0/19
I1656 Armenia Middle Bronze Age 1501–1402 BC 7/23
I1584 Asia Minor Copper Age 3943–3708 BC 0/3
I1290 Iran Neolithic 8179–7613 BC 0/2
I1945 Iran Neolithic 8000–7700 BC 0/1
I1671 Iran Late Neolithic 5837–5659 BC 0/3
I1670 Iran Copper Age 4839–4617 BC 0/1
I1662 Iran Copper Age 4831–4612 BC 0/2
I1661 Iran Copper Age 4696–4491 BC 2/4
I1674 Iran Copper Age 3972–3800 BC 0/2
I1665 Iran Copper Age 3956–3796 BC 0/8
I1955 Iran Recent 1430–1485 AD 9/17
I1701 Levant PPNB 7750–7569 BC 0/1
I1707 Levant PPNB 7722–7541 BC 1/1
I0867 Levant PPNB 7300–6750 BC 4/9
I1706 Levant Early Bronze Age 2490–2300 BC 0/20
I1730 Levant Early Bronze Age 2489–2299 BC 8/10
I1705 Levant Early Bronze Age 2198–1966 BC 0/5

Clearly the populace arrived from north of the Zargos mountains to the levant and mesopotamia

Tomenable
06-07-16, 12:38
and none of our WHG or ANE genomes have either mutation.

This is wrong, KO1 from Hungary was a WHG (he had no Neolithic admixture) - and had one mutation.

As for ANE - according to Genetiker, Afontova Gora 2 (ca. 17,000 years old) had one mutation as well.

bicicleur
06-07-16, 13:16
This is wrong, KO1 from Hungary was a WHG (he had no Neolithic admixture) - and had one mutation.

As for ANE - according to Genetiker, Afontova Gora 2 (ca. 17,000 years old) had one mutation as well.

so the mutation was present and spread long time ago
the question is when selection of this gene started

Fire Haired14
06-07-16, 22:57
This is wrong, KO1 from Hungary was a WHG (he had no Neolithic admixture) - and had one mutation.

As for ANE - according to Genetiker, Afontova Gora 2 (ca. 17,000 years old) had one mutation as well.
Afontova Gora 3 didn't have either mutation. Afontova Gora 2 is of lower coverage.

KO1 is confusing. Everyone thought he was the same as Loschbour but he isn't. I was skeptical of this but got convinced a little bit ago he isn't pure WHG. He has EHG and EEF admixture. D-stats I've looked at suggest he's 20% EHG and 10% EEF. LaBrana1 isn't the same either. He's about 20% ElMiron, so 10% Goyet(Paleo Beligium) and maybe something else. Loschbour might have even have EHG. All the "WHGs" were basically exactly the same but most had at least some other type of ancestry, and we can't really know what WHG is until we get tons of WHG genomes because a WHG we think is pure(eg, Loschbour) might be an unknown mix.

K01 also shared mtDNA R1b1 with Afontova Gora 3. IMO he got the R1b1 from his EHG/ANE ancestors.

Angela
07-07-16, 00:13
@Tomenable,

No one has ever claimed Levant_Neolithic had European ancestry. We don't have enough ancient DNA data to know if they had ancestry from Europe or not. They had lots of ancestry similar to Paleo Europeans, that's all we know. Their Paleo-Euro like ancestors could have lived in the Middle East. There's definitely nothing strongly suggesting they had EHG ancestry. At this point we can't conclusively say they did or not. It's definitely possible CHG and Iran_Neo had EHG ancestry though.

This is all we know so far.
Paleolithic and Mesolithic Western Europeans lacked Light skin mutations.
Paleo North Asia(ANE) lacked both or had a low frequency.
Paleo Caucasus and Iran had SLC24A5 but no or a low frequency of SLC45A2.
Levant and Anatolia Neolithic had SLC24A5 at a very high frequency, and a somewhat high frequency of SLC45A2.
Mesolithic Sweden and Russia had a high frequency of both SLC24A5 and SLC45A2.

We can't conclude much about the distant origins of those two mutations with this data. Frequencies of SLC24A5 and SLC45A2 drastically changed in some populations. Most Mesolithic Swedes had both even though they were ~50% WHG who had 0% for both. Most EHG had both even though they were ~50% WHG and ~50% ANE, and none of our WHG or ANE genomes have either mutation. Mesolithic Swedish results make no sense. Maybe there was a Near Eastern population 10,000 years ago who also mostly had both mutations. Anything is possible now.

Exactly so.




Afontova Gora 3 didn't have either mutation. Afontova Gora 2 is of lower coverage.

KO1 is confusing. Everyone thought he was the same as Loschbour but he isn't. I was skeptical of this but got convinced a little bit ago he isn't pure WHG. He has EHG and EEF admixture. D-stats I've looked at suggest he's 20% EHG and 10% EEF. LaBrana1 isn't the same either. He's about 20% ElMiron, so 10% Goyet(Paleo Beligium) and maybe something else. Loschbour might have even have EHG. All the "WHGs" were basically exactly the same but most had at least some other type of ancestry, and we can't really know what WHG is until we get tons of WHG genomes because a WHG we think is pure(eg, Loschbour) might be an unknown mix.

K01 also shared mtDNA R1b1 with Afontova Gora 3. IMO he got the R1b1 from his EHG/ANE ancestors.

Correct.

So, all we know for sure is that it appeared sporadically in certain ancient samples, that by the time the "farmers" reached Europe they were heavily derived for SLC24A5 and had relatively high percentages for SLC42A5, while the "WHG" were not, and did not, the Yamnaya, who were supposed to be the vector for light skin in Europe were not, and in far northeastern Europe among the SHG many of them were also derived for both. Our two EHG samples from far northeastern Europe were also derived for them.

That's it. There's certainly nothing yet to indicate that the SLC45A2 arose in EHG and diffused to the Levant.

If I wanted to speculate, I think I'd go for both of these first arising somewhere around the Caucasus, but as I said, that's sheer speculation.

Ed. Just a forum note. We now have multiple threads on "pigmentation". Don't start yet another new thread. Post further discussion on existing ones.

Tomenable
07-07-16, 08:24
Angela,


by the time the "farmers" reached Europe they were heavily derived for SLC24A5 and had relatively high percentages for SLC42A5, while the "WHG" were not, and did not, the Yamnaya, who were supposed to be the vector for light skin in Europe were not

The Yamnaya were at least as light-skinned as the EEF farmers, if not more. They were fixed for SLC24A5 (100% derived) - just like EEF farmers - and they had over 40% frequency of SLC45A2 - slightly more than EEF. So calling EEF farmers "light-skinned" and Yamnaya "dark-skinned", when both groups had the same skin colour, is wrong.

BTW - by whom were the Yamnaya supposed to be the vector for light skin?

Groups such as Corded Ware, Srubnaya, Sintashta, Andronovo - were lighter-skinned than Yamnaya (these groups were all 70% up to 99% derived for SLC45A2 - compared to 40-50% for Yamnaya and 35-45% for EEF). So we can assume that CWC and Srubnaya peoples were the vector for light skin in Northern Europe and Eastern Europe. Areas were CWC did not extend - France, Iberia, Italy, etc. - are still on average darker-skinned than Balts or Scandinavians.

========================

Average EEF skin colour was probably similar to that of Non-IE Mediterranean groups such as Etruscans:

http://s10.postimg.org/vwhqjp6k9/Etruscan_Latin.jpg

Dinarid
07-07-16, 08:42
I can't possibly see light-skin genes and Early European Farmers coming from the same source population. Maybe some Early European Farmer males carried Haplogroup R which may have brought light-skin genes, but this would be very far back and after that admixture being quite diluted. I read a study connecting the Early European Farmers to modern-day Armenians, whom they probably resembled. The dark hair, olive skin, and very elongated faces and noses seem to link them, only Armenians are brachycephalic.

The lightest-haired peoples are in the far northeast and rich in R1a, but also N1c1- and they are short and stocky, and have flat, broad faces and round heads. They seem to have the ability to become tanned by the sun in proper conditions.

LeBrok
07-07-16, 08:45
Areas were CWC did not extend - France, Iberia, Italy, etc. - are still on average darker-skinned than Balts or Scandinavians. You can't conclude that, or at least be certain in any way, because:
1. CWC didn't extend to Ireland where we can find lightest skin in Europe today.
2. CWC existed 4.5 kya. We know that lightening of skin was a long process and lasted till our times, and a lot changed in this regard in Northern Europe. You can't equal CWC genetics and light skin mutations in particular to modern Europeans. For that we need more research in all skin alleles and their phenotypical expression.

LeBrok
07-07-16, 08:59
Average EEF skin colour was probably similar to that of Non-IE Mediterranean groups such as Etruscans:

http://s10.postimg.org/vwhqjp6k9/Etruscan_Latin.jpg
Tomenable, how can we trust your impartial rational judgment about skin tone if you purposely picked a picture with the darkest skin Etruscan you could find. They also presented themselves like this:
https://s-media-cache-ak0.pinimg.com/564x/25/08/43/250843204ec51bfe8a491ee1826e4d11.jpg

Or if I would like to discredit paintings as a realistic depiction of ancient people I would post this:
https://www.usu.edu/markdamen/ClasDram/images/13/etruscandancers2.jpg
A black guy with blond hair in Etruria. Guy on the left must be Irish.

Angela
07-07-16, 16:48
You're spamming the same things over and over again, in thread after thread. It's getting annoying as well as boring. Re-read LeBrok's post. Then re-read mine. Then re-read the ones from Fire-Haired. Or, read Matthiesen et al and the other papers on the subject.
http://biorxiv.org/content/biorxiv/early/2015/10/10/016477.full.pdf

There's no inherent, absolute value to having lighter skin. It doesn't make some modern day nationality better or more important to have X% more ancestry than other groups from whatever now extinct ancient tribe of hunter-gatherers first developed the mutations, or in which now extinct group selection first acted upon them, or which now extinct group carried more of it into certain parts of Europe. Surely you're intelligent enough to know that.

As for who thought Yamnaya was the vector for light skin in Europe as well as for lactose tolerance, make that practically every hobbyist for the last ten years, all the way from the days of dna forums, and people who have written professionally on the subject as well.

Just give it a rest, Tomenable. Go outside and enjoy the sun; who knows, you might even turn a lovely shade of brown. :)

Greying Wanderer
07-07-16, 19:27
I think the depigmentation genes came from both the north and the EEF with (imo) the EEF originally getting it from the north before they expanded into Europe (via a CHG-like intermediary population).

It's the WHG who don't seem to have had it - apart from eyes - something i think you can still see a trace of with the black hair / blue eyes type you see around the Irish Sea.

Greying Wanderer
07-07-16, 19:49
Tomenable


Areas were CWC did not extend - France, Iberia, Italy, etc. - are still on average darker-skinned than Balts or Scandinavians.

The recent paper about the UK said lighter skin had been positively selected for.

If so it might be the case that x% of pigmentation genes arrived in different parts of Europe and in some places (more northerly) they were selected for and became 2x% and in other places (more southerly) they weren't selected for and stayed at x%.

Angela
07-07-16, 20:00
I think the depigmentation genes came from both the north and the EEF with (imo) the EEF originally getting it from the north before they expanded into Europe (via a CHG-like intermediary population).

It's the WHG who don't seem to have had it - apart from eyes - something i think you can still see a trace of with the black hair / blue eyes type you see around the Irish Sea.


Very nice look, imo.

Aidan Quinn

https://s-media-cache-ak0.pinimg.com/236x/0e/a3/d8/0ea3d8bb63816bb9239872031f67be30.jpg

Henry Cavill:
https://s-media-cache-ak0.pinimg.com/236x/90/8e/bf/908ebf9144baa884170cd124be1edfc2.jpg
However, I'm very partial to the Aidan Turner and Kit Harrington look as well. :)

http://cdn.collider.com/wp-content/uploads/2015/06/poldark-image-aidan-turner.jpg

http://eye-forward.com/blog/wp-content/uploads/2014/01/tumblr_mz4zgvnk4J1rtsxuto1_1280-e1390869271185.png

Love that Heathcliffe tousled curls look...:)

Not that the fairer version isn't very nice as well:
http://healthyceleb.com/wp-content/uploads/2013/10/Michael-Fassbender-2013.jpg

Lots of variety in Europe nowadays.

MOESAN
07-07-16, 20:26
I can't possibly see light-skin genes and Early European Farmers coming from the same source population. Maybe some Early European Farmer males carried Haplogroup R which may have brought light-skin genes, but this would be very far back and after that admixture being quite diluted. I read a study connecting the Early European Farmers to modern-day Armenians, whom they probably resembled. The dark hair, olive skin, and very elongated faces and noses seem to link them, only Armenians are brachycephalic.

The lightest-haired peoples are in the far northeast and rich in R1a, but also N1c1- and they are short and stocky, and have flat, broad faces and round heads. They seem to have the ability to become tanned by the sun in proper conditions.

No offense but your knowledge about European types seems a bit uperficial for shapes as for colour. Things are not so simple. And you are confusing modern Europoids differences in skin hues which are very slight compared to SSA or Veddoids or other Australoid influenced pops. Don't confuse basal skin colour and tanning. But as says Angela, it could be discussed in pigmentation or anthropology threads, and then we could exchange there.

MOESAN
07-07-16, 20:53
You can't conclude that, or at least be certain in any way, because:
1. CWC didn't extend to Ireland where we can find lightest skin in Europe today.
2. CWC existed 4.5 kya. We know that lightening of skin was a long process and lasted till our times, and a lot changed in this regard in Northern Europe. You can't equal CWC genetics and light skin mutations in particular to modern Europeans. For that we need more research in all skin alleles and their phenotypical expression.

I agree concerning the CWC as cultural, but in some surveys about distances, Irish people show among the closest to CWC (auDNA).
CWC pops were not completely homogenous but they contained types we find today as a respectable to important part of the pops of Northern Europe. CWC contained I think respectable %s of HG elements, surely more on the EHG side than on the WHG one. That said, someones said the WHG arisen again in Europe was not exactly the same as the pre-Neolithic one, at least in some regions; so? Elements came back (mixed) from Northeast where they could have underwent pigmentation selection as others there? And it would be interesting to look at the Irish people 's mtDNA? Just rambling thoughts.

Greying Wanderer
07-07-16, 23:09
Angela


Very nice look, imo.

yes, Cillian Murphy is another example

http://i2.birminghammail.co.uk/incoming/article11256820.ece/ALTERNATES/s1200/JS88492176.jpg

it's interesting as to me it looks kinda half-northern and half southern but not averaged out - more like elements plucked randomly from one or the other and stuck together - if you see what i mean.

i may be imagining it but i've always wondered if that look had an unusual history behind it

Fire Haired14
07-07-16, 23:15
Average EEF skin colour was probably similar to that of Non-IE Mediterranean groups such as Etruscans:


We don't have Etruscan DNA yet. IMO, they'll turn out to be similar to modern Central/North Italians with a big a load of Steppe admixture. Etruscans didn't go extinct they were conquered and became Latin/Italian speakers.

MOESAN
07-07-16, 23:32
Etruscans were a mix of diverse Neolithic people (not without some light taste of CHG) and Villanovian Italics and an elite of East Mediterranea origin, not too precisely localized; at least it's the last version of mainstream thoughts. As a whole, it it's true, they were not so different from other Central "Italians" of the time.

MOESAN
07-07-16, 23:40
Very uneasy to guess where the 2 principal mutations gave birth. We can suppose where they developped, but with some caution and without too big precision: around Western and Northern Black-Sea? The selection of these genes could be linked to other genes - close on same chromosome - selected for other purposes than pigmentation, as proposed by others here.

MOESAN
07-07-16, 23:41
Sorry - "found" birth