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Saturday, January 7, 2017

Higher caste, lighter skin


The Journal of Investigative Dermatology has a new paper on the pigmentation genetics of populations from the Middle Gangetic Plain in northern India. Its main finding is that upper caste Indians are generally lighter skinned than other Indians, particularly those from tribal groups.

This shouldn't be surprising to most people, but now we have a clearer idea of the genetics behind this phenomenon, including a new marker (SNP rs2470102) that helps to better explain skin pigmentation differences within South Asia.

Those of you wondering how the ancient samples likely to be relevant to the population history of South Asia stack up in terms of the alleles at rs2470102, check out the spreadsheet HERE. See anything interesting? I reckon I can; in terms of this one SNP, pre-Neolithic Western Europeans were potentially darker skinned than most modern-day Indians, because they're all homozygous for the G allele.

Our understanding of genetics of skin pigmentation has been largely skewed towards populations of European ancestry imparting much less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate the skin pigmentation variation in a cohort of 1167 individuals in Middle Gangetic Plain of Indian subcontinent. Our data confirms the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies and also reveals association for rs2470102 SNP. Our haplotype analyses further help us to delineate the haplotype distribution across the social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated SNPs explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated SNPs studied across 52 diverse populations of the Indian subcontinent, reveals wide presence of the derived alleles, albeit their frequencies vary across populations. Our results show that both of the polymorphisms (rs1426654 and rs2470102) play an important role in skin pigmentation diversity of South Asians.

...

However, some tribes show exceptionally high frequency of rs1426654-A allele for example Gujjar (Jammu and Kashmir -1) and Meena (Rajasthan -0.91) (Supplementary Table S3 online). These tribes have been also known to be fair skinned (Joshua project, https://joshuaproject.net/). Interestingly, Brahmins belonging to higher castes in the social hierarchy of the caste system (Supplementary text online), irrespective of their geographical locations (North- Kashmiri Pandits, Pandits of Haryana, Brahmins of Uttar UPradesh), Havik (Karnataka, South) show similar frequencies of rs1426654-A variant (0.83–1) (Supplementary Table S3 online).

Mishra, Anshuman et al., Genotype-phenotype study of Middle Gangetic Plain in India reveals association of rs2470102 with skin pigmentation, Journal of Investigative Dermatology, article in press, DOI: http://dx.doi.org/10.1016/j.jid.2016.10.043

85 comments:

mickeydodds1 said...

I can feel the firestorm gathering already.

Davidski said...

Judging by that spreadsheet I posted, Western Euro Hunter-Gatherers (WHG) were dark skinned, Eastern Euro Hunter-Gatherers (EHG), at least from Karelia, may have been light skinned, and Scandinavian Hunter-Gatherers (SHG) from the Motala site were of mixed pigmentation.

However, EHG and SHG probably weren't fair/mixed because they carried Ancient North Eurasian (ANE) ancestry, because ANE samples AfontovaGora3 (AG3) and MA1 were both dark.

All of the Bronze Age steppe samples are light, which isn't surprising since not only EHG, but also Caucasus Hunter-Gatherer (CHG) Kotias come out light in this comparison.

Onur Dinçer said...

@Davidski

I checked the spreadsheet. It seems the distribution of the light skin alleles of rs2470102 and rs1426654 (SLC24A5) are strictly correlated in both ancients and moderns. Do you think those alleles spread together?

Davidski said...

They probably did most of the time, but at different times with different populations, in all likelihood from the Near East and Eastern Europe.

Samuel Andrews said...

rs2470102 is in the SLC24A5 gene like rs1426654. Anyways the frequency difference between Tribes and Castes is pretty big...
“When populations were grouped by social status, caste populations showed higher A
allele frequencies compared to tribes (0.72 vs 0.39 for rs1426654 and 0.76 vs 0.45 in rs2470102)”

This is just a demenstration of Tribes having less West Eurasian ancestry. We already knew they had less WE ancestry right?

Davidski said...

Yeah, that's why I said it's nothing surprising, although there is a bit of new info there thanks to the new SNP that might be interesting.

Matt said...

Possible to run off the same spreadsheet for rs1426654? I want to look at the correlation structure between the variants.

Olympus Mons said...

So... Yamnaya were extremely light skinned right? So full of ehg and being the dominating force in such a genetic diverse chalco europe... They had to ve extremely light skin, hence helping to fixate those alleles in western europe. Right?

a said...


https://genetiker.wordpress.com/2015/03/07/phenotype-snps-from-prehistoric-europe/

SLC24A5, rs1426654, Caucasoid light skin
Karelia HG I0061 8/8
Samara HG I0124 3/3
Yamnaya I0231 4/4
Yamnaya I0370 1/1
Yamnaya I0441 1/1
Yamnaya I0443 3/3
Yamnaya I0444 1/1

SLC45A2, rs16891982, Caucasoid light skin

Karelia HG I0061 16/28
Samara HG I0124 2/2
Yamnaya I0231 11/22
Yamnaya I0370 0/1
Yamnaya I0438 1/1
Yamnaya I0443 9/23
Yamnaya I0444 0/2

rs2470102

Karelia_HGI0061 AA
Samara_EneolithicI0122A
Samara_EneolithicI0433AA
Yamnaya_KalmykiaRISE240AA
Yamnaya_KalmykiaRISE548AA
Yamnaya_KalmykiaRISE552AA
Yamnaya_SamaraI0231AA
Yamnaya_SamaraI0429AA
Yamnaya_SamaraI0443AA
Yamnaya_SamaraI0444AA

http://www.snpedia.com/index.php/SLC24A5

MaxT said...

@Olympus Mons

"So... Yamnaya were extremely light skinned right? So full of ehg and being the dominating force in such a genetic diverse chalco europe... They had to ve extremely light skin, hence helping to fixate those alleles in western europe. Right?"

Both rs1426654 and rs16891982 existed in Pre-Yamnaya Europe. (SHG) sample have both of them and were lighter than Yamnaya. I'm guessing it was already fixated in some HG before Yamnaya migration.

https://2.bp.blogspot.com/-9faAor2hsHU/VQTCpkYlwdI/AAAAAAAAKAY/66NrPHxDoJ4/s1600/change.jpg

Mathison et al chart shows Yamnaya were darker than Southern Europeans due to lower frequnchy of AA alleles. I think it's probably due to (EHG) who were 75% (ANE).

Alberto said...

Davidski: in terms of this one SNP, pre-Neolithic Western Europeans were potentially darker skinned than most modern-day Indians, because they're all homozygous for the G allele.

Mickeydodds1: I can feel the firestorm gathering already.

No, this is old news. Just another small proof of it. And fortunately it never caused any storm to discover that "white" people spread from the Near East. Except a few crackpots, everyone has accepted this fact with normality.

a said...

SLC45A2, rs16891982, Caucasoid light skin

Karelia HG I0061 16/28----[Yuzhnyy Oleni Ostrov [I0061 / UzOO 74; Karelia in Fu 2016]M6850-6000 BC]

Samara HG I0124 2/2-------Sok River, Samara [I0124/SVP 44] M5650-5555 CR1b1a

Yamnaya I0231 11/22------[Ekaterinovka, Southern Steppe, Samara [I0231/SVP 3] M2910-2875 BC]

https://anthropologynet.files.wordpress.com/2008/10/worldwide-distirbution-of-rs16891982-slc45a2-allele.jpg

http://www.snpedia.com/index.php/Rs16891982(C;G)

SLC45A2-

"...........be one of the significant components of the skin color of modern Europeans through its Phe374Leu (rs16891982[54]) allele that has been directly correlated with skin color variation in mixed-race populations.[40][51.....This variation is ubiquitous in European populations but extremely rare elsewhere and shows strong signs of selection.[52][53][55]"

https://en.wikipedia.org/wiki/Human_skin_color

MaxT said...

It's actually surprising to see on spreadsheet that one Bell_Beaker_Germany sample was dark skinned (GG) while other Bell_Beaker_Germany had light skin alleles (AA). Looks like some dark skinned (WHG) existed well into bronze age!

Pr V said...

In India, its very common to see one sibling who is lighter (olive complexioned) and the other one being dark skinned like african americans. Since Indians are a mix of ANI (Neolithic Iranian) and ASI (Onge-like), its not surprising.

Lista04 said...

Hello @Alberto:
"And fortunately it never caused any storm to discover that "white" people spread from the Near East. Except a few crackpots, everyone has accepted this fact with normality."

Technically speaking, white people did not come from the Near East but from the Eastern Europe (Southwest Russia) as the earliest white people originated in the European Caucasus and spread to other parts of Europe from there. The Near Easterners inherited such genes through the Southern Caucasus where the source of oldest available white-skinned genomes is located. However, regarding the initial source for all, I can tell you that an upcoming study is to reveal that even 27,000-25,000 year-old burials in the Northwest Caucasus had people who all carry not only the genes for Caucasoid white skin but also for the light eyes and hair. This is probably the most interesting news although there was already an oral tradition that such genes stem from that particular region in Eastern Europe (Northwest Caucasus-Pontic steppe where some autochthonous Europeans famed for fairness still live https://s30.postimg.org/xh9el5975/3491275.jpg). I assure everyone that so many good studies are on the way. All we have to do is to wait.

MaxT said...

@Lista04

Are you talking about (CHG)? There is some truth to this since they were really light skinned compared to other ancient population but their auDNA is predominantly Near Eastern/Basal Eurasian so white skinned genomo as most scientific studies says ultimately came from Near East.

(EEF) farmers introduced AA alleles & Basal Eurasian ancestry to Europe before the (CHG).

Alberto said...

@Lista04

Technically speaking, white people did not come from the Near East but from the Eastern Europe (Southwest Russia) as the earliest white people originated in the European Caucasus and spread to other parts of Europe from there

Do you mean modern day Georgia? That's where we might have the oldest samples so far.

However, regarding the initial source for all, I can tell you that an upcoming study is to reveal that even 27,000-25,000 year-old burials in the Northwest Caucasus had people who all carry not only the genes for Caucasoid white skin but also for the light eyes and hair.

Thanks for this scoop. Interesting indeed, since I was going to write in my previous post that Caucasians might be from the Caucasus, as it was first speculated (hence the name) ,since SHG/EHG could only have got them from there, not from WHG or ANE.

Will be interesting to see how these genomes look like. They're probably not ancestral to either WHG or ANE, so the question would be if they are some kind of Basal Eurasians???

Any idea of when these might be published?

Rob said...

A 26ky BP sample from NW Caucasus ?
Marvellous . That's MUP, ~ developed Gravettian (but might be local distinct Caucasus culture).
? Mezmaiskaya Cave

Unknown Singh said...

Davidski: which population introduced to this to South Asia? Iran Neolthic-related or steppe-related? from your spreadsheet data...

Brahmins : A1 A2
Gupta : A1 A2

Tribals
Santal : G A2
Gond : A1 A2

Gond tribe are not very light even if they carry A1A2. Did this first come with Iran Neolthic related people?

Davidski said...

@Matt

https://docs.google.com/spreadsheets/d/1_WGl09Xm5gZgdcC3o8Ijj678WFEGmPL47KL8ElKkS5o/edit?usp=sharing

@Alberto

It's hard to believe that Basal Eurasians lived in the Northwest Caucasus and nearby steppes at any stage. But it's plausible that the UP/Mesolithic foragers there did have some Basal Eurasian admixture, considering that foragers from Georgia were part Basal Eurasian.

Davidski said...

@Singh

Light skin alleles arrived in South Asia with early farmers from Iran and with Indo-Iranians from the steppe.

Davidski said...

@Lista04

I can tell you that an upcoming study is to reveal that even 27,000-25,000 year-old burials in the Northwest Caucasus had people who all carry not only the genes for Caucasoid white skin but also for the light eyes and hair.

Nice, though I'm skeptical that all of them will turn out to be light haired and eyed.

Olympus Mons said...

well,
Regarding light skin... are you talking before going to the beach or after? I am always confused.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485197/

As one can see in this study Skin pigmentation for a Portuguese and a Polish is exactly the same! when measured where it should (armpit) not where Portuguese enjoy expose to sun 90% of the days.

However, Irish are really fair skinned and Italians a bit darker skin.

Davidski said...

That study also claims Irish have lighter hair than Poles, which is nonsense.

The results don't look credible.

Olympus Mons said...

@Davidski.

Lol. - Give me a break. Read the paper.

And stop saying that sort of thing. You not liking the results, posits or statements of a paper is not indicative of anything but your personal bias.

Davidski said...

I did read the paper. It doesn't reflect reality. Maybe due to sampling bias.

A lot of nonsense gets published in peer reviewed papers. Get used to it.

Olympus Mons said...

@davidski.
And I have been many time in Warsaw and Wroclaw (love the place) and many times in Dublin... and did not notice a difference... as the paper shows a small difference.

Note: the difference was just that in Wroclaw girls are much, but much, prettier.

a said...

If I were to speculate....Basal Eurasian not the source but sink for light genes based on Natufian/Iranian+0%Neaderthal
https://s30.postimg.org/xh9el5975/3491275.jpg

Perhaps-Mezmaiskaya /
https://en.wikipedia.org/wiki/Mezmaiskaya_cave
Dmanisi-is pretty old
https://en.wikipedia.org/wiki/Dmanisi

Archaic human-...." The proportion of Neanderthal-derived ancestry was estimated to be 1–4% of the Eurasian genome.[2] In 2013, the same team of researchers revised the proportion to an estimated 1.5–2.1%.[3] They also found that the Neanderthal component in non-African modern humans was more related to the Mezmaiskaya Neanderthal (Caucasus) than to the Altai Neanderthal (Siberia) or the Vindija Neanderthals (Croatia).[3] In the modern human population, at least those of East Asians and Europeans, the total introgressed Neanderthal DNA found spans about 20% of the Neanderthal genome.[4]"
https://en.wikipedia.org/wiki/Archaic_human_admixture_with_modern_humans

Speculate that the white genes are from non-basal Eurasian that contributed to Kartvelians ancient ancestors that comprises the element/component- that fits Yamnaya.
http://eurogenes.blogspot.ca/2015/10/yamnayas-exotic-ancestry-kartvelian.html

All pure speculation.

Olympus Mons said...

@Davidski

"
I did read the paper. It doesn't reflect reality. Maybe due to sampling bias."

Well, all I can do is show you my butt cheeks.
You will understand what I mean. :=)

Tobus said...

One major frequency difference with these SLC24A5 SNPs is in East Asians - rs1426654 is pretty much 100% ancestral in East Asia, while the derived rs2470102 variant is about 20-30% in all the East Asian pops in 1000 genomes: https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?q=rs2470102

As one can see in this study Skin pigmentation for a Portuguese and a Polish is exactly the same!

Jablonki's original 2000 paper using skin reflectance samples from the armpit also showed very little variation across Europe.. most of the difference we see between North/South Europe is due to tanning response.

Samuel Andrews said...

@Alberto,
"And fortunately it never caused any storm to discover that "white" people spread from the Near East."

If anything European levels of light skin derive from natural selection not an ancestor. The "light skin" in Neolithic Anatolia, EHG, CHG, Yamnaya, modern Near East might be what we would call light brown skin.

@Lista04
"However, regarding the initial source for all, I can tell you that an upcoming study is to reveal that even 27,000-25,000 year-old burials in the Northwest Caucasus had people who all carry not only the genes for Caucasoid white skin but also for the light eyes and hair."

This would be a bit of a surprise. The reason is EHG, CHG, and EEF probably didn't exist 25-27ky. Who were these people in the Caucasus 25-27ky? I wouldn't be surprised those pale mutations existed back then because EHG and CHG and SHG and EEF had them 8ky-10ky.

As I said before *natural selection* is the source not an ancestor. Maybe an ancestor introduced the mutations for paleness but they didn't cause them to be popular.

Samuel Andrews said...

@Olympus Moons,
"As one can see in this study Skin pigmentation for a Portuguese and a Polish is exactly the same! when measured where it should (armpit) not where Portuguese enjoy expose to sun 90% of the days."

Who cares? This post's discussion topic is rs2470102 and it's higher frequency in Higher Castes in India(reflective of more ANI).

Do you want your people(Portugese) to be ultra pale? Besides it's a fact Iberians are slightly swarthier or whatever you wanna call it than most Europeans. There's no reason to argue this and there's nothing wrong with it.

You have to understand as far as we know Europeans aren't descended from a proto-white European population, that they're a mixture of mostly the same ancestors at different proportions. You also have to understand we should be open minded about European genetics and all types of genetics, be open to lots of possibilities. We should be open to the idea there was no proto-white population, that skin color varies by region.

I think you think Europeans are descended from a proto-white European population hence I think you think all Europeans are "white", that they're all equally light skinned. That's a hypothesis, based on modern skin color and genetics, but it isn't proven. So far ancient DNA isn't consistent with that idea. So far ancient DNA suggests European genetics are more diverse and Europeans are more unrelated than that. It also suggests the origin of lighter skin in Europe is still a mystery. Skin color can definitely vary by region in Europe because we know Europeans vary genetically by region.

No one here has argued Steppe people, who contributed more to Poles than Portugese, are the source of light skin in Europe, which you seem to think. My opinon is natural selection is the main cooperate. Because of Andronovo results I think maybe mostly Steppe/part MN populations could have been a big contributer.

Would if light skin natural selection affected some Europeans more than others or would if light skinned ancestor contributed more to some Europeans than others? So what? There's diversity in Europe. Big deal. We already knew that. One population isn't less European or inferior because they're darker.

MaxT said...

@a
Nope, take look at Matheson et al. 2015 chart. Yamnaya had very low frequency** for AA alleles, they were darker* than your average Spaniard or Italian.

Matheson et al. 2015 allele frequencies chart https://2.bp.blogspot.com/-9faAor2hsHU/VQTCpkYlwdI/AAAAAAAAKAY/66NrPHxDoJ4/s1600/change.jpg

We can clearly see (SHG) were lighter than Yamnaya. Yamnaya had very low frequency of AA alleles, they were darker than both Neolthic farmers (EEF) and (SHG). In modern context, Yamnaya would not be considered "white" anywhere.

I agree with what Samuel Andrews said
"If anything European levels of light skin derive from natural selection not an ancestor. The "light skin" in Neolithic Anatolia, EHG, CHG, Yamnaya, modern Near East might be what we would call light brown skin."

a said...

MaxT said...

"Nope, take look at Matheson et al. 2015 chart..."

I have no problems with natural selection. However tracking source of particular light skin mutations;without the risk of sounding autistic[some have made fun of me] the 11km cluster of samples from Sok river[Kurgan/HG R1b have oldest samples of Yamnaya-R1b-L23-IO443[L51-Z2103*]&R1b-M73-I0124[Y13872]on tree
notice the relative close distance H/G-Kurgan maybe 5km+/-?
R1b-L23+6200YBP+/-
-http://www.kumbarov.com/ht35/aDNA_02_11_30_2015.png


SLC24A5, rs1426654, Caucasoid light skin
Karelia HG I0061 8/8
Samara HG I0124 3/3
Yamnaya I0443 3/3


SLC45A2, rs16891982, Caucasoid light skin
Karelia HG I0061 16/28
Samara HG I0124 2/2
Yamnaya I0443 9/23


rs2470102
Karelia_HGI0061 AA
Yamnaya_SamaraI0443AA



a said...

To compare:Basal Rich/Neaderthal poor regions-
https://genetiker.wordpress.com/2016/06/22/phenotype-snps-from-the-ancient-near-east/

SLC24A5, rs1426654, Caucasoid light skin
I1072 Levant Natufian 11840–9760 BC 0/1
I1707 Levant PPNB 7722–7541 BC 0/1
I0867 Levant PPNB 7300–6750 BC 3/3

SLC45A2, rs16891982, Caucasoid light skin
I1290 Iran Neolithic 8179–7613 BC 0/2
I1945 Iran Neolithic 8000–7700 BC 0/1
I1701 Levant PPNB 7750–7569 BC 0/1
I1707 Levant PPNB 7722–7541 BC 1/1
I0867 Levant PPNB 7300–6750 BC 4/9
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
I1584 Asia Minor Copper Age 3943–3708 BC 0/3

Tobus said...

@MaxT: We can clearly see (SHG) were lighter than Yamnaya. Yamnaya had very low frequency of AA alleles, they were darker than both Neolthic farmers (EEF) and (SHG)

The pigmentation alleles on that chart are the blue and green lines - 100% of Yamnaya have SLC24A5 and 40% have SLC45A2, which means that 40% of Yamanaya were as light as we can tell and 60% are halfway. SHG have 75% of each, meaning that ~56% were as light as we can tell, ~38% where halfway and ~6% were as dark as we can tell. EEF had frequencies of 90% and 20% meaning light, middle and dark frequencies of roughly 18%, 84% and 8%.

So Yamnaya as a group were decidedly lighter than EEF, and within the extremes of SHG. As I think we all agree, all 3 were darker than any modern European "white" population.

a said...

https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1330589433

Karelian-R1a-Yuzhnyy Oleni Ostrov [I0061 / UzOO 74; Karelia in Fu 2016]M6850-6000 BC] 0% BASAL Eurasian # possible markers for light skin.
Karelia_HG:I0061-54.5-0-3.67-0-0.6-0.43-40.8

SLC24A5, rs1426654, Caucasoid light skin
Karelia HG I0061 8/8
SLC45A2, rs16891982, Caucasoid light skin
Karelia HG I0061 16/28
rs2470102 light skin
Karelia_HGI0061 AA
-----------------------------------------------------

Israel_NatufianI1072-Levant Natufian 11840–9760BC:74.39% Basal Rich Eurasian
0.1-74.39-0.37-1.46-0.05-0.65-22.98
SLC24A5, rs1426654, Caucasoid light skin
I1072 Levant Natufian 0/1
----------------------------------------------
Iran_Neolithic:I1290-Iran Neolithic 8179–7613 BC:57.04%Basal Rich Eurasian
39.55-57.04-0.41-1.3-0.79-0.86-0.06
SLC45A2, rs16891982, Caucasoid light skin
I1290 0/2
------------------------------------------
I1945 Iran Neolithic 8000–7700 BC:52.93% Basal Rich Eurasian
42.75-52.93-1.05-0.77-2.49-0.01 0
SLC45A2, rs16891982, Caucasoid light skin
I1945 0/1


Tobus said...

It's actually a bit more complex than that, as the effect of each SLC24A5 allele is twice as strong as SLC45A2, and if we allow for heterozygous individuals there are 9 different combinations that we can calculate frequencies for.

Here's some charts which show the frequency breakdowns for each possible allele combination: https://drive.google.com/file/d/0B1Z5v96nWWmhSmRER2FOMzY5aW8/view?usp=sharing

I've assigned 35% and 15% lightening effect to SLC24A5 and SLC45A2 respectively, the X-axis number (50, 42..etc) is the total lightening affect, lighter is to the left. You can see that close to 50% of SHG would have been darker than the darkest Yamnaya.

Krefter said...

mtDNA match between LBK farmers and Mesolithic Greek hunter gatherers.

http://mtdnaatlas.blogspot.com/2017/01/the-first-mtdna-from-mesolithic-greece.html

If you want to say something about this do the posting at my blog.

Matt said...

Re: selection on skin colour, Samuel is correct that this had to be the main driver of change, rather than migration introducing new alleles.

For me particularly interesting phenomena, is that among the EEF, the earliest Anatolians seem to have had the lightest skin / eyes (http://www.nature.com/nature/journal/v528/n7583/images_supplementary/nature16152-sf4.jpg and http://www.nature.com/nature/journal/v528/n7583/images_article/nature16152-f3.jpg).

For the early Anatolian Farmers, SLC24A5 is fixed among them (1.0), and SLC245A2 is at 0.4, as it is among the Yamnaya in isolation in this graph (https://2.bp.blogspot.com/-9faAor2hsHU/VQTCpkYlwdI/AAAAAAAAKAY/66NrPHxDoJ4/s1600/change.jpg), while the HERC2 allele associated with blue eyes is at a higher frequency (0.4) than the Yamnaya (0.1).

So the Yamnaya were likely to have been the same in skin as the earliest Anatolian Farmers, and darker in eye.(On this data, with statistical error bounds).

Yet the HG admixed descendents of the earliest Anatolian Farmers, in Europe, the Early European Farmers, seem to have had lower frequencies of skin lightening alleles in anything other than the HERC2 blue eye allele (and even that has mixed results for Iberians).

Matt said...

To compare to my above post, some stories I saw we had a few years ago, with the first publishing of data were something like

"Oh, the early farmers had SLC24A5, but not anything else. Then they got blue eyes from WHG via HERC2. Then SLC45A2 mutation happened. Finally Yamnaya brough blonde hair alleles to Europe. Through all this, slow but steady, natural selection happened, with sustained but very low fitness boosts."

Instead it seems like the "ingredients" needed for a modern European pigmentation, SLC24A5 and SLC45A2 and HERC2, were basically already present in Anatolia, at the same frequencies as among the much later Yamnaya.

But selection just stood still on these for thousands and thousands of years, all through the Neolithic, up to the Bronze Age. (Or it went back and forth and we haven't got the resolution, so I doubt this). Even appears to have gone back more towards ancestral, with the introduction of ancestry from darker skinned WHG. These skin pigment related alleles must've not been associated to reproductive fitness (number of children) or survival, for thousands of years. Then selection became very rapid in the Bronze Age, both on the steppe and in Europe.

So the question is now what made the change on selection (on fitness) happen?

Gioiello said...

This time I agree with Sam: selection (all our hgs are deeply rooted in Western Europe from their origin)

SLC24A5, MYEF2 48433494 rs2470102 A or G
AA Francesca Guarino (NA, K1c1f)
not genotyped Gioiello Tognoni (R-L23-Z2110, K1a1b1e)
AA Giorgio Tognarelli (R-L23-Z2109 (not terminal), H6a1)
AA Monica De Conti (NA, H41a)
AA Silvana Vagelli (NA, K1a1b1e)
AA Velthur Tognoni (K1c1f, R-L23-Z2110)

SLC24A5 48426484 rs1426654 A or G
AA Francesca Guarino
AA Gioiello Tognoni
AA Giorgio Tognarelli
AA Monica De Conti
AA Silvana Vagelli
AA Velthur Tognoni


Rob said...

@ Matt

"So the question is now what made the change on selection (on fitness) happen?"

Diet ? by the Bronze Age, the last of the fisher -foragers had died, it become assimilated.
What if temporary halt in Fat-Vit D rich Sea Fish required accelerated selection of light skin, for more optimal in vivo processing of skin cholesterol esters -> vit D.

Olympus Mons said...

@rob
Increase artisan activities indoors? Or overall activities indoors?

How many men it takes to Sheppard,or hunt, or do the overall outdoors activities? So lots of people started to spend more time without so many sun exposure.
Were not those activities closer to elites?

Matt said...

Spent 10 minutes or so of procrastination stitching together the Yamnaya only part of the graphic from Mathieson's March 2015 preprint with the October 2015 preprint that amalgamates some regions over time and includes Anatolian farmers:

http://i.imgur.com/XMbiBXl.png

So it's clearer where the Yamnaya alone sit, in contrast to the later samples of more diverse Steppe Bronze Age, also including Sintashta, Andronovo, etc. (Admittedly there would be more statistical uncertainty in the Yamnaya alone sample, which is probably why Mathieson amalgamated it with the much more diverse later steppe samples in the final print.).

@ Rob, it could be something like that, where introducing marine diet into EEF who moved into Europe, perhaps through trade with WHG or other means, halted a pattern of selection for lighter skin among cultures on an agricultural diet that picked up again by the Bronze Age when marine consumption was interrupted. I don't know if carbon and nitrogen isotope data is promising on that, though, as you can directly test that way (though, if the consumption changed at the margins maybe it's not sensitive enough for that).

Alberto said...

Yes, selection is what brought modern levels, like in everything else.

Excluding he Iberian samples (which might be a bit special), what's the total number of samples tested for these alleles from the Middle Neolithic Europe? Is it enough to have statistical significance?

Matt said...

In Mathieson's first print of the paper, n as:
Yamnaya: 9

In Mathieson's second print of the paper, n as:

Anatolia Neolithic : 24
Central European Neolithic: 31
CLB (European Bronze Age): 64
STP (Steppe Bronze Age): 47 (24 Early Steppe type (15 Yamnaya, 5 Afanasievo, 4 Poltavka), 23 Later Steppe Type (5 Sintashta, 3 Potapovka, 12 Srubnaya, 3 Andronovo)).

bmdriver said...

Racial Christian eugenics of colonial imperialism never goes away, why do white European people like to assume White skinned blue eyed blonde haired people are chosen by God to enslave the people dark skinned slaves of Hamites.,


Again David and European eugenic scientist are overlaying their own racial profiling to lay claim of others. Surely north India being of colder climate than the south would have lighter pigmentation. Surely East Asians from a more northerly altitude are lighter than their southern tropical counterparts.

Surely native Americans from North America are lighter than their central and southern counterparts.

Surely Northern European are lighter than their Souter. Mediterranean counterparts.

Why not claim these light skinned native Americans, East Asian and Indians as your own to give you that racial sense of superiority, or white mans burden.

All this talk reminds me of the good old Jim Crowe laws.

bmdriver said...

Plus it also makes sense northern Indian farmering societies migrated into Central Asia and Europe. The source of Caucasians are Indians, the population source for Middle East, Europe, steppes is of south Asian ancestry, now go and debate the smaller migrations that ventured back into South Asia as being white Caucasian (.Christian stock) rather than south Asian migrants settling west Asia and then migrating back.

Also amusing how almost all Vedic deities are described as dark skinned.

a said...

So I guess the oldest samples of SLC24A5-rs1426654 samples to date are-
1]Satsurblia cave in Western Georgia dated to the Late Upper Palaeolithic 13,132–13,380 cal. BP.
2]Kotias-a rockshelter also in Western Georgia ,529–9,895 cal. BP
rs-2470102-good bet that Satsurblia is also positive for 2470102-Kotias-K1-AA
tps://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1330589433

Kotias:KK1 44.22 49.1 0.01 1.55 0 0 5.13
Since 8.5K+/- R1a Karelia has 0% Basal Rich component- but both white skin markers/maybe 3, only possible way of transmission would be either ANE or Villabruna?


Norther Caucasus[Georgia] & Southern Russia sweet spots for
frequencies of skin-lightening derived alleles rs1426654 and rs16891982:

Western HG = 12,5% and 0% (combined 13) ---> darkest-skinned of them all
Caucasus HG = 100% and 0% (combined 100)
Sweden HG = 58,3% and 66,7% (combined 125)
Anatolia NF = 100% and 34,8% (combined 135)
Russian HG = 100% and 75% (combined 175)

Showing, that Eastern HG (from Russia) were the lightest-skinned group.

Alberto said...

@Matt

Thanks for the numbers. Though it seems that the Central European Neolithic are all the early and middle neolithic together. But the Middle Neolithic ones listed in their supp. data Table 1 are: 3 Baalberge_MN, 1 Esperstedt_MN, 1 Salzmuende_MN, 1 Hungary Copper Age. Of these 6, 2 are < 0.1x coverage, 1 less than 0.2x coverage and 1 less than 0.5x coverage, so I don't think that more than 3-4 could be tested successfully for each allele, and probably only 2 for all of them.

So it's hard to say how gradual the process was. With more samples we might see that it was more or less steady. Or maybe indeed there was some reason for a stronger selection from the Bronze Age. Not that this really matters much, anyway.

Romulus said...

In Reich's latest talk from a few months ago he says that modern Europeans received their light skin from EEF, which is obvious after the Anatolian Neolithic samples came back positive for both SLC24A5 and SLC45A2.

Grey said...

"In Reich's latest talk from a few months ago he says that modern Europeans received their light skin from EEF"

""white" people spread from the Near East"

"spread from" and "originally derived from" are still separate though and the reasons for both may be informative i.e.

1) where and why were they derived?

2) if they were derived elsewhere than Anatolia (which seems most likely if SHG had them) then why did they spread so much among the Anatolian farmers?

diet is my guess for #2

For the king said...

@David

When you have time, you should run Iran/Levant/Anatolia Neolithic/ChL, Armenian ChL/EBA/MLBA, Natufians, Huto and Iran IA/JordanEBA in your phenotype calculator. They should produce interesting results.

Annie Mouse said...

I cant believe I am commenting on a skin colour discussion.

Armpit skin colour is not particularly interesting as it does not tell you anything about sun sensitivity. Folk can be a range of colours depending on sun exposure. Armpits just give you the bottom end of the range, which really does not say much. Not many people go about looking at peoples armpits. The colour of your armpits does not affect Vitamin D or sun protection.

In hot climates southern Europeans tan more than the North Western Europeans. Thems the visible facts. You can visit any warm climate and see that.

The 1 Polish lady I knew in the tropics was very pale (well red), but Scandinavians can get quite brown also despite the pale hair and eyes. Portuguese and Spaniards can get very dark. But there is a also lot a variation. In my own family most of us remain super pale (or red) even after decades in the sun. But my father used to tan so very darkly that when he visited his home town local pub in the north of England he would hear whispered racist mutterings from folk who did not know him, and thought he must be from Pakistan.

So there is diversity, but no amount of armpit studies change the fact that southern europeans tan darker than others. As you would expect since southern europeans need more sun protection and northern europeans need more Vitamin D. Let us not forget the role of natural selection. Neanderthals were also pale for a climatic reason.

AWood said...

Lista04

You're a bit vague here, and I'm guessing that it's because you don't speak English as a first language. If you have inside information that's great, but are you referring to the Caucasus mountains or the steppes? These seem to be two different populations? One would be CHG or their hypothetical ancestors, or the European Steppes themselves which would be north of the Caucasus mountains and west of the Ural mountains. So which is it? It cannot be both.

Samuel Andrews said...

@Romulus,
"In Reich's latest talk from a few months ago he says that modern Europeans received their light skin from EEF, which is obvious after the Anatolian Neolithic samples came back positive for both SLC24A5 and SLC45A2."

Yamnaya and Catacomb had as much SLC24A5 and SLC45A2 as EEF. Light skin isn't from a single source. Reich may have been simplifying things. The ancestors of Europeans weren't complete strangers, they shared Paleo ancestry and shared mutations He's done that before. like the ones in SLC24A5 and SLC45A2. He's done that before.

Davidski said...

@bmdriver

This new paper on Indian skin pigmentation genetics was authored by Indians.

So shut the hell up.

Romulus said...

@Samuel

Are you sure about Yamnaya having SLC45A2? I'm pretty sure they only had SLC24A5.

The Anatolian Neolithic samples are from 8300 B.C. and I'm also fairly sure that makes them the oldest samples which have tested positive for SLC45A2.

Romulus said...

https://youtu.be/EfHGhWfxWoA?t=2586

"The main variants affecting light skin seem to, for the most part, to have come from the ancient near east"

Romulus said...

There was another study from Fu awhile back that said the genotype responsible for light skin was found in WHG so obv something still not well understood.

bmdriver said...

@david

As I said when Indians are educated from an Indian perspective not a colonially induced White Caucasian perceptive enforced into the education system of India, we will have a truer reflection of the past. And with a nationalistic government in place for the foreseeable future the shoots of true discourse minus European colonial nationalism will soon start to spring up.

Charles E. Trevelyan, brother-in-law of Macaulay, stated: " Familiarly acquainted with us by means of our literature, the Indian youth almost cease to regard us as foreigners. They speak of "great" men with the same enthusiasm as we do. Educated in the same way, interested in the same objects, engaged in the same pursuits with ourselves, they become more English than Hindoos, just as the Roman provincial became more Romans than Gauls or Italians.."

House of Lords on the Government of Indian Territories on 23rd June, 1853: "..... the effect of training in European learning is to give an entirely new turn to the native mind. The young men educated in this way cease to strive after independence according to the original Native model, and aim at, improving the institutions of the country according to the English model, with the ultimate result of establishing constitutional self-government. They cease to regard us as enemies and usurpers, and they look upon us as friends and patrons, and powerful beneficent persons, under whose protection the regeneration of their country will gradually be worked out. ....."

(Culture and Consumption: Fiction, the Reading Public, and the British Novel in Colonial India) writes: "Often, the implementation of a new education system leaves those who are colonized with a lack of identity and a limited sense of their past. The indigenous history and customs once practiced and observed slowly slip away. The colonized become hybrids of two vastly different cultural systems. Colonial education creates a blurring that makes it difficult to differentiate between the new, enforced ideas of the colonizers and the formerly accepted native practices."

Lord Canning (1812 - 1862) Governor General of India from 1856 - 1862 and the first Viceroy in India. “As we must rule 150 millions of people by a handful (more or less small) of Englishmen, let us do it in the manner best calculated to leave them divided (as in religion and national feeling) and to inspire them with the greatest possible awe of our power and with the least possible suspicion of our motives.”

bmdriver said...

@david

....never forget the past and the people you think you lay claim over.

“Philosophers have long conceded, however, that every man has two educators: 'that which is given to him, and the other that which he gives himself. Of the two kinds the latter is by far the more desirable. Indeed all that is most worthy in man he must work out and conquer for himself. It is that which constitutes our real and best nourishment. What we are merely taught seldom nourishes the mind like that which we teach ourselves.

When you control a man's thinking you do not have to worry about his actions. You do not have to tell him not to stand here or go yonder. He will find his 'proper place' and will stay in it. You do not need to send him to the back door. He will go without being told. In fact, if there is no back door, he will cut one for his special benefit. His education makes it necessary.

you teach the Negro that he has accomplished as much good as any other race he will aspire to equality and justice without regard to race. Such an effort would upset the program of the oppressor in Africa and America. Play up before the Negro, then, his crimes and shortcomings. Let him learn to admire the Hebrew, the Greek, the Latin and the Teuton. Lead the Negro to detest the man of African blood--to hate himself.”

― Carter G. Woodson, The (colonial) MIS-Education of the Negro

End.

Tobus said...

@Annie: Armpit skin colour is not particularly interesting as it does not tell you anything about sun sensitivity.

That's the whole point.

Tobus said...

@Romulus: Are you sure about Yamnaya having SLC45A2? I'm pretty sure they only had SLC24A5.

Yamnaya had SLC45A2 at about 40%, according to Matthieson et. al..

Worth remembering that although lots of ancients has SLC45A2, it didn't get to high frequencies until the Bronze Age. It's unclear what triggered the selection, but it does coincide somewhat with the incursion from the Steppe.

Samuel Andrews said...

@bmdriver,

Genetics facts are genetic facts. There's no way around it. A European or Indian way of thinking of genetics doesn't change genetic facts. Once we get DNA from ancient DNA of people with high amounts of Steppe ancestry in India there will be little room for debate, Bronze age European Steppe migration will be fact. It doesn't promote white supremacy unless you want it to. These Bronze age European Steppe folk contributed 50% or less ancestry to modern Europeans btw, they weren't exactly the same. They're an ancestor of SC Asians and Europeans.

Anytime you think of something in absolutes you should question yourself. You think of Europeans absolutely. You think they're horrible evil people, have a evil culture, hate all non-Europeans, and twist facts to promote belief in their supremacy. Can't you see how your opinion is driven by hate aswell? There's truth to what you say about European racism and colonialism but you exaggerate big time.

You are an embarrassment for Indians.

Balaji said...

The significant finding in this paper is not that on the average the amount of pigment in the skin is correlated with position in the caste hierarchy. This has been known for centuries to even casual observers without the use of spectrometers. It has also long been known that within each caste, there is considerable variation in pigmentation and that some high caste individuals are darker than some low caste ones. The important finding is that the SLC24A5 gene is so polymorphous in all the Indian populations with variations in both rs1426654 and rs2470102 being necessary to account for pigment variations. In Europe and the Middle East almost every one has the same version of SLC24A5 and therefore this gene cannot be used to explain within-population variation of skin color.

Davidski has suggested that the light-skin version of SLC24A5 was introduced by agriculturalists from Iran. But in Iran there is not much variation in rs2470102 so the immigrants would have had the derived version of the allele at both rs1426654 and rs2470102 which is not always the case in India where the authors of this paper have identified three significant haplotypes - one of these has the derived type allele at rs1426654 and the wild type allele at rs2470102. This suggests to me that these variations originated in the Indian Subcontinent and then spread from there to the Middle East and to Europe. In Europe and the Middle East the derived version of SLC24A5 reached close to 100% of the population while India remained polymorphous.

The authors have not looked into SLC45A2 of which the light-skin version is also present in small amounts in India. This, too, is probably polymorphic in India and accounts for some of variation of pigment. SLC24A5, SLC45A2 and lactase persistence all probably originated in the Indian Subcontinent though all of these are now most prevalent in Europe. Similarly Indo-European languages also probably originated in the Indian Subcontinent and spread from there. We will know for sure soon with aDNA.

Gioiello said...

@ Balaji

"We will know for sure soon with aDNA".

Of course.

Grey said...

Romulus

"The main variants affecting light skin seem to, for the most part, to have come from the ancient near east"

There's one debate about how light skin genes came into Europe and another about why and where those genes developed originally so "come from the ancient near east" may be correct in the first context but incorrect in the second (which i'm interested in).

(And doubly so if it originated in one place but spread much faster among early farmers in another place as that might be a clue as to the reason it developed.)

#

@bmdriver

I understand your point but sometimes the only way to fix things is to start somewhere you don't like.

Qagan said...

@Matt

Sorry for off topic, but if you don't mind do you know how much West Eurasian admix do North Asian/Siberians like Mongolian, Altaian, Evenk, Yakut, Tuvan have?

In thes case of Mongolians and closely related grops, they seem to be able to be divided into distinct subgroups genetically: Daur, Mongola (from China), Mongolian (from Mongolia), Buryatm, Kalmyk. Do you know how much West Eurasian admix each group have on average?

Thank you very much.

Open Genomes said...

David, you're a bit wrong here about the skin pigmentation SNPs in the Early Neolithic, but you may be right about how they spread:

SLC24A5 rs2470102 (ancestral: A derived: G)
SLC24A5 rs2470102 WC1 GD13A Rev5 Klei10 AH2 Bar8 Tep002 Bon002

Iran:
AH2: ancestral
WC1: heterozygous
GD13A: heterozygous

Central Anatolia:
Bon002: heterozygous
Tep002: heterozygous

NW Anatolia
Bar8: derived
Bar31: derived

Greece:
Rev5: no read
Kle10: derived

SLC45A2 rs16891982 (ancestral: C derived: G)
SLC24A5 rs2470102 WC1 GD13A Rev5 Klei10 AH2 Bar8 Tep002 Bon002

Iran:
AH2: ancestral
WC1: ancestral
GD13A: ancestral

Central Anatolia:
Bon002: no read
Tep002: no read

NW Anatolia
Bar8: heterozygous
Bar31: heterozygous

Greece:
Rev5: derived
Kle10: ancestral

As we can see, both light skin pigmentation SNPs some of the earliest Iranian, Anatolian, and Greek Neolithic farmers were not yet fixed in the populations:

AH2 (J2b-M12*), who is possibly a Neolithic Iranian Western Zagros goat herder, but not a cereal farmer - from AH2 Early PPN Tepe Abdul Hosein Iran 8205-7756 calBCE and who is almost completely "ANI" was ancestral for both SNPs.

GD13A-I1290, another Neolithic Iranian Western Zagros goat herder, and also not a cereal farmer,from Ganj Dareh Iran 8179-7613 is heterozygous for SLC24A5 rs2470102 but ancestral for SLC45A2 rs16891982.

WC1 (G2b2a-Z8022), who is a Neolithic cereal farmer from the Iranian Western Zagros, from WC1 Wezmeh Cave, Iran 7455-7082 calBCE (9465-9092 ybp), is heterozygous for SLC24A5 rs2470102 but ancestral for SLC45A2 rs16891982.

The early Central Anatolians however are heterozygous for SLC24A5 rs2470102 and derived for SLC45A2 rs16891982, and so is Klei10, a Late Neolithic sample from Central Greece.

WC1 has a extra "Near Eastern Neolithic" set of components that are lacking in AH2.

So we see that SLC24A5 rs2470102 began to appear with the advent of the Neolithic in Western Iran, while SLC24A5 rs16891982 became fixed in Central Anatolia contemporary with the earliest Neolithic herders in Western Iran, who were ancestral for it.

Note that while most Brahmins are in Y haplogroup R1a1a1b2a1-L657 with a tMRCA of only 2,200 BCE (4,200 BP), there are Iyer and Iyengar Brahmins in G-Z30522 under G-Z40458 with a tMRCA of 4,800 BCE (6,800 BP) with an Iraqi in G-Z40458 from Baghdad. G-Z40458 is also found among 10% of Iranians from the Caspian provinces of Gilan and Mazandaran. There are also Iyer Vadama (northern) Brahmins in G-L91 which has a tMRCA of 6,300 BCE (9,300 BP) and which was found in NW Anatolia as well as in Europe (Klei10, Otzi, etc.)

G-Z30503 also has a separate Punjabi-Kalash G-Z31387 clade with a tMRCA of 6,000 BCE (8,000 BP) with the G-Z40458 Iraqi-Iranian-Brahmin clade.

YFull Tree G-Z30503

We also know that at least some Punjabi Jatts in G-PF3170 are also homozygous derived for SLC24A5 rs2470102 while ancestral for SLC24A5 rs16891982, so this isn't restricted to Brahmins. G-PF3170* is yet another Neolithic Y clade, found in Halberstadt-Sonntagsfeld in the LBK.

The conclusion is that SLC24A5 rs2470102 is a Near Eastern Early Neolithic SNP, which gradually increased in frequency in both directions, Iran and Anatolia, and later South Asia and Europe, because it was under positive selection as a result of a primarily grain and dairy diet without vitamin D sources from fishing. We can actually see this process unfold. It does represent Near Eastern Neolithic ancestry, but we can't ignore the process of selection that drove it to high frequency in both South Asia and Europe.

Davidski said...

David, you're a bit wrong here about the skin pigmentation SNPs in the Early Neolithic.

The genotypes in my samples are correct, except all of my samples are pseudo haploid, while yours are haploid.

The problem with haploid genotypes at less than 20x coverage is that they're not very reliable, especially for formal stats.

Most of my samples are from here...

https://reich.hms.harvard.edu/datasets

Tobus said...

@Balaji:these variations originated in the Indian Subcontinent and then spread from there to the Middle East and to Europe. In Europe and the Middle East the derived version of SLC24A5 reached close to 100% of the population while India remained polymorphous.

So pop A is polymorphic, pop B is fixed ancestral, they mix and the resulting pop C is fixed derived? That would require a severe bottleneck or extremely strong selection only in pop C.

Much more simple is that pop A was fixed derived, pop B was fixed ancestral, they mixed resulting in a polymorphic pop C... I think this is the reasonable assumption (until aDNA proves otherwise ;)).

Open Genomes said...

Correction, the second link is suppose to read:
SLC45A2 rs16891982 WC1 GD13A Rev5 Klei10 AH2 Bar8 Tep002 Bon002

David, I wasn't saying your data was wrong, it's just that the overall picture is incomplete.

These samples, if they have reads, all have at least two reads as you can see. The higher quality genomes, WC1, GD13A, and Bar8 all have higher read depths. Generally many of these have enough read depth to determine heterozygosity.

Would you agree that SLC24A5 rs2470102 started to go to higher frequencies because of positive selection in the Early Neolithic, but wasn't yet fixed in the Near Eastern Early Neolithic population?

That would mean that while this SNP appears to have a single Near Eastern origin, it was still under selection as it moved out both east and west.

It seems that the earliest Neolithic people were rather dark, like darker South Asians.
Their descendants became lighter as time went on.

Do you think diet played a role, seeing that the latitudes were basically the same?

Davidski said...

Well, if the Anatolian and Iranian farmers were heterozygous at that site, then I would expect at least a couple of them to be homozygous for the G allele in my mostly pseudo haploid dataset.

But they're not. This might be a coincidence, but I have been told that it's very difficult to call true haploid genotypes for samples with coverage of less than 20x.

This comes from Harvard, and even though I do criticize them regularly for their interpretations of their ancient data, I won't argue with them when it comes to technical things like this.

However, if the early farmers do carry the G allele, and my dataset is simply missing this fact, then yes, diet could be one explanation. Another explanation might be social selection.

Grey said...

*if* light skin developed to compensate for a dietary deficiency that could potentially explain how it might have originated in one region and yet spread faster among farmers in an adjacent region - that is if the farmer diet created the same deficiency but more so, for example if say WHG had a 0% deficiency, SHG/EHG had a 5% deficiency and the farmers a 20% deficiency

(although once started other factors could come into play as well)

(although apparently SHG didn't contribute much to modern European DNA i think them having these genes points to a northern/interior origin)

a said...


Blogger bmdriver said...

"....... What we are merely taught seldom nourishes the mind like that which we teach ourselves..............."
― Carter G. Woodson, The (colonial)

How about trying to get some ancient Egyptian dynasty information;like genetic result's, from some labs[like the one with 1000 samples; maybe to busy to publish results on Egypt]. For example King Tut's results could be shared with OP project and Eurogenes, providing that would be okay with the proper authorities . I'm sure they would step up to the plate and happily contribute their expertise in deciphering some interesting Egyptian/African results, and generating admix[they could even use Mota and Natufian]. It would be good public gesture to show interest in other genomes; other than the Europe/Steppe/Caucasus or Iran[white gene mutations]. I can't think of a better way to generate interest, can you?

Grey said...

"(although apparently SHG didn't contribute much to modern European DNA i think them having these genes points to a northern/interior origin)"

SHG/EHG/6-8k+/- Northern Caucasus 13k+/-
I think the vitamin D fish oil/whole grain diet isn't going to cut it. It's looking like some kind of Quantum Teleportation miracle via Iran/Anatolia/SHG/EHG/CHG bypassing "Villabruna like/Bichon cluster" to the North, and Natufian=craniometric African like, to the South.

Tobus said...

a: It's looking like some kind of Quantum Teleportation miracle via Iran/Anatolia/SHG/EHG/CHG bypassing "Villabruna like/Bichon cluster"

Look at a map - the shortest path from Iran to Sweden goes through Anatolia, Georgia and Western Russia, but doesn't go anywhere near Italy/Switzerland. No teleportation needed.

a said...


Tobus said.
"
Look at a map - the shortest path from Iran to Sweden goes through Anatolia, Georgia and Western Russia, but doesn't go anywhere near Italy/Switzerland. No teleportation needed."

https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1330589433

SLC24A5, rs1426654/rs16891982 Caucasoid light skin

Motala_HG:I0015=0%Natufian
Karelia=0%Natufian
They are almost pure ANE/Villabruna. Just how did they get these mutations found in Natufia?

Tobus said...

a: They are almost pure ANE/Villabruna. Just how did they get these mutations found in Natufia?

From a common ancestor or admixture. In that same table the Barcin samples are almost 50/50 Basal/Villabruna, CHG are almost 50/50 Basal/ANE... there's plenty of common ancestry with SHG/EHG that these mutations could have originated in.

Don't be confused by the K7 having reference pops that are more recent than the likely origin of the SLC variants.

Grey said...

a

"I think the vitamin D fish oil/whole grain diet isn't going to cut it. It's looking like some kind of Quantum Teleportation miracle via Iran/Anatolia/SHG/EHG/CHG bypassing "Villabruna like/Bichon cluster" to the North, and Natufian=craniometric African like, to the South."

If it was connected to a dietary deficiency connected to seafood/seacoast then there'd be no reason for it to spread among people who had lots of that in their diet

(like maybe WHG, Anatolian and Natufian HGs)

but if the switch to farming recreated that same deficiency but on a larger scale then maybe it would spread like wildfire among the farmers (except where it was too hot and lighter skin created a problem that balanced out the advantage).

If it developed among people furthest from the sea e.g. somewhere north of the Caucasus / Himalayas it could spread west to SHG, sw into Anatolia, south into mid-east/India etc

a said...


Blogger Lista04 said...

Technically speaking, white people did not come from the Near East but from the Eastern Europe (Southwest Russia) as the earliest white people originated in the European Caucasus and spread to other parts of Europe from there....... I can tell you that an upcoming study is to reveal that even 27,000-25,000 year-old burials in the Northwest Caucasus had people who all carry not only the genes for Caucasoid white skin but also for the light eyes and hair.......https://s30.postimg.org/xh9el5975/3491275.jpg). I assure everyone that so many good studies are on the way. All we have to do is to wait."

Nice map-Quite old region.
Hopefully you will test for some of these markers, and give this enigma some answers. :)

დღესაც კი ევროპის მთელ გაყოლებაზე წინაინდოევროპული სამყაროს მემკვიდრეობა შეინიშნება Rh ნეგატიური სისხლის ჯგუფის გავრცელების მეშვეობით,
ჯგუფისა, რომელიც მხოლოდ ევროპული წარმომავლობის მოსახლეობისათვის არის დამახასიათებელი. Rh ნეგატიური გენის ყველაზე მაღალი პროცენტული შემადგენლობა, 55%, და Rh ნეგატიური ინდივიდუალებისა, 25-30%, გვხვდება ბასკებს შორის. რამდენადმე ნაკლებია ჩრდილო-დასავლეთ ევროპაში და კიდრვ უფრო ნაკლებია, 12-15%
- ცენტრალურ ევროპაში, 9-12% - ჩრდილოეთ-ცენტრალურ- და ჩრდილოაღმოსავლეთ ხმელთაშუაზღვისპირეთსა და ახლო აღმოსავლეთში[ 11 Ammerman/Cavalli-Sforza 1984, 87, 92, 156ნ.4; Cavalli-Sforza 1991, 73.]. მისი სიხშირე უმნიშვნელოა მსოფლიოს ყველა სხვა ნაწილში[12 Ammerman/Cavalli-Sforza 1984, 86f.]. კავკასიაში, ძირითადად დასავლეთ ამიერკავკასიის დასავლეთ ნაწილში, ანუ დასავლეთ საქართველოში, Rh ნეგატიური ფენოტიპის სიხშირე ზოგჯერ20% აღემატება[13
Inasaridze et al. 1990, Table 1.ზ. ინასარიძის მონცემებით, დასავლეთ საქართველოს ზოგიერთ რაიონში Rh ნეგატიური ინდივიდუალების სიხშირე აღწევს 25-30% . Rh სისტემასთან დაკავშირებით,d გენის სიხშირე ქართულ მოსახლეობაში უფრო მაღალია ვიდრე კავკასიის სხვა ეთნიკურ ჯგუფებში და აგრეთვე აღემატება ახლო აღმოსავლეთისა და ევროპის მოსახლეობის უმეტეს ნაწილთან შედარებით, მაგ. ზუგდიდის რაიონში იგი48%-ზე მეტია (Nasidze et al.1990, 612, Table2;
Inasaridze et al. 1990, 718,Ta ble 2).]. აშკარა ხდება, რომ ევროპაში შედარებით გვიანდელი იმიგრან/გვ.55:/ტები, სავარაუდოდ ინდოევროპულ ენებზე მოლაპარაკენი, უპირატესად Rh პოზიტიურის მატარებლები უნდა ყოფილიყვნენ. ABO სისხლის ჯგუფების მონაცემთა განხილვის დროსაც, ისევ პირენეები (“კელტურ” დასავლეთ ევროპასთან და ხმელთაშუაზღვის კუნძულებთან ერთად) და დასავლეთ ამიერკავკასია ავლენენO ჯგუფის მაღალ სიხშირეს[14 Mourant 1954, 10, 44-53, 57f.; Mourant/Kopec/Domaniewska-Sobczak 1976, 63-65, 70-74, 144, 176,Table 1.1.მ თლიანობაში, ABO

სისტემასთან დაკავშირებით,O გენის ყველაზე მაღალი სიხშირე კავკასიაში - 69% (დასავლეთ საქართველოში - 72-78%, ფენოტიპების სიხშირით - 54-62%) დაB გენის ყველაზე დაბალი სიხშირე - 8% (დასავლეთ საქართველოს ზოგიერთ რაიონში - 2-4%)საქართველოში (A გენის სიხშირე აქ არის - 22.6%)შეინიშნება (Nasidze et al. 1990, 611f., Table 1; Inasaridze et al. 1990, 715-718, Tables 1 and 17).]. გენების სიხშირის საშუალო მაჩვენებლები ნათელყოფენ ორივე ამ რეგიონის უნიკალურ გენეტიკურ ადგილს ევროპის, ხმელთაშუაზღვისპირეთისა და ახლო აღმოსავლეთის სხვა მოსახლეობასთან მიმართებაში[15შდრ. Ammerman/Cavalli-Sforza 1984,
86f.; Inasaridze et al. 1990, 722.]. ვინაიდან იმ სახის მონაცემები, როგორიცაა Rh ფაქტორი და ABO სისტემა მიგვანიშნებენ ისტორიული ხასიათის მოვლენების მნიშვნელოვან როლზე მათ გეოგრაფიულ გავრცელებაში[16 Ammerman/Cavalli-Sforza 1984, 136.შეგვიძლია გავიხსენოთ, რომ მრავალი წლის წინათ, ანთროპოლოგიური მონაცემების საფუძველზე მიიჩნევდნენ, რომ ლინგვისტური ოჯახი, რომელიც გადაშენდა ევროპაში ჯერ კიდევ იყო შემორჩენილი კავკასიაში, ძველ კავკასიურ ენებზე, ქართულზე და სხვებზე მოლაპარაკეთა შორის (Ungand 1936, 15).],

Lukasz M said...

@Olympus Mons said...
Well, all I can do is show you my butt cheeks. You will understand what I mean. :=)

This paper is nonsense because hair color (and other also) were self-reported. People usually are not very trustfull in it, especially women:)

In old good days, scientist used color scales which was objecitve. Self-reporting by people who doesn't know what is ligh brown and dark blond is useless:)

I also read such paper about polish hair color from some Polish dermatologist. Also data were self-reportef by his patients. It's reveal thaht Poland as I remember has 70% light hair which is also nonsense of course.

Antoni Małkowski said...

Tak co niezwykle ciekaw dla mnie.
Należę do CTS9219/L23EE grupa krwi B –
Chyba pójdę w formalne.

Gioiello said...

@ Antoni Malkowski
Tak co niezwykle ciekaw dla mnie.
Należę do CTS9219/L23EE grupa krwi B –
Chyba pójdę w formalne.

You are very likely B0 --, my father was 00--, my mother was A0--, I am 00+- (it is difficult to explain my +, but it is a case that theory explains). Thus I think you have a deep Western European hunter-gatherers ancestry, as you R-CTS9219 demonstrates.