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Fire Haired14
01-12-15, 17:32
http://www.anthrogenica.com/attachment.php?attachmentid=6773&stc=1
The only dramatic change in pigmentation between 6000 BC and 2800 BC was in skin color. The difference between Yamnaya and Corded Ware/Sintashta isn't evolution, because Yamnaya isn't ancestral to Corded Ware/Sintashta. Poltavka was contemporary to Corded Ware but they had differnt skin color.

Mathieson 2015 gave allele frequencies for phenotype SNPs but their categories "Steppe", "EF", etc. were too broad. Geneticker has just posted calls for each individual: More phenotype SNPs from prehistoric Eurasia (https://genetiker.wordpress.com/2015/12/01/more-phenotype-snps-from-prehistoric-eurasia/). So, the broad categories is no longer a problem. Some of Geneticker's results are probably wrong. He has been slightly inconsistent with published papers before. Keep that in mind. What I'm doing with this post is presenting the information Geneticker provide about the phenotype of Pre-Historic Europeans and their implications on the origins of traits in Europe today. Geneticker did not test many of the SNPs Mathieson found signs of selection for, you can find information on those SNPs in my first post (http://www.anthrogenica.com/showthread.php?5602-Traits-that-were-Selected-for-in-the-last-8-000-years).

I've added the results from Geneticker's recent work to my spreadsheet: Pre-Historic West Eurasian Phenotype (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1993675580&vpid=A1) and Ancient Hair Color Predictions (https://docs.google.com/spreadsheets/d/1WN9qwNyju93dVXxkTMaYbzT4cBdMq9wZF-mIe1aMMcQ/edit#gid=15711752&vpid=A1).

Essentially all the data comes from a handful of locations and Time Periods.
6000-5000 BC
Hunter Gatherers N=11: West Europe, Sweden
Farmers: Anatolia(N=23+), Central Europe(N=17+), Spain(N=18+).

3000 BC
"Steppe"(N-20+): Yamnaya, Afanasievo, Poltavaka.

2800-2000 BC:
R1a Dominated(N=20): Corded Ware, Srubnaya, Sintashta, Andronovo. Equal representation of R1a-Z93 dominated and Corded Ware.


Note: There's other data. But the data above is the only data with enough samples to make population categories. Most from from 2800-2000 BC LNBA North Europeans not dominated by R1a and Russian Mesolithic+Eneolithic. There's also a handful of data from 3000 BC EEFs in Italy.


This information is important concerning pigmentation results in ancient DNA
It is important to understand in pigmentation only Eye color and Red or non-Red hair can be predicted accurately with the SNPs tested. Skin color and Hair color can not be predicted accurately. We can track the frequency of the two mutations most associated with Light skin in Europe. But that doesn't tell us for fact what skin color any ancients had it only suggests they had Dark or Light skin.

The same goes for Hair color. We can predict hair color but the results are just suggestions. Also, the two most popular Red hair variants often pop up in ancient DNA because of DNA damage according to Ian Mathieson. So, it's difficult to track Red hair.

Here are four graphs depicting the frequency of Blue eye color, frequencies of Light skin mutations, and frequencies of a Lactose Tolerance mutation(rs4988235 T). I only included Anatolia Neolithic, North European EEF, R1a Dominated LNBA, and modern North Europe for the Skin color mutation frequencies. For the Blue eye color frequency I included those four and West/North Hunter gatherers. For Lactose Tolerance I included West/North Hunter Gatherer and lots of modern Europeans.

Note: This the below graphs for Skin+Eye Color are not allele frequencies. They are the frequency of people with two-derived alleles in 3 SNPs associated with eye and skin color. The frequency of the Lactose Tolerance mutation(rs4988235 T) are allele frequencies though.

Blue eye Frequency.
7549

Light skin mutation #1(rs1426654).
7550
Light skin mutation #2(rs16891982).
7551

Lactose Tolerance(rs4988235) frequency.


7552

The graphs above show three things.
>No Selection For Pale Skin rs1426654: It's high frequency is mostly do to migration of Anatolian farmers and "Steppe" into Europe.

>No Selection For Blue eyes: Hunter gatherers in West/North Europe were almost uniformly Blue eyed. The migration of Anatolian_HGs caused the frequency to go down, however EEF Central Europeans still had 44% Blue eyes. The Frequency went down to about 20% in R1a dominated LNBA because they were mostly "Steppe". It's much higher today in modern North Europeans at 65%(on average). A combination of further admixture with EEF/WHG and selection could have caused the frequency to go up. It appears Unetice, Andronovo, and Nordic LN had a similarly high frequency as North Europeans today. The most unexpected results are for Srubnaya because only one had Blue eyes while the majority of their close relatives(essentially the same people) Andronovo had Blue eyes. There's variation on eye color in LNBA North Europeans, so it's hard to say if there's been selection or not since then.

>Selection For Pale Skin rs16891982: Only 1/5 "Steppe" and "EEF" had the Light skin version while 3/4 LNBA R1a dominated people did. The majority of other LNBA North Europeans had the Light skin version, so the selection wasn't exclusive to R1a dominated people. In North Europe we can see the frequency is even higher today, almost 100% have the Light skin version. In Italy and Balkans we see the same frequency. However in Greece just over 85% have it and in Iberia just under 70%. So, all over Europe this mutation was selected for after 3000 BC and even after 2000 BC.

>Selection For Lactose Tolerance rs4988235: It makes its first appearance in LNBA North Europe but it was much less popular than it is today. Today the vast majority of North Europeans have a derived allele. A high percentage in Iberia and S/C Asia do to. However in Italy and Balkans it isn't very popular.

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In the case of Red hair Geneticker has found carriers in Sweden(6000 BC), Anatolia(6300 BC), and Russia(5200-4000 BC, R1b1 guy he was almost 100% EHG). This means Red hair was widespread by 6000 BC. There's only two carriers though from Neolithic Europe. He has found carriers of Red hair in R1a-Z93 dominated groups but none in Corded Ware, so probably very few in R1a-M417 dominated Bronze age groups had Red hair.

The highest frequency is in Neolithic Anatolia. Ian Mathieson found the same high frequency but suspects it is DNA damage. He says derived allele in rs1805007 and rs1805008(the most popular Red hair variants) in ancient DNA can be the result of DNA damage. It might DNA damage and it might not be. I don't understand how Neolithic Anatolians from the same time period and same village could constantly get DNA damage in rs1805008. It makes more sense this mutation ran in their family/village. There's no way to know for sure. But we should keep the derived alleles in those two SNPs in mind, they might reveal information about the origins of Red hair.

Carriers have been found in other SNPS associated with Red hair that don't suffer from DNA damage. It doesn't look like Red hair was selected for or not selected for. The R1a dominated groups don't have a much lower frequency than today's NorthEast Euroepans. It's very likely IMO that random drift caused Red hair to rise in frequency in the British Isles and Volga Russia. It also seems there's a lot more Red hair in NorthWest Europe today than in any of the ancients.

Frequency of Red hair Carriers.
7553

Tomenable
01-12-15, 20:03
I can't see most of images.

Angela
01-12-15, 21:24
Fire-Haired, I really think you should take it slower and review your post. You're saying at one and the same time, sometimes in the same paragraph, that there was no selection and then that there was selection. Some, maybe a lot of Genetiker's actual calls on snps are correct. His interpretations are almost always incorrect and agenda driven.

Look at the data again, even from the Bronze Age until now, but also before that.

Tomenable
01-12-15, 21:49
Angela, I think we should differentiate between two kinds of things:

- 1) selection "in situ" = processes taking place within the original population

And:

- 2) replacement of one population by another one, with different phenotypes

If we don't do this, then we can as well claim that - for example - between years 1600 AD and 1900 AD there was a strong positive selection on blue eyes and light hair in North America. But after 1900 AD brown eyes started to be selected for again, at least in California and Texas, etc. While in fact we know, that those weren't Cherokee Indians becoming blue-eyed, but at first a lot of blue-eyed immigrants from Europe, and later a lot of brown-eyed and dark-haired Chinese and Mexican immigration to California, Texas, etc.

Of course some traits were really being selected for in Europe (for example, it seems that lactase persistence was).

But other traits simply arrived with waves of new migrants who came in large numbers (to some areas).

If some trait arrived with new migrants, but in low frequency, and later increased in frequency, then I count this as selection. But if some trait arrived with new migrants already in large frequency, and later its frequency didn't really change, then I don't.

Fire Haired14
01-12-15, 22:25
The images should be viewable now.

@Angela,

I'm very confident Geneticker doesn't lie to push what he wants to be true. He isn't as DNA savvy as geneticist that's all. His results have been confirmed to be correct by academic papers many times. I have no doubt most of the time he's correct.

I have the data organised well. I'm repreating the point Tomenable made. Srubna/Corded Ware as far as I know had significantly more Steppe than anyone today. This can explain why they had such a high frequency of Brown eyes. The only obvious selection is in rs4988235. rs16891982 are basically the same as today, but I guess there could be selection on it since Late Neolithic.

I'm contradicting what I've said in earlier posts, like about blue eyes rising in frequency since 2000 BC, but in this post I'm not contradictory. I didn't take into account that Srubna/Corded Ware were 65%+ Steppe.

Athiudisc
01-12-15, 23:01
Genetiker still insists R1b-M269 spread from western Europe. All of his theories proceed from that basis.

Greying Wanderer
01-12-15, 23:41
Genetiker still insists R1b-M269 spread from western Europe. All of his theories proceed from that basis.

I think people's data and interpretation can be treated separately if they have a track record with the data.


edit: nb i don't know if Genetiker has a good track record on the data or not except by other's comments but so far all the comments I've seen have been pro on the data side at least.

Greying Wanderer
01-12-15, 23:48
Fire-Haired

It's very likely IMO that random drift caused Red hair to rise in frequency in the British Isles and Volga Russia.

The distribution of R1b and R1a would be consistent with R1b expanding first with R1a expanding later and in the process displacing R1b on the steppe.

If so a founder effect from the region of Volga Russia seems more likely to me.

Tomenable
05-12-15, 22:00
About very recent (last 200 years) changes in eye pigmentation in Europe, a publication from 1995 (in Polish):


https://repozytorium.amu.edu.pl/bitstream/10593/7344/1/07_L_Gronkiewicz_S_Gronkiewicz_ZR__NICOWANIE_BARWY _OCZU_53-67.pdf


Translation to English:


"(...) Results of extensive studies on territorial diversification and secular changes of eye pigmentation, carried out already from the 19th century onward in many European countries, were collected by Chamla and Gloor [1986]. (...) These authors think, that in general, among the European population, we can observe decreasing frequencies of light-pigmented eyes in modern populations when compared to populations of the past. This refers to populations of France, Italy and Switzerland, but a similar phenomenon can also be observed in South-Eastern Europe: in Bulgaria, Greece and Yugoslavia. Even in Sweden frequency of light eyes has decreased from 80-90% by the end of the 19th century to 70-80% nowadays [1995]. In France between 1880 and 1960 a considerable increase in frequency of dark eyes was observed, but it took place mostly in connection with a drastic decline in frequency of intermediate-colored eyes, while frequency of light-colored eyes remained throughout that period at a stable level of around 47 percent [Chamla 1964] (...)"


And here is how the authors define "light", "intermediate" and "dark" eyes:


"(...) Basing on amount of pigment in iris of eye, expressed with use of grades on the scale of eye color, subjects were grouped into three categories: 1. people with light eyes; 2. people with intermediate-colored eyes; 3. people with dark eyes. Category of light eyes (according to Martin's scale 16-12, 10, 9) includes irides of blue or grey color, without any insertions of yellow or russet pigments (except for naevi); intermediate eyes had irides of blue or green color with clearly visible groupings of yellow or russet pigment (according to Martin's scale 11, 8, 7); dark eyes had irides of various intensivity of brown color (according to Martin's scale 6-1). (...)"

Tomenable
05-12-15, 22:05
About very recent (last 200 years) changes in eye pigmentation in Europe, a publication from 1995 (in Polish):

https://repozytorium.amu.edu.pl/bitstream/10593/7344/1/07_L_Gronkiewicz_S_Gronkiewicz_ZR__NICOWANIE_BARWY _OCZU_53-67.pdf

Translation to English:

"(...) Results of extensive studies on territorial diversification and secular changes of eye pigmentation, carried out already from the 19th century onward in many European countries, were collected by Chamla and Gloor [1986]. (...) These authors think, that in general, among the European population, we can observe decreasing frequencies of light-pigmented eyes in modern populations when compared to populations of the past. This refers to populations of France, Italy and Switzerland, but a similar phenomenon can also be observed in South-Eastern Europe: in Bulgaria, Greece and Yugoslavia. Even in Sweden frequency of light eyes has decreased from 80-90% by the end of the 19th century to 70-80% nowadays [1995]. In France between 1880 and 1960 a considerable increase in frequency of dark eyes was observed, but it took place mostly in connection with a drastic decline in frequency of intermediate-colored eyes, while frequency of light-colored eyes remained throughout that period at a stable level of around 47 percent [Chamla 1964] (...)"

And here is how the authors define "light", "intermediate" and "dark" eyes:

"(...) Basing on amount of pigment in iris of eye, expressed with use of grades on the scale of eye color, subjects were grouped into three categories: 1. people with light eyes; 2. people with intermediate-colored eyes; 3. people with dark eyes. Category of light eyes (according to Martin's scale 16-12, 10, 9) includes irides of blue or grey color, without any insertions of yellow or russet pigments (except for naevi); intermediate eyes had irides of blue or green color with clearly visible groupings of yellow or russet pigment (according to Martin's scale 11, 8, 7); dark eyes had irides of various intensity of brown color (according to Martin's scale 6-1). (...)"

MOESAN
06-12-15, 19:11
About very recent (last 200 years) changes in eye pigmentation in Europe, a publication from 1995 (in Polish):


https://repozytorium.amu.edu.pl/bitstream/10593/7344/1/07_L_Gronkiewicz_S_Gronkiewicz_ZR__NICOWANIE_BARWY _OCZU_53-67.pdf


Translation to English:


"(...) Results of extensive studies on territorial diversification and secular changes of eye pigmentation, carried out already from the 19th century onward in many European countries, were collected by Chamla and Gloor [1986]. (...) These authors think, that in general, among the European population, we can observe decreasing frequencies of light-pigmented eyes in modern populations when compared to populations of the past. This refers to populations of France, Italy and Switzerland, but a similar phenomenon can also be observed in South-Eastern Europe: in Bulgaria, Greece and Yugoslavia. Even in Sweden frequency of light eyes has decreased from 80-90% by the end of the 19th century to 70-80% nowadays [1995]. In France between 1880 and 1960 a considerable increase in frequency of dark eyes was observed, but it took place mostly in connection with a drastic decline in frequency of intermediate-colored eyes, while frequency of light-colored eyes remained throughout that period at a stable level of around 47 percent [Chamla 1964] (...)"


And here is how the authors define "light", "intermediate" and "dark" eyes:


"(...) Basing on amount of pigment in iris of eye, expressed with use of grades on the scale of eye color, subjects were grouped into three categories: 1. people with light eyes; 2. people with intermediate-colored eyes; 3. people with dark eyes. Category of light eyes (according to Martin's scale 16-12, 10, 9) includes irides of blue or grey color, without any insertions of yellow or russet pigments (except for naevi); intermediate eyes had irides of blue or green color with clearly visible groupings of yellow or russet pigment (according to Martin's scale 11, 8, 7); dark eyes had irides of various intensivity of brown color (according to Martin's scale 6-1). (...)"


Concerning ancient DNA we have genetics based evaluated pigmentation: it's not phoenotypical but rely on solid ground; the question is we have too little samples as a whole; concenring pigmentation states between 19° and 21° century we have unreliable states made on life by different people with with different cirteria; I know a good bit concerning France; what doesn't contradict the fact that an increasing and constant immigration of southern Europeans took place in France at those periods, explaining a darker pigmentation a sa whole, the most in middle and big towns, less in country, and with regional variations (economic attractiveness) of course..
concerning ancient population (10000 BC to 1000 AC, I propose we wait more data. NO offense to anybody.