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View Full Version : Update: Natural Selection in last 8,000 years.



Krefter
12-01-2015, 03:47 PM
Click to enlarge.
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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.
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Light skin mutation #1(rs1426654).
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Light skin mutation #2(rs16891982).
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Lactose Tolerance(rs4988235) frequency.


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.
http://www.anthrogenica.com/attachment.php?attachmentid=6769&stc=1

Tomenable
12-01-2015, 05:21 PM
I can't see graphs from spoilers, except for the last one ("Frequency of Red hair Carriers").

paulgill
12-01-2015, 05:53 PM
I don't think that Natural Selection have anything to do with conscious decisions, though man and the mind are also a part of the Nature.

Krefter
12-01-2015, 07:09 PM
I can't see graphs from spoilers, except for the last one ("Frequency of Red hair Carriers").

Can you see them now?

Tomenable
12-01-2015, 07:36 PM
Nope, I still can't see them. Here is what I see (http://s28.postimg.org/fczazfmnx/here.png):

http://s28.postimg.org/fczazfmnx/here.png

Krefter
12-01-2015, 07:39 PM
Nope, I still can't see them. Here is what I see (http://s28.postimg.org/fczazfmnx/here.png):

http://s28.postimg.org/fczazfmnx/here.png

How about now?

Tomenable
12-01-2015, 09:11 PM
Yes, now I can see them! Thanks!

Tone
12-02-2015, 01:58 AM
Very interesting graphs, Krefter. :)

I'm not very steeped in this stuff. What are your thoughts on the origin of light (blond) hair at this time? Was it originally an EHG trait, or did it originate in EEF and hence selected for a higher frequency in Northern Europe? Maybe a SHG-EHG trait that's always been frequent where it is today around the Baltic?

drobbah
12-02-2015, 02:34 AM
What does it mean if one has AG for snp rs1426654?

Krefter
12-02-2015, 09:04 AM
What does it mean if one has AG for snp rs1426654?

It suggests someone has Dark Brown skin. But there are white skinned people with AG in that SNP. There's no perfect way to predict skin color with DNA yet.


Very interesting graphs, Krefter. :)

I'm not very steeped in this stuff. What are your thoughts on the origin of light (blond) hair at this time? Was it originally an EHG trait, or did it originate in EEF and hence selected for a higher frequency in Northern Europe? Maybe a SHG-EHG trait that's always been frequent where it is today around the Baltic?

The origins are mysterious. There's no very accurate way to know whether someone had blonde hair or not with DNA. There is a method to predict hair color from DNA Police use called Hirisplex. According to Hirisplex, some EHG and Anatolia_Neolithic had Blonde hair. But there's no way to know whether they had Blonde hair or not. My guess is the ultimate origins of Blonde hair are deep in the Upper Palaielthic. The question is not when it originated but when it became frequent.

The only Pre-Historic people we can be confident had a higher frequency of Blonde hair are Late Neolithic North Europeans around 2800-2000 BC. Late Neolithic North Europeans were hyprids, a mixture of "Steppe" from Russia and "EEF/WHG" who was native to North Europe. So, the question then is who gave them Blonde hair. If anything EEF/WHG are the source but there's no way to know for sure.

In conclusion the origins are unknown. It's an interesting question. Events, whether admixture of evolution, that occurred in North Europe sometime between ????-2000 BC caused it to be fairly frequent. It isn't only popular around Scandinavia and Baltic. It's pretty common in Ireland and deep in Central Europe. And it used to be common in Central Asia, because immigrants from Europe settled there in 2000 BC. That's more evidence by 2000 BC it was frequent.

parastais
12-02-2015, 11:16 AM
It (blond hair) correlates best with EHG % in Europe. WHG% does not really work and EEF% absolutely does not work.
But I am not sure if EHG was the source or Euro folk that brought EHG around.

Hando
12-02-2015, 04:02 PM
It (blond hair) correlates best with EHG % in Europe. WHG% does not really work and EEF% absolutely does not work.
But I am not sure if EHG was the source or Euro folk that brought EHG around.
Who are these Euro folk? EHG was a hybrid of WHG and ANE so are you suggesting blonde hair originated with ANE in Siberia?

Krefter
12-02-2015, 08:00 PM
It (blond hair) correlates best with EHG % in Europe. WHG% does not really work and EEF% absolutely does not work.
But I am not sure if EHG was the source or Euro folk that brought EHG around.

It's a stretch to associate blonde hair with EHG or WHG or whoever else that lived 8,000 years ago. This is because, EHG/WHG/EEF/CHG were not given to modern Europeans 8,000 years ago. All four elements came together circa 4,800 years ago. And modern Euros are not overwhelmingly any of those things.

Hando
12-03-2015, 02:56 AM
It's a stretch to associate blonde hair with EHG or WHG or whoever else that lived 8,000 years ago. This is because, EHG/WHG/EEF/CHG were not given to modern Europeans 8,000 years ago. All four elements came together circa 4,800 years ago. And modern Euros are not overwhelmingly any of those things.
Do you mean that modern Europeans are mostly descended from an ancestor that has nothing to do with EHG/WHG/EEF/CHG? I don't thnk that's what you intended to suggest...

Krefter
12-03-2015, 05:44 AM
Do you mean that modern Europeans are mostly descended from an ancestor that has nothing to do with EHG/WHG/EEF/CHG? I don't thnk that's what you intended to suggest...

I'm saying no one is like 70% WHG or EEF or CHG or EHG. No one is overwelhmingly one of those things.

parastais
12-03-2015, 01:09 PM
Who are these Euro folk? EHG was a hybrid of WHG and ANE so are you suggesting blonde hair originated with ANE in Siberia?
Nah, it is simple linear regression.
% of EHG vs % of blond hair. Very strong correlation (R over 0.95) of course does not mean causality, also not sure if it is kosher to try linearily correlate two ratios.
It is just mathematical thingy.

As to Euro folk, I was not very precise, what I meant was - either it was EHG as the source OR it was population that brought EHG around the Europe specifically (Yamna, Corded, something else?), because this correlation works charmingly in Europe, but most likely not so well outside Europe.

Intuitively, if you check folk with top EHG in Europe, they are also blondest (Finns, Estonians, Balts, Nordic folk), but for some reason it does not work so well for WHG.

I made that math based on Haak's ratios a time ago.

Tomenable
12-05-2015, 08:50 PM
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). (...)"

Krefter
12-06-2015, 02:58 AM
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). (...)"

Maybe natural selection is going on now. But serisously I can't see how this is possible. 100 years isn't long enough. Maybe immigration is why.

Kale
12-06-2015, 03:57 AM
The guy in 1880 might not have had the same standards of eye color as the guy in 1960. It's not like we have color photographs from 1880 to do a real scientific comparison.

Constantine
12-06-2015, 07:41 AM
So is EDAR exclusively Mongoloid like Genetiker says? Why would it occur in such unlikely people as the Yoruba if it is?

Kale
12-06-2015, 06:16 PM
Where are you getting that?

Krefter
12-07-2015, 02:46 AM
So is EDAR exclusively Mongoloid like Genetiker says? Why would it occur in such unlikely people as the Yoruba if it is?

If it exists in Yoruba it isn't exclusively Mongoloid. I imagine the Motala_HGs were an isolated and drifted group. They're related to ancestors of modern Euroepans but not direct ancestors. So, in that sense people like them died out. So, I'm not surprised to see weird results for them like in EDAR.

parasar
12-07-2015, 04:48 AM
So is EDAR exclusively Mongoloid like Genetiker says? Why would it occur in such unlikely people as the Yoruba if it is?

The Yoruba have seen a relatively recent influx of Eurasian genes. Even then I do not see much of a presence in the Yoruba: http://alfred.med.yale.edu/alfred/mvograph.asp?siteuid=SI663326A

Brent.B
12-07-2015, 05:08 AM
I don't know much about this subject, but am curious. What would the original Indo-European R1a/R1b people have looked like then? I remember reading that they would have been blonde and white. I also read that pre-indoeuropean Europe would have been semi-dark skinned and blue eyed.

Is that consistent with the data here?

Ignis90
12-07-2015, 05:39 AM
So is EDAR exclusively Mongoloid like Genetiker says? Why would it occur in such unlikely people as the Yoruba if it is?

Genetiker uses obsolete and counterproductive racial "-oid" terms to begin with.

It's also known that some African population have the derived version of EDAR and that some East Asian/American population have the derived versions for light eyes and/or hair. In each case, the mutations don't have the same effect as they are known for respectively. It's just part of the variation and doesn't always have to do with geneflow.
Yoruba people could have inherited it from their very small Eurasian ancestry but it's also highly possible that it is part of the African variation.

Constantine
12-07-2015, 08:23 AM
I respect a lot of the old "-oid" anthropology--esp. that of Coon--but its abuse on the Internet by people with personal/emotional hangups has giving it a bad name it seems.

Anyway, this sort of reminds me of blood types. Years ago people were declaring that having blood type B was indicative of "Mongoloid" ancestry.


Genetiker uses obsolete and counterproductive racial "-oid" terms to begin with.

It's also known that some African population have the derived version of EDAR and that some East Asian/American population have the derived versions for light eyes and/or hair. In each case, the mutations don't have the same effect as they are known for respectively. It's just part of the variation and doesn't always have to do with geneflow.
Yoruba people could have inherited it from their very small Eurasian ancestry but it's also highly possible that it is part of the African variation.