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Thread: The evolution of skin pigmentation-associated variation in West Eurasia.

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    It’s hard to know the exact de***mentation effects of the so called ‘derived’ genes.
    If a rely on the maps of distribution of the mutated forms for SLC24A5 and SLC45A2 in the world, and on what I think I know about all these people skin ***mentation, i’m tempted to say :
    - SLC24A5 is almost alone or very very dominant in Europe (a bit less roughly said in South, the lest in Sardigna) and in Levant and Northern Arabia ; it’s very dominant too among northern Iranians and ethnic Afghans, even more north-east, Hindu Kush and north of western Himalaya ; Mozabites have significantly less, but they are not on the maps I’ve. In western Algeria (Sahel) it accounts for around 80% (what ethny?) so les than in the northern Indo-Iranian lands.
    - SLC45A2 is still very dominant among Europeans, but less than SC24A5 ; the doc I’ve is unprecise for some regions, and I don’t know precisely but it seems the derived alleles spite dominant, are very less present in a southern region of Italy (Sicily ? Basilicate ? Calabre?) ; in Levant and Nth-Arabia, it represents about 50 %, and in Iran, Hindu Kush and around it’s around 20 % only. In western Algeria (Sahel), it’s around 40-45 % so more than in northern Indo-Iranian lands.
    So, what about the « whiting power » of these derived alleles ?
    In Europe, the skin colours are very close (light or very light) in winter time, from milky white to yellowish olive, not as dark (brunet white) as Levantines and Nth-Arabians or Iranians and Afghans.
    I have to say that at the individual level, Levantines, eg Druzes and Kurds, show often the same skin colour than the most of darkest Europe regions inhabitants (Southerners is a « bag term » in Europe which covers a lot of different and diverse people, all Mediterranean are not ‘mediter’like) ; Jordanians, Saudi Arabs and Asia ‘europoids’ are a bit darker but not so much.
    I don’t speak about the pops with more ‘mongoloid’ crossings, where the specific east-asian mutation has produced visible lightening effects, whatever would be the %’s of specific Europoid mutations.
    I see that SLC24A5 derived alleles has surely more effects than SLC45A2 derived alleles, since the Iranian, Afghan and Tadjik pop’s, very dominant for the SLC24A5 mutation close here to Europeans but very poor for the SLC45A2, opposed here to Europeans and even neatly poorer than Levantines Arabians, have skin colours not too far from the darkest Europeans, if not so close (and this could be discussed but the reflectance measures of not exposed skin colour confirms it: Sth-West Asia, Near-East, Nth of Sth-Asia and NW Africa are very close one to another : the slightly darkest would be due too to some input of SSA genes, concerning the Semitic-Hamitic pop’s. (BTW, among the less dark ones, we have some Kurds and Northern Amazighs).
    I avow that my conclusion about both SLC’s is a bit fast made, because I don’t know the input that could have other loci, even if weak everyone of them… Just a bet.


    Concerning « black » skin, let’s remember that SSAfricans have derived alleles for reinforced***mentation so we aren’t obliged to believe our far ancestors in Africa were « blackish black » skinned (BTW it seems their ***mentation has changed there and then, according to families, darker or lighter).

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    Quote Originally Posted by matp View Post

    P.S have a look at the Whitehawk woman reconstruction of a neolithic farmer - do you agree this is an accurate portrayal? Given we actually have living populations living in far hotter climates (Sardinians) that have very similar ***mentation variants to EEF and in no way look anything like the Whitehawk reconstruction..
    Given the fact that the Whitehawk woman was a Neolithic farmer, it is rather likely that she was several shades lighter than the reconstruction. That said, the researchers explained that they think the Whitehawk women's complexion was that dark due to the fact, that she had significant WHG admixture. So, to these researchers the WHG genetic input didn't lighten the Anatolian farmers' complexion, but made them rather darker.

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    So far as I know there is no dna available for the "Whitehawk" Neolithic woman, so it's impossible to gauge the accuracy of the skin tone.

    I personally know people who are homogeneous derived for SLC24A5, but heterogeneous for derived SLC45A2 who look like normal Mediterranean Europeans, although slightly on the darker side. That combination is pretty common in parts of Iberia. However, the ones I know have other depigmentation snps. I don't know any Europeans who are completely ancestral for SLC45.

    As I've said a thousand times, you can't tell predicted pigmentation without a bunch of snps, as pigmentation is CUMULATIVE in nature.


    What I can say is that if you go back and check the pigmentation snps of the early farmers in the Balkans, and compare them to the early farmers in Iberia where the farmers have more WHG, the farmers in Iberia would be predicted to be "darker".

    As always, these things are relative.

    Has anyone run La Brana through the online calculator? Are there enough good quality snps to fit the requirement for the calculator?


    Non si fa il proprio dovere perchè qualcuno ci dica grazie, lo si fa per principio, per se stessi, per la propria dignità. Oriana Fallaci

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    2 members found this post helpful.
    Quote Originally Posted by Angela View Post
    So far as I know there is no dna available for the "Whitehawk" Neolithic woman, so it's impossible to gauge the accuracy of the skin tone.

    I personally know people who are homogeneous derived for SLC24A5, but heterogeneous for derived SLC45A2 who look like normal Mediterranean Europeans, although slightly on the darker side. That combination is pretty common in parts of Iberia. However, the ones I know have other depigmentation snps. I don't know any Europeans who are completely ancestral for SLC45.

    As I've said a thousand times, you can't tell predicted pigmentation without a bunch of snps, as pigmentation is CUMULATIVE in nature.


    What I can say is that if you go back and check the pigmentation snps of the early farmers in the Balkans, and compare them to the early farmers in Iberia where the farmers have more WHG, the farmers in Iberia would be predicted to be "darker".

    As always, these things are relative.

    Has anyone run La Brana through the online calculator? Are there enough good quality snps to fit the requirement for the calculator?
    Again, I've posted these before, but for newcomers...



    This is the only study of which I'm aware that has data for each province. That's because the data is from a melanoma study.

    However, Lucotte et al has spotty data from the rest of West Eurasia for 374f or 45A2:





    Table 1. Distribution of 374F allele frequencies in 32 populations of West Europe and North Africa (N = sample size).
    No.
    Country
    Region/population
    Latitude (°)
    N
    Frequency of 374f
    References
    1
    Germany
    Northrhine-Whestphali
    50.9
    241
    0.965
    Yuasa et al. (2006)
    2
    Munich
    48.1
    93
    0.962
    3
    France
    Rheims
    49.2
    98
    0.893
    4
    Italy
    Genoa
    44.5
    97
    0.85
    5
    Denmark
    Copenhagen
    56
    51
    0.98
    Lucotte et al.(2010)
    6
    England
    London
    51.5
    56
    0.955
    7
    Belgium
    Brussels
    50.5
    53
    0.934
    8
    France
    Lille
    50.5
    64
    0.945
    9
    Rennes
    48
    52
    0.971
    10
    Marseilles
    43.2
    312
    0.888
    11
    Perpignan
    43
    101
    0.827
    12
    Corsica
    42
    328
    0.878
    13
    Germany
    Mulheim
    50
    59
    0.975
    14
    Switzerland
    Basel
    47.2
    51
    0.961
    15
    Italy
    Roma
    41.9
    64
    0.898
    16
    Napoli
    41
    128
    0.859
    17
    Sicily
    38
    39
    0.833
    18
    Sardinia
    40
    100
    0.805
    19
    Spain
    Barcelona
    41
    59
    0.856
    20
    Sevilla
    37.5
    71
    0.725
    21
    Portugal
    North
    42
    79
    0.725
    22
    South
    38
    59
    0.780
    23
    Morocco
    Tangier
    35.8
    123
    0.691
    24
    Algeria
    Algier
    36.5
    141
    0.709
    25
    Tunisia
    Tunis
    36.5
    73
    0.610
    26
    England
    Orcades
    59
    16
    1
    Norton et al. (2007)
    27
    France
    46
    29
    0.91
    28
    Basque
    43
    24
    0.94
    29
    Italy
    Bergamo
    46
    14
    0.96
    30
    Tuscan
    43
    8
    0.94
    31
    Sardinia
    40
    28
    0.68
    32
    Algeria
    Mozabite
    32
    30
    0.40




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    Quote Originally Posted by Angela View Post
    So far as I know there is no dna available for the "Whitehawk" Neolithic woman, so it's impossible to gauge the accuracy of the skin tone................


    The researchers indirectly gauged the complexion of the Whitewawk woman by comparing her to other Neolithic Brits, and by going from the information they've got from the "Cheddar Man" team.
    From recalling reading the British Neolithic folks had substantial WHG genetic input.


    The same team of scientists released results of research to the public in 2018 about ‘Cheddar Man’, a ten thousand year old modern human from the Mesolithic Period, whose ancient DNA demonstrated that he was dark skinned.
    While DNA could not be retrieved from Whitehawk Woman, the ‘Cheddar Man’ team advised that she would probably have had dark skin of a southern Mediterranean/Near Eastern/North African colour, brown hair and brown eyes. This is based on the genetic analysis of ancient individuals dating to the Neolithic from around Europe as well as from Britain specifically. This information was passed on to our forensic artist who included it within the facial reconstruction on display in the new gallery.
    The same analysis produced predictions of lighter skin for other individuals included in the gallery and these predictions were also included in their facial reconstructions.
    In each instance where ancient DNA was not recoverable from our individuals, we followed the same scientific advice on likelihood of their physical characteristics.
    https://brightonmuseums.org.uk/disco...has-dark-skin/

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    Quote Originally Posted by real expert View Post
    The researchers indirectly gauged the complexion of the Whitewawk woman by comparing her to other Neolithic Brits, and by going from the information they've got from the "Cheddar Man" team.
    From recalling reading the British Neolithic folks had substantial WHG genetic input.




    https://brightonmuseums.org.uk/disco...has-dark-skin/
    Sorry to be a pain in the neck, but unless I see all the snps they used from these other Neolithic people and then some evidence those snps were run through the algorithm, color me sceptical.

    If you take a look at the parts of Europe where the people are 100% derived for SLC 24A5, as were most of the Early Neolithic farmers, and had only one or no derived SLC 45A2, they are no where near as dark as that.

    So, everything depends on which "modern" depigmentation snps those "other" Neolithic farmers carried in addition to derived SLC24A5. It's unlikely the early ones carried derived SLC45A2, but there are other depigmentation snps coded on the newest algorithms.

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    Quote Originally Posted by Angela View Post
    Sorry to be a pain in the neck, but unless I see all the snps they used from these other Neolithic people and then some evidence those snps were run through the algorithm, color me sceptical.

    If you take a look at the parts of Europe where the people are 100% derived for SLC 24A5, as were most of the Early Neolithic farmers, and had only one or no derived SLC 45A2, they are no where near as dark as that.

    So, everything depends on which "modern" depigmentation snps those "other" Neolithic farmers carried in addition to derived SLC24A5. It's unlikely the early ones carried derived SLC45A2, but there are other depigmentation snps coded on the newest algorithms.

    I’m actually skeptical, too. As you can see from my response to matp, I doubt that she was that dark. However, I brought the arguments of the researchers why they assume that she was of a dark complexion.

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    ........................
    Last edited by matp; 08-08-21 at 22:02.

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    ..............................
    Last edited by matp; 08-08-21 at 22:02.

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    Quote Originally Posted by matp View Post
    I have run La Brana and several other higher coverage WHG through on the calculator, they all get lighter skin predictions when you swap the blue eye associated variants for the ancestral brown eye alleles. I cannot post screenshots but if you want to put the data through yourself here is the number of alleles to input for each snp for La Brana for the darker prediction range suggested in the original study:

    12: 2
    13: 2
    16: 1
    19: 1
    27: 2
    29: 1
    35: 2
    39: 1

    Then see how the skin prediction changes when you plug in 2 alleles for snps:

    20, 31 & 32

    You will notice that whilst the blue eyes are totally gone, the skin prediction changes to dark from dark to black.
    So, academics putting out a major paper just decided not to input the snps for eye color???

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    ......................
    Last edited by matp; 09-08-21 at 05:14.

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    Quote Originally Posted by matp View Post
    I have run La Brana and several other higher coverage WHG through on the calculator, they all get lighter skin predictions when you swap the blue eye associated variants for the ancestral brown eye alleles. I cannot post screenshots but if you want to put the data through yourself here is the number of alleles to input for each snp for La Brana for the darker prediction range suggested in the original study:

    12: 2
    13: 2
    16: 1
    19: 1
    27: 2
    29: 1
    35: 2
    39: 1

    Then see how the skin prediction changes when you plug in 2 alleles for snps:

    20, 31 & 32

    You will notice that whilst the blue eyes are totally gone, the skin prediction changes to dark from dark to black.
    did you enter NA for all the others?

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    ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
    Last edited by matp; 08-08-21 at 22:03.

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    Quote Originally Posted by matp View Post
    All of the other snps you leave as '0' with no inputs as 'NA'
    is that really correct? we don't know the data for those snp's right? i assume you are using this right? https://hirisplex.erasmusmc.nl/

    i already wrote this somewhere else but i don't get that site.

    for example for rs1129038(31) it says "G" but when i google that snp it says that there is a C and a T allele not G

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    ......................
    Last edited by matp; 09-08-21 at 05:15.

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    Quote Originally Posted by matp View Post
    Have a look on snpedia and search for 'orientation' - in this instance the C/G allele represents the ancestral brown eye associated variant, and the T/A allele represents the derived associated blue eye variant at highest frequency to North Europe
    thanks. i thought that it might be because of the reversed/non-reversed strand. but didn't think people would actually label SNP's based on the non-coding strand or mix everything up.

    tried the different snp's and it seems for the different HERC2 variants nr.20, 28, 30 leads to darker skin prediction while 31 and 32 lead to a lighter one. it's a bit strange but i'm not sure how accurate this is if you just put in 0 in those where we don't know the value.

    something that might be a sign of this problem that you really shouldn't just add 0 everywhere: if you leave everything at 0 and just change 31 and 32 then they actually lead to somewhat darker skin prediction while before with the values of la brana they lead to lighter skin prediction.

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    ........................
    Last edited by matp; 09-08-21 at 05:15.

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    Quote Originally Posted by matp View Post
    Yes 20 and 28 are giving what I would consider a consistent effect as with modern populations, 31 and 32 are inconsistent with modern populations - especially 31 - and the derived allele is almost unique to North Europe and does not appear anywhere else at any great frequencies bar the Americas of course.

    So what you have here is alleles most unique to North Europe contributing directly to heightened likelihood of black skin...

    Now see what happens when applying the same conditions to this modern day Finnish prediction; inputs are:

    12: 1
    13: 1
    22: 1
    24: 1
    25: 1

    All other snps are left as '0'



    And also Loschbour:

    12: 1
    13: 2
    15: 2
    16: 2
    27: 2
    29:2
    35: 2

    for those predictions ancestral version of 31 and 32 lead to higher likelyhood of dark skin. isn't that what you would expect?

    imo it shows that it is highly dependant on the context and that it's probably not accurate if we put in 0 everywhere instead of NA.

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    .....................
    Last edited by matp; 09-08-21 at 05:15.

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    Quote Originally Posted by matp View Post
    Yes that is my point. The Loschbour WHG prediction of 0.90 for intermediate is consistent - so 31 and 32 ancestral give the darkening effect to the prediction just like the modern day Finnish.

    However with La Brana the identical ancestral alleles at highest frequency to Africa/ East Asia contribute significantly to a lighter prediction. Remember these HGs were relatively homogenous, so any factors such as epistasis or variants not included in the model that could be influencing skin pigmentation on the hirisplex-s database subjects is not likely to be relevant to such similar individuals.

    We have to also remember that there is not a single actual WHG on the hirisplex database - but, of all potential comparative subjects, would it be more relevant to compare a WHG to say a Finnish person, or a heavily mixed African American - of which there will be numerous on the hirisplex database? I should also mention that on the snipper skin prediction model, all WHG score intermediate - Loschbour and La Brana actually score identical on the snipper.
    can you link me to the allele table for the WHG's? are those values you put in 0 really not there or are they NA?

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    Quote Originally Posted by matp View Post
    Yes that is my point. The Loschbour WHG prediction of 0.90 for intermediate is consistent - so 31 and 32 ancestral give the darkening effect to the prediction just like the modern day Finnish.

    However with La Brana the identical ancestral alleles at highest frequency to Africa/ East Asia contribute significantly to a lighter prediction. Remember these HGs were relatively homogenous, so any factors such as epistasis or variants not included in the model that could be influencing skin pigmentation on the hirisplex-s database subjects is not likely to be relevant to such similar individuals.

    We have to also remember that there is not a single actual WHG on the hirisplex database - but, of all potential comparative subjects, would it be more relevant to compare a WHG to say a Finnish person, or a heavily mixed African American - of which there will be numerous on the hirisplex database? I should also mention that on the snipper skin prediction model, all WHG score intermediate - Loschbour and La Brana actually score identical on the snipper.

    i tried Snipper now too and i have one question. in Snipper rs16891982 is C among 84% of "whites" so i assume if you enter C in Snipper for that snp it will give you a lighter skin prediction. however i believe the C from Hirisplex is actually not the C from Snipper because if you google that snp the ancestral allele is C and there are 2 possible mutations either A or G which means depending on which strand people look at, in case of the G muation couldn't it be that this mutation and the ancestral allele potentially get confused for each other?
    in that case i would enter G instead of C in snipper for that SNP and then you will get intermediate and black prediction.

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    Quote Originally Posted by Ailchu View Post
    i tried Snipper now too and i have one question. in Snipper rs16891982 is C among 84% of "whites" so i assume if you enter C in Snipper for that snp it will give you a lighter skin prediction. however i believe the C from Hirisplex is actually not the C from Snipper because if you google that snp the ancestral allele is C and there are 2 possible mutations either A or G which means depending on which strand people look at, in case of the G muation couldn't it be that this mutation and the ancestral allele potentially get confused for each other?
    in that case i would enter G instead of C in snipper for that SNP and then you will get intermediate and black prediction.

    i checked again, the variant most common in europe is derived not ancestral, which means you probably really have to enter G instead of C in Snipper which will yield an intermediate to black skin prediction.

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    .........................
    Last edited by matp; 09-08-21 at 05:16.

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    .....................
    Last edited by matp; 09-08-21 at 05:16.

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