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Thread: Cheddar Man near totally debunked (the "blue eyed black skinned" ancient Briton)

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    Cheddar Man near totally debunked (the "blue eyed black skinned" ancient Briton)

    A couple of years ago this had already been debunked. When they used the tool to calculate his skin colour the scientists made a typo or a data input error because they didn't read the manual for the tool.

    This is like calling someone up but getting one digit wrong in the number when putting it in and getting throw to the wrong person but never knowing it was the wrong number because they didn't pick up the phone.

    Specifically they inverted rs6119471 (flipped a bit) and that inversion switches Cheddar Man to black.

    Though this is a fundamental error in their paper, I've been able to confirm it and many others with the tool.

    Cheddar Man's SNPs are here:

    https://www.nhm.ac.uk/content/dam/nh...tion-data.xlsx

    You can put them into the tool here:

    https://hirisplex.erasmusmc.nl/

    Without reading the manual, I got black with blue eyes. After reading the manual I got intermediate with blue eyes.

    The manual is here:

    https://hirisplex.erasmusmc.nl/pdf/h...asmusmc.nl.pdf

    "*if you are using sequencing data, than you may need to flip strand orientation in your
    result before inputting into this prediction model. The only SNP that may cause
    confusion and therefore must be converted (from NCBI’s forward orientation) is
    rs6119471. All other G/C, A/T SNPs are in the correct orientation for input or are
    opposite alleles i.e. SNP G/A, input requests C/T."

    I couldn't do this as thoroughly the first time around with Cheddar Man and HIrisPlex-S as I didn't have another sample with a known correct result for a point of comparison.

    This isn't the only error with the tool. This is what is likely just one in a very large number of scientific errors producing a large amount of noise and garbage in scientific publications.

    You can view a full write up here which explores the original research and several categorical problems stemming from it:

    https://www.quora.com/What-is-the-ev...ohn-Baker-1665

    There have been threads on here previously questioning this such as this one:

    https://anthrogenica.com/showthread....-Briton/page56

    I've been able to advance much further on this because I was fully sequenced last year rather than just partially allowing me to use myself to evaluate the tool and compare their results. IF you try this with something like 23andme results or other standard ones you'll usually get many missing SNPs for the tool.

    I really want to stress that this isn't just about Cheddar Man. The errors and uncertainties observed in my full write up after peer reviewing the research are certain to have played out many times and this really means we have to question a lot of what we think we know where based on scientific publications in genetics. These errors are particularly prone with ancient samples because you don't have the real live specimen on hand to falsify your work.
    Last edited by John Baker; 10-17-2021 at 01:50 AM.

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    absurd!

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    Thank you for sharing the link with the snps.
    I did run these snps through the hirisplex tool.

    Keep in mind:

    - A = T
    - C = G
    - Don’t forget to put N/A for the 3 missing loci.
    - When you see a combination of 2 different letters such as AG or CT you always put 1.
    - When you only see one letter such as A or G and it is matching, you always put 2.

    Here the result:

    34AF278F-8C61-4BC9-BBBF-E381A67E5770.jpeg

    3103FA20-4A45-4A04-8837-9E4B8C4BF8CC.jpeg



    Predicted phenotype

    p-value
    blue eye 0.564
    intermediate eye 0.189
    brown eye 0.247
    blond hair 0
    brown hair 0.015
    red hair 0.984
    black hair 0.001
    light hair 1
    dark hair 0
    very pale skin 0
    pale skin 0
    intermediate skin 0.047
    dark skin 0
    dark to black skin 0.953

    AUC Loss
    blue eye 0
    intermediate eye 0
    brown eye 0
    blond hair 0.003
    brown hair -0
    red hair 0.013
    black hair 0
    light hair 0
    dark hair 0
    very pale skin 0.011
    pale skin 0.002
    intermediate skin 0.001
    dark skin 0.001
    dark to black skin -0


    A probability of almost 100% dark to black skin prediction.
    A blue eye probability of 56%.
    There is some brown eye pigmentation so it is possible he had hazel/green eyes.

    Who knows what changes when we have the 3 missing loci.
    But this definitely won’t make him suddenly very pale skinned.
    All the most important pigmentation genes are covered.

    So what is debunked?
    I think more better quality European Hunter gatherers samples are available for hirisplex since this year. Several recent studies of other European hunter gatherers came to the same conclusion.
    And there is a similar pattern: a lack of depigmentation mutations for skin and a higher probability for blue eyes.

    Keep mind that a Southern European with the perceived olive tan which some of us socially call darker skin never ever gets a dark to black skin probability of nearly 100% with the same amounts of covered genes.
    The prediction is usually between pale and intermediate for these type of modern olive pigmented people.
    So we can only speculate how dark the Cheddar man had been…


    Here the supplementary information from Harvard:

    https://reich.hms.harvard.edu/sites/...Supplement.pdf

    Hirisplex result on page 18:

    Cheddar Man (UK, Mesolithic)
    Eye colour —There is 1 locus (LOC105374875 (formally known as SLC24A4) rs12896399) with low coverage (1x) hence a heterozygote is possible. Prediction includes a range that includes what the 1x coverage found (ancestral G allele) and the possibility of an A derived allele being present.

    LOC105374875 rs12896399 (homozygote GG)
    Blue eye 0.564
    Int. eye. 0.189
    Brown eye. 0.247

    LOC105374875 rs12896399 (heterozygote GA)

    Blue eye. 0.711
    Int. eye. 0.143
    Brown eye. 0.145

    Prediction range:
    Blue eye 0.564 - 0.711
    Int. eye 0.189 - 0.143
    Brown eye 0.247 - 0.145

    Final prediction: Intermediate (blue/green) eye colour

    Explanation: This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced SNP would clarify this but blue/hazel cannot be ruled out.
    It is certainly not a brown eyed or clear blue-eyed individual.

    Hair colour—There is 1 locus PIGU rs2378249 with low coverage (1x) hence a heterozygote is possible. Prediction is a range that includes what the 1x coverage found, ancestral A allele, but also includes the possibility of a heterozygote being present.


    PIGU rs2378249 (homozygote AA)
    Blond hair 0.009
    Brown hair 0.692
    Red hair 0.006
    black hair 0.292
    Light hair 0.999
    Dark hair 0.001

    PIGU rs2378249 (heterozygote CA)
    Blond hair 0.009
    Brown hair 0.741
    Red hair 0.012
    Black hair 0.237
    Light hair 0.999
    Dark hair 0.001

    Prediction range:
    Brown 0.692 – 0.741
    Black 0.292 – 0.237

    Final Prediction: Dark Brown/Black hair colour
    Explanation: The probability value of black is >0.2 so it has an impact on prediction, and will darken the high brown probability. However, there are light pigment alleles indicating a lighter shade phenotype. Better coverage at the low sequenced SNP would help clarify this. This individual would be perceived as having dark brown hair. However, black cannot be ruled out.


    Skin pigmentation—There are 3 loci (BNC2 rs10756819, TYR rs1126809, MC1R rs3212355) missing, and the profile does contain 2 loci (LOC105374875 rs12896399 and PIGU rs2378249) with low coverage (n=1x) hence a heterozygote is possible at those sites. When factoring in possible genotype combinations, a prediction range may be generated. The range consists of assuming the two loci with low coverage are correct as homozygote for their sequenced allele (LOC105374875 rs12896399 G allele and PIGU rs2378249 A allele) and omitting the 3 missing loci from the prediction model as they have no coverage, to including these SNPs with their ancestral (BNC2 rs10756819-GG, TYR rs1126809-GG, MC1R rs3212355-CC) and also their derived allele counterparts. The following range for skin pigmentation prediction is possible for this individual with these parameters:

    Ancestral alleles used
    Very Pale 0
    Pale. 0
    Intermediate 0.152
    Dark. 0
    Dark - Black. 0.848

    Derived alleles used
    Very Pale. 0
    Pale. 0
    Intermediate 0.038
    Dark. 0
    Dark - Black. 0.962

    Prediction range:
    Very Pale 0
    Pale 0
    Intermediate 0.152 - 0.038
    Dark 0. - 0
    Dark-Black. 0.848. - 0.962

    If we omit the intermediate and dark-black category respectively, changing the prediction ranges to 0.752- 0.038 and 0.248-0.962. However, note that this completely removes the locus from the prediction model; hence the prediction will not perform optimally (how the prediction model was made). It is therefore best to have some allele present to infer the most probable range for Cheddar Man and we derive the ranges above from the extreme allele constellations only.

    Final prediction: Dark/Dark-to-black skin

    Explanation: The missing loci certainly impact on this prediction; however, utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.152 for intermediate and 0.848 for Dark-to-Black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also, this effect of skipping a skin pigmentation prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is present. It is unlikely that this individual has the darkest possible pigmentation, but it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion.
    Last edited by Ylang-Ylang; 10-17-2021 at 07:55 AM.

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    According to the scientists that decoded the genome of La Braņa, these Mesolithic HGs carried ancestral alleles for skin pigmentation that aren't found in present-day Europeans. This means that virtually all Europeans have a much lighter skin pigmentation (even the ones with olive skin) than these HGs.

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    The hirisplex result of La Brana man by this Harvard paper:

    https://reich.hms.harvard.edu/sites/...Supplement.pdf

    Page 16.

    La Braņa (Spain, Mesolithic)
    Eye colour —All loci are present and have good coverage.
    Blue eye Int. eye Brown eye
    0.459 0.155 0.387
    Final prediction: Intermediate (hazel/green) eye colour
    Explanation: All probabilities are less than 0.5 so it is a combination of all categories, as brown is relatively high, it is more than likely a light hazel eye colour individual, but perceived green (blue/yellow) cannot be ruled out.
    Hair colour—There is 1 locus (TYRP1 rs683) with low coverage (1x), hence a heterozygote is possible. Prediction is a range that includes what the 1x coverage found (derived G allele) and the possibility of an A ancestral allele being present.

    TYRP1 rs683
    (homozygote GG)

    Blond 0.018
    Brown 0.612
    Red 0
    Black 0.37
    Light 0.033
    Dark 0.967


    TYRP1 rs683 (heterozygote GA)

    Blond 0.014
    Brown 0.595
    Red 0
    Black 0.391
    Light 0.025
    Dark 0.975

    Prediction range:
    Brown 0.612 – 0.595
    Black 0.37 – 0.391


    Final Prediction: Black/Dark Brown hair colour

    Explanation: The probability value of black is >0.25 so it has a significant impact on prediction, and will darken the high brown probability. This individual would be perceived to have black hair. However, Dark Brown cannot be ruled out.

    Skin pigmentation—Only 1 locus (BNC2 rs10756819) is missing; however, the profile contains 3 loci with low coverage (n=1x), hence a heterozygote is possible. When factoring in possible genotype combinations, a prediction range has been generated. The range consists of assuming the 3 loci with low coverage are correct as homozygous for their sequenced allele (ASIP rs1667394 A allele (derived), OCA2 rs1545397 A allele (ancestral), TYRP1 rs683 A allele (ancestral)) and omitting BNC rs10756819 in the prediction model as it has no coverage, to including this SNP with a homozygote ancestral G allele and also derived A allele. The following range for skin pigmentation prediction is possible for this individual with these parameters:

    Omitting rs10756819
    Very Pale 0
    Pale0
    Intermediate 0.174
    Dark 0.463
    Dark-Black 0.363

    G ancestral allele
    Very Pale 0
    Pale 0
    Intermediate 0.042
    Dark 0.209
    Dark-Black 0.749

    A derived allele
    Very Pale 0
    Pale 0
    Intermediate 0.205
    Dark 0.435
    Dark-black 0.360

    Prediction range:
    Very Pale Pale Intermediate Dark Dark-Black
    0
    0 0.042 0.209 0.749
    - 0.205 - 0.435 - 0.36

    Final prediction: Dark/Dark-to-Black skin

    Explanation: The combined effect of probabilities in the dark and dark-to-black colour categories provide an indication that the individual has darkly pigmented skin, it is unlikely that this individual has the darkest possible skin pigmentation, but it cannot be ruled out as the missing SNP does influence that detail, but certainly skin pigmentation is dark in complexion.


    Prediction range:
    Very Pale 0
    Pale 0
    Intermediate 0.042 - 0.205
    Dark 0.209 - 0.435
    Dark-Black

    Final prediction: Dark/Dark-to-Black skin

    Explanation: The combined effect of probabilities in the dark and dark-to-black colour categories provide an indication that the individual has darkly pigmented skin, it is unlikely that this individual has the darkest possible skin pigmentation, but it cannot be ruled out as the missing SNP does influence that detail, but certainly skin pigmentation is dark in complexion.
    Last edited by Ylang-Ylang; 10-17-2021 at 09:05 AM.

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    It's fascinating that evolution didn't gave them pale skin. It's like Darwin failed and left them vitamin D deficient. Or maybe pale skin is not an evolutionary trait but a random mutation? Or maybe social selection? Why EEF had lighter skin? Was diet a factor? Lot of questions...

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    Quote Originally Posted by Milkyway View Post
    According to the scientists that decoded the genome of La Braņa, these Mesolithic HGs carried ancestral alleles for skin pigmentation that aren't found in present-day Europeans. This means that virtually all Europeans have a much lighter skin pigmentation (even the ones with olive skin) than these HGs.
    You haven't seen a certain video where it is supposed, as a second "option", that Cheddar Man (in particular) could also have had genes (not the combination of alleles) linked to a certain pigmentation which is not found currently anymore in Europe?

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    Unmixed Native Americans completely lack the derived (light pigmentation) alleles of SLC24A5 and SLC45A2 yet they don't have black skin or skin as dark as some of the Cheddar Man or other WHG reconstructions. Also WHGs seem to have lacked alleles for dark pigmentation found in very dark skinned populations today like subsaharan Africans and some south Asians.
    Last edited by Philjames; 10-17-2021 at 04:45 PM.

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    Quote Originally Posted by Philjames View Post
    Unmixed Native Americans completely lack the derived (light pigmentation) alleles of SLC24A5 and SlC45A2 yet they don't have black skin or skin as dark as some of the Cheddar Man or other WHG reconstructions. Also WHGs seem to have lacked alleles for dark pigmentation found in very dark skinned populations today like subsaharan Africans and some south Asians.
    The prediction of pigmentation is very complicated.
    You should not focus on only 1 copy of a specific pigmentation gene. This is why the hirisplex tools use 41 loci to predict the pigmentation accurately. It includes typical skin depigmentation mutations of the East Asians too.
    This pigmentation prediction is dependent on many pigmentation genes together, not one one specific gene.
    A human can lack one specific pigmentation gene and have other light skin mutations. And this would make these people not black skinned, but perhaps between intermediate and dark or even between pale and intermediate.
    Many East Asian people lack specific pigmentation you find in Europe, but still would look light/intermedite skinned.

    People of full East Asian and Native American origins can lack specific depigmentation mutations which is more common with Europeans.
    There are typical East Asian depigmentation mutations which you rarely find with West Eurasian and African people. Perhaps you find this with some Eastern Europeans who carry significant East Asian genetics. Slavic people sometimes have the very typical East Asian Edar gene.
    So you can think the other way: because most Europeans lack these specific East Asian light skin mutations does not mean Europeans are black skinned…

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5671666/
    “ In East Asia however, two non-synonymous variants in the OCA2 gene; rs1800414 (His615Arg) and rs74653330 (Ala481Thr) have been associated with light skin and eye color (Edwards et al., 2010; Abe et al., 2013; Eaton et al., 2015; Edwards et al., 2016; Norton et al., 2016; Yang et al., 2016).”


    More about the East Asian rs1800414:

    https://selfdecode.com/snp/rs1800414/
    rs1800414 : each copy of the ''C'' allele decreases skin pigmentation by approximately 1.3 melanin units (p = 0.002). The TC heterozygote decreases skin pigmentation by 1.6 melanin units (p = 0.046) and CC homozygotes by 2.6 melanin units (p = 0.002) [R].



    There is already a study about pigmentation of full Native Americans.
    It seems very accurate to me: between intermediate and dark skin.
    Which we socially observe as brown pigmentations.

    https://www.fsigenetics.com/article/...108-3/fulltext

    Insights on hair, skin and eye color of ancient and contemporary Native Americans

    Highlights


    We have predicted pigmentation phenotypes for seven ancient Native Americans.

    The HIrisPlex-S and Snipper systems were used for the predictions.

    Except for a Karitiana sample, eye colors were predicted as intermediate/brown.

    Except for a Karitiana sample, all individuals were predicted with black hair.

    Snipper and HIrisPlex-S presented differences regarding skin color prediction.
    Abstract

    Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.
    Last edited by Ylang-Ylang; 10-17-2021 at 04:35 PM.

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    Quote Originally Posted by Ylang-Ylang View Post
    There is already a study about pigmentation of full Native Americans. It seems very accurate to me: between intermediate and dark skin. Which we socially observe as brown pigmentations.
    Brown skin or as historically described 'copper' or 'dark red' skin, which is quite different both in tone and colour to very dark skinned populations like sub-Saharan Africans and some South Asians, and to some of the Cheddar Man/WHG reconstructions. The claim was that Cheddar Man had skin colour like sub-Saharan Africans, whereas skin colour similar to Native Americans seems much more likely given the DNA and also the more recent common ancestry between Europeans and Native Americans.

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