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Thread: Phenotype SNPs Late Neolithic Spain

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    Elite member Fire Haired14's Avatar
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    Phenotype SNPs Late Neolithic Spain


    Geneticker has done analysis of Phenotype SNPs in Late Neolithic genomes from Burgos Spain published from a recent study: Phenotype SNPs from Copper and Bronze Age Spain. I've added the results to my spreadsheet: Pre-Historic West Eurasian Phenotype. Like with other results from Pre-Historic Europe they suggest Light skin mutation Phe374Leu and Lactose Tolerant mutations T-13910 and T-22018 have rising in frequency across all of Europe since 3000 BC.

    Mostly Brown eyed
    : As of far 8/8 Neolithic Spanish are Brown eyed while 43%(9/21) Neolithic Hungary/Germany/Sweden were Blue eyed. 5/10 of Early Neolithic LBK from Germany had Blue eyes, which means the difference in eye color difference LBK-derived and Cardiel-derived groups may have origins in Anatolia not Europe. Ultimately uniformly Brown eyed Cardial-groups and largely Blue eyed LBK-groups may be the source of eye color difference in Europe today.

    Darker skinned than modern Spanish: 3/3 of Late Neolithic Spanish have Light skin mutation Ala111Thr but 2/3 lacked Light skin mutation Phe374Leu. This is consistent with results from all over Europe dating earlier than 3000 BC. Today 80%+ in most of Europe are completely derived for Ala111Thr and Phe374Leu. This suggests Pale skin was selected for in all of Europe from 3000 BC and afterwards.

    Some were Lactose Tolerant: 1/3 Late Neolithic Spanish had T-13910. This Lactose Tolerance mutation has been found in other Late Neolithic Spanish and also in Neolithic Germany/Sweden and Yamnaya. Its frequency rose in Bronze age but it wasn't at modern frequencies. The frequencies of T-13910 vary by region today but its obvious after 3000 BC and even 2000BC or 1500 BC it was selected for and rose in frequency.

    Carriers for Red hair: Late Neolithic Spaniard ATP2 dating 2899–2678 BC had Red hair variant R151C. ATP2 had typical Neolithic European("EEF") genetic makeup(see here) and is the first of kind to besampled to be a carrier of Red hair. Before this R151C was only found in Pre-Historic Europeans with a high amount of "EHG"-ancestry. Today R151C is found in all West Eurasians and also in some parts of East Asia and America.

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    Quote Originally Posted by Fire Haired14 View Post

    Geneticker has done analysis of Phenotype SNPs in Late Neolithic genomes from Burgos Spain published from a recent study: Phenotype SNPs from Copper and Bronze Age Spain. I've added the results to my spreadsheet: Pre-Historic West Eurasian Phenotype. Like with other results from Pre-Historic Europe they suggest Light skin mutation Phe374Leu and Lactose Tolerant mutations T-13910 and T-22018 have rising in frequency across all of Europe since 3000 BC.

    Mostly Brown eyed
    : As of far 8/8 Neolithic Spanish are Brown eyed while 43%(9/21) Neolithic Hungary/Germany/Sweden were Blue eyed. 5/10 of Early Neolithic LBK from Germany had Blue eyes, which means the difference in eye color difference LBK-derived and Cardiel-derived groups may have origins in Anatolia not Europe. Ultimately uniformly Brown eyed Cardial-groups and largely Blue eyed LBK-groups may be the source of eye color difference in Europe today.

    Darker skinned than modern Spanish: 3/3 of Late Neolithic Spanish have Light skin mutation Ala111Thr but 2/3 lacked Light skin mutation Phe374Leu. This is consistent with results from all over Europe dating earlier than 3000 BC. Today 80%+ in most of Europe are completely derived for Ala111Thr and Phe374Leu. This suggests Pale skin was selected for in all of Europe from 3000 BC and afterwards.

    Some were Lactose Tolerant: 1/3 Late Neolithic Spanish had T-13910. This Lactose Tolerance mutation has been found in other Late Neolithic Spanish and also in Neolithic Germany/Sweden and Yamnaya. Its frequency rose in Bronze age but it wasn't at modern frequencies. The frequencies of T-13910 vary by region today but its obvious after 3000 BC and even 2000BC or 1500 BC it was selected for and rose in frequency.

    Carriers for Red hair: Late Neolithic Spaniard ATP2 dating 2899–2678 BC had Red hair variant R151C. ATP2 had typical Neolithic European("EEF") genetic makeup(see here) and is the first of kind to besampled to be a carrier of Red hair. Before this R151C was only found in Pre-Historic Europeans with a high amount of "EHG"-ancestry. Today R151C is found in all West Eurasians and also in some parts of East Asia and America.
    ATP9 looks interesting............seems like its admixture fits western Anatolians
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    Interesting

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    Quote Originally Posted by Fire Haired14 View Post

    Geneticker has done analysis of Phenotype SNPs in Late Neolithic genomes from Burgos Spain published from a recent study: Phenotype SNPs from Copper and Bronze Age Spain. I've added the results to my spreadsheet: Pre-Historic West Eurasian Phenotype. Like with other results from Pre-Historic Europe they suggest Light skin mutation Phe374Leu and Lactose Tolerant mutations T-13910 and T-22018 have rising in frequency across all of Europe since 3000 BC.

    Mostly Brown eyed
    : As of far 8/8 Neolithic Spanish are Brown eyed while 43%(9/21) Neolithic Hungary/Germany/Sweden were Blue eyed. 5/10 of Early Neolithic LBK from Germany had Blue eyes, which means the difference in eye color difference LBK-derived and Cardiel-derived groups may have origins in Anatolia not Europe. Ultimately uniformly Brown eyed Cardial-groups and largely Blue eyed LBK-groups may be the source of eye color difference in Europe today.

    Darker skinned than modern Spanish: 3/3 of Late Neolithic Spanish have Light skin mutation Ala111Thr but 2/3 lacked Light skin mutation Phe374Leu. This is consistent with results from all over Europe dating earlier than 3000 BC. Today 80%+ in most of Europe are completely derived for Ala111Thr and Phe374Leu. This suggests Pale skin was selected for in all of Europe from 3000 BC and afterwards.

    Some were Lactose Tolerant: 1/3 Late Neolithic Spanish had T-13910. This Lactose Tolerance mutation has been found in other Late Neolithic Spanish and also in Neolithic Germany/Sweden and Yamnaya. Its frequency rose in Bronze age but it wasn't at modern frequencies. The frequencies of T-13910 vary by region today but its obvious after 3000 BC and even 2000BC or 1500 BC it was selected for and rose in frequency.
    I don't think we have enough information to make claims about the pigmentation snps of all Cardial versus all LBK people, Fire-Haired.

    As to whether blue eyes existed in the Anatolian farmers before they got to Europe, perhaps we'll know in a few days. I suppose that if they did exist there, it could be that just based on the "luck of the draw", or which precise group went into central Europe after they reached the Balkans versus the group that took off by sea, LBK could have been established by a group of farmers some of whom were brown eyed and some of whom were blue eyed, whereas the group that left by boat could have been all brown-eyed or the blue eyed were such a minority that through drift the trait died out.

    Or it could be that it was picked up by the farmers who established LBK from the WHG they encountered either further north in the Balkans or in central Europe itself. There is that maybe 5% of WHG that they picked up in Europe, if that turns out to be the operative number.

    As for the Lactose tolerant gene, I thought the first sign of it in central or northern Europe was in a Bell Beaker genome, and that it was not present in any Neolithic samples in central or northern Europe at all. If my memory serves it was also not in Yamnaya, or if it was it was extremely minimal.

    The only place that had a pocket of it was late Neolithic Spain.

    If you have a chance, could you check that data again?


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    Elite member Fire Haired14's Avatar
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    Quote Originally Posted by Angela View Post
    I don't think we have enough information to make claims about the pigmentation snps of all Cardial versus all LBK people, Fire-Haired.
    I agree. I was only speculating.

    Quote Originally Posted by Angela View Post
    As for the Lactose tolerant gene, I thought the first sign of it in central or northern Europe was in a Bell Beaker genome, and that it was not present in any Neolithic samples in central or northern Europe at all. If my memory serves it was also not in Yamnaya, or if it was it was extremely minimal.

    The only place that had a pocket of it was late Neolithic Spain.

    If you have a chance, could you check that data again?
    I got my Lactose-Tolerance data from here. TRB and PWC(Part EEF) in Sweden had some. Allentoft claimed Yamnaya did and articles online took that and claimed Yamnaya is the source of Lactose Tolerance.

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    Quote Originally Posted by Fire Haired14 View Post
    I agree. I was only speculating.



    I got my Lactose-Tolerance data from here. TRB and PWC(Part EEF) in Sweden had some. Allentoft claimed Yamnaya did and articles online took that and claimed Yamnaya is the source of Lactose Tolerance.
    I don't see any Yamnaya samples on Jean Manco's page.

    Where did Allentoft state that he found lactase persistence in the Yamnaya? I just went over the whole supplement and the tables once again and I find absolutely nothing like that.

    Does anyone have access to the full paper? All I can see is this comment on page 39 or the Supplementary Info about their Table 13-Derived Allele Frequencies for Putative Selection: "The results from this analysis revealed a surprisingly low frequency of lactase persistence among BA Europens. However, the allele frequencies are limited to ancient individual's with sequencing coverage at the SNP of interest. We therefore used imputation to infer the likely genotype at rs49882530 in all ancient individuals."

    I'm not sure how reliable such imputed results might be, but it's really irrelevant to this particular question because if you just go to Table 13 it's clear that in terms of their samples they found O % of the derived allele in ba Step, Hunter, neol, and paleo. The only place where they found any derived alleles for lactase persistence is in Bronze Age Europe, with a value of .07, which they define as starting with Bell Beaker, and which they moreover seem to see as coming out of Iberia.

    So, unless there's something that contradicts this in the body of the paper, or I'm totally misinterpreting the table, it's absolutely incorrect that Allentoft said there were derived alleles for lactase persistence on the steppe and therefore there would be no basis for stating that Yamnaya is the source of lactase persistence.

    I don't know where it originated or the exact direction of spread, but given that it was present in quite a few farmers in Iberia I'd say an argument could be made that it spread from there. Either that or from the EEF Swedish farmers. The 1 Pitted Ware sample might be an anomaly...a spread from farmers, given their genetic population history.

    From Jean Manco's table:

    Swedish TRB farmers, 3300 BC: 2-4 derived, 4-6 ancestral
    San Juan Ante Portan Latinam, Spanish farmers 3000 BC: 10 derived, 28 ancestral
    Pitted Ware, 2800 BC: 1 derived, 19 ancestral
    Longar Spain, 2500 BC: 2 derived, 12 ancestral

    Then in starts with Central European Bell Beaker and then the Bronze Age samples of later European cultures.

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    The TRB we have is a "Scandinavian" and TRB is a relatively late neolithic sample if I don' mistake, with a lot of diverse cultural (so genetic?) influences from Atlantic, Central Europe and maybe already some IE imput (Globular Amphora)?

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