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Thread: Italian study 40000 years in southern Europe

  1. #1
    Regular Member torzio's Avatar
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    Italian study 40000 years in southern Europe

    https://link.springer.com/article/10...39-021-02328-6




    Through 40,000 years of human presence in Southern Europe: the Italian case study

    The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
    Fathers mtdna ...... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ...... K1a4p
    Mothers line ..... R1b-S8172
    Grandmother paternal side ... I1-CTS6397
    Wife paternal line ..... R1a-PF6155

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    Regular Member Salento's Avatar
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    Otzi raw-data ... 23andme format:

    https://www.mediafire.com/file/tq491...ceman.zip/file

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    Quote Originally Posted by Salento View Post
    Salento, thanks, great work. Can use this file on GEDMATCH and do kit to kit comparison.

    thanks again, PT

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    Regular Member Salento's Avatar
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    Quote Originally Posted by Palermo Trapani View Post
    Salento, thanks, great work. Can use this file on GEDMATCH and do kit to kit comparison.
    thanks again, PT
    ... it can get complicated with ancient raw-data :)
    but, just in case, ... same file: GedM... # UT4561244

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    Quote Originally Posted by Salento View Post
    ... it can get complicated with ancient raw-data :)
    but, just in case, ... same file: GedM... # UT4561244
    Ok, got it, you used the GEDMATCH kit you mentioned above. I already looked at the raw data and looked at some snps. Otzi was had the following SNPs

    SLC24A5 rs1426654 AA
    SLC45A2 rs16891982 (N/A)
    BNC2 rs10756819 GG
    OCA2 rs1800401 GG
    HERC2 rs12913832 AA

    So the snps on SLC2A45 and BNC2 would point to lighter skin to intermediate (did not have SLC45A2). OCA2 GG would relate to lighter skin and the HERC2 snp rs1291382 AA predicts brown eyes 80% of the time from what I think 23 and Me states. Interestingly, he was CC on the ACTN3 gene which is consistent with power athlete (TT more endurance and cold adaptation) which I guess allowed him to hike very easily in the Alps (with proper clothing!).


    ACTN3 rs1815739 CC

    Thanks again, really neat to search Otzi's SNPS.

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    Satyavrata Maciamo's Avatar
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    It's nice that they calculated the average frequencies of alleles related to pigmentation by era and region. Interesting to see that about 87% of Iron Age Central Italians (samples mostly from Latium) had the G allele for Rs12913832 (GG correlates with blue eyes 99% of the time), but that it dropped to about 30% in Imperial times (of course there were many East Med immigrants in places like Ostia among Imperial samples, so it isn't representative of the native Latin population).



    Regarding fatty acid metabolism, the C allele of Rs174546 is linked with lower LDL cholesterol levels and lower risk of metabolic syndrome. This beneficial allele has been positively selected over time at a relatively constant rate in all regions, except in Sardinia where it appears to have dropped in modern times for some reason.
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    Moderator Pax Augusta's Avatar
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    Quote Originally Posted by Maciamo View Post
    I like their timeline.



    It's nice that they calculated the average frequencies of alleles related to pigmentation by era and region. Interesting to see that about 87% of Iron Age Central Italians (samples mostly from Latium) had the G allele for Rs12913832 (GG correlates with blue eyes 99% of the time), but that it dropped to about 30% in Imperial times (of course there were many East Med immigrants in places like Ostia among Imperial samples, so it isn't representative of the native Latin population).



    Regarding fatty acid metabolism, the C allele of Rs174546 is linked with lower LDL cholesterol levels and lower risk of metabolic syndrome. This beneficial allele has been positively selected over time at a relatively constant rate in all regions, except in Sardinia where it appears to have dropped in modern times for some reason.


    I would not take this paper very seriously, just see how shamefully it pretends that ancient DNA studies on the Etruscans do not exist (at least three studies on mitochondrial DNA had already been published, and the one on ancient Rome in 2019 shows that Etruscans and Latins have the same genetic position). A paper that writes in 2021 where the Etruscans came from is still uncertain is a paper of no credibility at all. The author of the paper is one of a group of Italian geneticists who have always gone against the archaeological and anthropological record, basing their conclusions on circular reasoning, and have often been contradicted by ancient DNA.

    As for the difference between the Iron Age and Imperial Age in the frequency of G allele for Rs12913832, the Iron Age samples are too few, about ten, to draw any conclusions, although the idea that it dropped in Roman imperial times due to migrations from the eastern Mediterranean is a plausible one.

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    Regular Member Salento's Avatar
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    @PT ... that file file shows rs16891982 as GG and rs10756819 as AA, ... obviously your screen was blurry :)

    rs1426654 AA
    rs16891982 GG
    rs10756819 AA
    rs1800401 GG
    rs12913832 AA
    rs1815739 CC

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    Quote Originally Posted by Salento View Post
    @PT ... that file file shows rs16891982 as GG and rs10756819 as AA, ... obviously your screen was blurry :)

    rs1426654 AA
    rs16891982 GG
    rs10756819 AA
    rs1800401 GG
    rs12913832 AA
    rs1815739 CC
    You are correct. My screen could use a cleaning, those 2 SNPS are:

    rs16891982 is GG (SLC45A2)
    rs10756819 is AA (BNC2)

    I think the BNC2 gene has high association with Neanderthal admixture and the A allele is related to lighter skin tone (Danneman and Kelso 2017, "The Contribution of Neanderthals
    to Phenotypic Variation in Modern Humans").

    Relative to Otzi, I am AA, GG, AG, AG, AA, and TT on those 5 SNPs.

    Two other SNPS on the MCR1 gene for Otzi, both related to skin cancer risk, tone, red hair, etc.

    MC1R rs1805006 CC
    MC1R rs1805009 GG

    These SNPS are associated with Skin cancer risk and sunburn. The risk alleles according to SNPedia for rs1805006 is A and it is also associated with Freckling and red hair, higher risk of skin cancer. On rs1805009, the risk allele is C, so CC would be associated again with Red hair and freckling and increase risk of skin cancer.

    Regarding the OCA2 rs1800401 snp, GG here makes blue eyes more likely, but according to SNPedia regarding the rs12913832 SNP being AA, brown eyes are 80% likely. Reading down, it lists 13 SNPS and the allele that has to be homozygous on 13 SNPS where 97% of individuals with Blue eyes have such alleles.
    Last edited by Palermo Trapani; 18-05-22 at 05:37. Reason: editing, clarification

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