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Thread: Leaked Uniparental Marker Data

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    Leaked Uniparental Marker Data

    It's what the title suggests - I've found data on a whole bunch of Y DNA and mtDNA of samples (no auDNA), some of which have not yet been formally published and most of which are preprints. Sometime later today, I'll post on all the info.

    A word of warning though - while most of the Y DNA calls are accurate (as most are from published, existing papers and I can check if it matches with the accepted results), several are incorrect calls of results already known (which is how I know they're incorrect), but I think it's pretty easy to tell when it's accurate and when it isn't when you see the context.
    Last edited by ToBeOrNotToBe; 21-01-19 at 11:14.

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    Holy mother of God there are some potentially REALLY big bombshells lol, PROVIDED they aren't mistakes. A couple of them definitely aren't mistakes, most are.
    Last edited by ToBeOrNotToBe; 21-01-19 at 11:15.

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    Okay there are lots of mistakes, but still a couple of things that aren't published and accurate (petrous bone samples seem to be considerably more reliable). Bones seem to be worse than teeth.

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    Is there any alternative to Genetiker now that he's gone? To get Y SNP calls from an already published sample?

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    Quote Originally Posted by ToBeOrNotToBe View Post
    Is there any alternative to Genetiker now that he's gone? To get Y SNP calls from an already published sample?
    Just post them here and we'll all work together :)

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    Quote Originally Posted by JajarBingan View Post
    Just post them here and we'll all work together :)
    I'd guess that this would be R1b-V88, but nobody has gotten the Y SNP calls for SC2 from Iron Gates. This is what Genetiker said about SC2:

    "SC2 and OC1 are reported to be R1 and R1b. The data for those samples is unaligned. I could align it, but it takes a very long time, so I'm probably not going to. It's not worth the effort. They're probably V88 or pre-V88, like SC1."

    What I have here says that it's M269, but there are loads of wrong calls all over the place.

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    Okay I'll post one thing, I'm getting a bit tired now.

    There's been an ancient DNA paper, actually published, from Israel, and I haven't seen anybody mention it (Reich gave a reference to it in a talk):

    http://sci-hub.tw/https://doi.org/10...4.2017.1368204

    Essentially, the study took DNA from a Canaanite elite in an Egyptian sarcophagus (who had an amulet with Seti's name on it), and somebody not buried in a sarcophagus, both from Tel Shadud. The study showed that both cluster somewhere in between modern Lebanese and Palestinians. However, I have the Y DNA of the elite in the Egyptian sarcophagus and the person with similar ancestry not in the sarcophagus: the elite was in great condition, and they extracted DNA from his petrous bone, and his Y DNA is R1b M269+. The other guy had DNA extracted from a tooth, which was lesser quality and assigned to Y DNA J+. I'm sure they could go further than this with both assignments, but the SNPs aren't available I don't believe

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    The paper is more interesting than the Y DNA really, and it was in the open all along.

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    Quote Originally Posted by ToBeOrNotToBe View Post
    I'd guess that this would be R1b-V88, but nobody has gotten the Y SNP calls for SC2 from Iron Gates. This is what Genetiker said about SC2:

    "SC2 and OC1 are reported to be R1 and R1b. The data for those samples is unaligned. I could align it, but it takes a very long time, so I'm probably not going to. It's not worth the effort. They're probably V88 or pre-V88, like SC1."

    What I have here says that it's M269, but there are loads of wrong calls all over the place.
    judging from the context, I would be surprised it they were M269, and not V88

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    Quote Originally Posted by ToBeOrNotToBe View Post
    Okay I'll post one thing, I'm getting a bit tired now.

    There's been an ancient DNA paper, actually published, from Israel, and I haven't seen anybody mention it (Reich gave a reference to it in a talk):

    http://sci-hub.tw/https://doi.org/10...4.2017.1368204

    Essentially, the study took DNA from a Canaanite elite in an Egyptian sarcophagus (who had an amulet with Seti's name on it), and somebody not buried in a sarcophagus, both from Tel Shadud. The study showed that both cluster somewhere in between modern Lebanese and Palestinians. However, I have the Y DNA of the elite in the Egyptian sarcophagus and the person with similar ancestry not in the sarcophagus: the elite was in great condition, and they extracted DNA from his petrous bone, and his Y DNA is R1b M269+. The other guy had DNA extracted from a tooth, which was lesser quality and assigned to Y DNA J+. I'm sure they could go further than this with both assignments, but the SNPs aren't available I don't believe
    Some crazy guy has an hypothesis that merimde beni salama in delta Nile 4000bc were M269+

    Crazy crazy world.

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    Quote Originally Posted by bicicleur View Post
    judging from the context, I would be surprised it they were M269, and not V88
    Yes. Some crazy guy has an hypothesis.....
    That M269 lived in the South Balkans, south of Iron Gates, and those moved to South Caucasus where L23 was born...
    Crazy crazy people.

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    this is Y-DNA from an unpublished study :

    The new Ancient Iberian Genomes unpublished study, PRJEB29189, has three whole genomes that have high-coverage Y-DNA sequences from 4500-3500 ybp. Vadim, can you add these to the YFull tree?
    No "Steppe" / "Bell Beaker" ancestry in Iberia yet.
    The haplogroups are as follows.
    Who are the "lucky winners" here who match them on the YFull tree?

    A spreadsheet of all the Y SNPs for these ancient Iberian individuals:
    https://docs.google.com/…/1thcQUVLKg...kXD…/edit…

    https://www.ebi.ac.uk/ena/data/view/PRJEB29189

    LU339 "partial" I-Y3749:
    https://yfull.com/tree/I-Y3749/
    AMM080/Y4661/FGC7133+
    FGC7139/Y3749-

    COV20126 I-Y34539*:
    https://yfull.com/tree/I-Y34539/

    LD270 "partial" H-Y20838:
    https://yfull.com/tree/H-Y20838/
    Z19077+
    Z19083+
    Z19118+
    Y21665-
    Y21636-
    Y20840-
    Y20836-
    Y21673-
    Y21633-
    Y21635-
    Y21640-

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    Quote Originally Posted by bicicleur View Post
    this is Y-DNA from an unpublished study :
    The new Ancient Iberian Genomes unpublished study, PRJEB29189, has three whole genomes that have high-coverage Y-DNA sequences from 4500-3500 ybp. Vadim, can you add these to the YFull tree?
    No "Steppe" / "Bell Beaker" ancestry in Iberia yet.
    The haplogroups are as follows.
    Who are the "lucky winners" here who match them on the YFull tree?
    A spreadsheet of all the Y SNPs for these ancient Iberian individuals:
    https://docs.google.com/…/1thcQUVLKg...kXD…/edit…
    https://www.ebi.ac.uk/ena/data/view/PRJEB29189
    LU339 "partial" I-Y3749:
    https://yfull.com/tree/I-Y3749/
    AMM080/Y4661/FGC7133+
    FGC7139/Y3749-
    COV20126 I-Y34539*:
    https://yfull.com/tree/I-Y34539/
    LD270 "partial" H-Y20838:
    https://yfull.com/tree/H-Y20838/
    Z19077+
    Z19083+
    Z19118+
    Y21665-
    Y21636-
    Y20840-
    Y20836-
    Y21673-
    Y21633-
    Y21635-
    Y21640-
    Regretfully, regarding Portugal all we can get is samples from people thrown into caves, buried in caves, not related to archeological places that are known, such as the ones related to Bell beakers or places such as VNSP and zambujal.
    Good news are that new samples from places like perdigões (olimplicly ignored thus far in aDna) are of more relevant type of people or castes.
    Also good news is that VNSP is going to have new archeological jobs, which has not happen since 1983 and prior 1963. So no inhumations or Cemitery found yet but must be really near...

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    Quote Originally Posted by ToBeOrNotToBe View Post
    Okay I'll post one thing, I'm getting a bit tired now.

    There's been an ancient DNA paper, actually published, from Israel, and I haven't seen anybody mention it (Reich gave a reference to it in a talk):

    http://sci-hub.tw/https://doi.org/10...4.2017.1368204

    Essentially, the study took DNA from a Canaanite elite in an Egyptian sarcophagus (who had an amulet with Seti's name on it), and somebody not buried in a sarcophagus, both from Tel Shadud. The study showed that both cluster somewhere in between modern Lebanese and Palestinians. However, I have the Y DNA of the elite in the Egyptian sarcophagus and the person with similar ancestry not in the sarcophagus: the elite was in great condition, and they extracted DNA from his petrous bone, and his Y DNA is R1b M269+. The other guy had DNA extracted from a tooth, which was lesser quality and assigned to Y DNA J+. I'm sure they could go further than this with both assignments, but the SNPs aren't available I don't believe
    Who made these calls?

    If it's some anonymous person or some t-roll site this is a waste of time.


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    Quote Originally Posted by Angela View Post
    Who made these calls?

    If it's some anonymous person or some t-roll site this is a waste of time.
    If only named persons were always accurate in making calls. It's surprising how often calls in academic studies need subsequent correction, even when they are rather vague.

    I find the most reliable and precise calls are usually from corporations (FTDNA, yfull etc.), where the actual tester is not identified.

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    Quote Originally Posted by bicicleur View Post
    this is Y-DNA from an unpublished study :

    The new Ancient Iberian Genomes unpublished study, PRJEB29189, has three whole genomes that have high-coverage Y-DNA sequences from 4500-3500 ybp. Vadim, can you add these to the YFull tree?
    No "Steppe" / "Bell Beaker" ancestry in Iberia yet.
    The haplogroups are as follows.
    Who are the "lucky winners" here who match them on the YFull tree?

    A spreadsheet of all the Y SNPs for these ancient Iberian individuals:
    https://docs.google.com/…/1thcQUVLKg...kXD…/edit…

    https://www.ebi.ac.uk/ena/data/view/PRJEB29189

    LU339 "partial" I-Y3749:
    https://yfull.com/tree/I-Y3749/
    AMM080/Y4661/FGC7133+
    FGC7139/Y3749-

    COV20126 I-Y34539*:
    https://yfull.com/tree/I-Y34539/

    LD270 "partial" H-Y20838:
    https://yfull.com/tree/H-Y20838/
    Z19077+
    Z19083+
    Z19118+
    Y21665-
    Y21636-
    Y20840-
    Y20836-
    Y21673-
    Y21633-
    Y21635-
    Y21640-
    Curious in some ways that these samples from 2,500 to 1,500 BC were I2a1, I2a2a and H, as I thought Reich had them all wiped out by Yamnayans around 2,500 BC.

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    Quote Originally Posted by Angela View Post
    Who made these calls?

    If it's some anonymous person or some t-roll site this is a waste of time.
    Reich worked as part of the study, but this was petrous bone data and was clearly high quality. It could very well be a coincidence this elite was M269, and I reckon it probably is coincidental even though I usually assign R1b-M269s elite status all the time.

    Here's where I found the data:

    https://www.biorxiv.org/highwire/fil.../322347-5.xlsx

    There were many reasons I got excited, but all seemed to turn out to be bad Y DNA calls. However, if they mistakenly call, say, L21 for something clearly not L21, can it reasonably be claimed that it was still R1b?

    There is so much in there that COULD have been amazing, but yeah sadly it looks like bad SNP calls. A Chinchorro mummy got Y DNA E1b1a+ by the way, which I got SO excited about, until I checked and realised that that lineage is SSA. Still, does that mean it is likely Chinchorro was Y DNA E? The Guanches, who have been linked to this group that theoretically moved into the Americas from West Eurasia/North Africa, are mostly E1b1b+, so it makes sense potentially.

    Still though, at least it lead to that Israel paper that everyone missed

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    Quote Originally Posted by Pip View Post
    Curious in some ways that these samples from 2,500 to 1,500 BC were I2a1, I2a2a and H, as I thought Reich had them all wiped out by Yamnayans around 2,500 BC.
    we have to await the publication of the actual study to know the actual places, dates and context in which these samples are found
    but check YFull for all 3 subclades, and you'll notice, at least YFull doesn't have any Iberian individuals alive in them

    when is this Reich study about 4.5 ka Iberia going to be published?

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    Quote Originally Posted by bicicleur View Post
    we have to await the publication of the actual study to know the actual places, dates and context in which these samples are found
    but check YFull for all 3 subclades, and you'll notice, at least YFull doesn't have any Iberian individuals alive in them

    when is this Reich study about 4.5 ka Iberia going to be published?
    Which one is this?

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    Quote Originally Posted by ToBeOrNotToBe View Post
    Reich worked as part of the study, but this was petrous bone data and was clearly high quality. It could very well be a coincidence this elite was M269, and I reckon it probably is coincidental even though I usually assign R1b-M269s elite status all the time.

    Here's where I found the data:

    https://www.biorxiv.org/highwire/fil.../322347-5.xlsx

    There were many reasons I got excited, but all seemed to turn out to be bad Y DNA calls. However, if they mistakenly call, say, L21 for something clearly not L21, can it reasonably be claimed that it was still R1b?

    There is so much in there that COULD have been amazing, but yeah sadly it looks like bad SNP calls. A Chinchorro mummy got Y DNA E1b1a+ by the way, which I got SO excited about, until I checked and realised that that lineage is SSA. Still, does that mean it is likely Chinchorro was Y DNA E? The Guanches, who have been linked to this group that theoretically moved into the Americas from West Eurasia/North Africa, are mostly E1b1b+, so it makes sense potentially.

    Still though, at least it lead to that Israel paper that everyone missed
    How do we know which calls are bad and which are good?

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    Quote Originally Posted by Olympus Mons View Post
    Some crazy guy has an hypothesis that merimde beni salama in delta Nile 4000bc were M269+

    Crazy crazy world.

    Reality can be stranger than fiction, statistically speaking.
    “Man cannot live without a permanent trust in something indestructible in himself, and at the same time that indestructible something as well as his trust in it may remain permanently concealed from him.”

    Franz Kafka

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    Quote Originally Posted by bicicleur View Post
    we have to await the publication of the actual study to know the actual places, dates and context in which these samples are found
    but check YFull for all 3 subclades, and you'll notice, at least YFull doesn't have any Iberian individuals alive in them
    FTDNA has some Iberian I-Y3749, but the SNP overall currently looks British.
    It has plenty of Iberian I-L1228 - either Y34539 or a close relative.

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    Quote Originally Posted by Pip View Post
    How do we know which calls are bad and which are good?
    Well usually just seeing if it's from a petrous bone

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    Quote Originally Posted by ToBeOrNotToBe View Post
    Well usually just seeing if it's from a petrous bone
    There's a U106 from Malawi 6,000 BC that's from petrous bone - looks odd.

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    0 out of 1 members found this post helpful.
    Quote Originally Posted by Pip View Post
    There's a U106 from Malawi 6,000 BC that's from petrous bone - looks odd.
    Good spot, that study though just seems off altogether. They got high quality data (you can see how many autosome SNPs hit), so I think the only conclusion is time-travelling Nazis

    As evidence, check this out: https://genetiker.wordpress.com/2017...aharan-africa/

    A blonde!

    Just kidding obviously, but yeah that's very surprising given it's from the petrous bone.

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