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Thread: Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY)

  1. #4471
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    Question

    Anyone want to take an extra look at sample I5441 from Olalde et al's "The Beaker Phenomenon and the Genomic Transformation of Northwest Europe"?

    In the original paper, the authors didn't go any further with I5441 than P312. Now Reich's ancient DNA data site .anno file has him listed as DF41 (R1b1a1b1a1a2c1a1d).

    I5441 is an Early Bronze Age sample from Neale's Cave in Paington, Devon, England, dated 2000-1600 BC.

    Doesn't seem unreasonable.

    I5441_screenshot_DF41_Reich Ancient DNA anno file.jpg

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  3. #4472
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    Sorry to be a pest, but here's another one from the anno file of Reich's new Allen Ancient DNA Resource (AADR) worthy of a closer look: I7288, a Beaker man from Radosevice in the Czech Republic, from Olalde et al's "The Beaker Phenomenon".

    The original paper only went as far as CTS11468, an M269 equivalent, but now Reich and company have him listed as R1b-L21 (R1b1a1b1a1a2c1). The date for I7288 is 2500-2000 BC. If this call is correct, he is our first continental R1b-L21, so this could be important.

    Good call, or not?

    I7288_Czech Beaker_L21_Reich's ancient DNA anno file.jpg

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  5. #4473
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    Quote Originally Posted by rms2 View Post
    Anyone want to take an extra look at sample I5441 from Olalde et al's "The Beaker Phenomenon and the Genomic Transformation of Northwest Europe"?

    In the original paper, the authors didn't go any further with I5441 than P312. Now Reich's ancient DNA data site .anno file has him listed as DF41 (R1b1a1b1a1a2c1a1d).

    I5441 is an Early Bronze Age sample from Neale's Cave in Paington, Devon, England, dated 2000-1600 BC.

    Doesn't seem unreasonable.

    I5441_screenshot_DF41_Reich Ancient DNA anno file.jpg
    Unless the Y-chromosome data has been re-sequenced since the last release, this is it...

    P310 DER
    L151 DER
    P312 DER

    Quote Originally Posted by rms2 View Post
    Sorry to be a pest, but here's another one from the anno file of Reich's new Allen Ancient DNA Resource (AADR) worthy of a closer look: I7288, a Beaker man from Radosevice in the Czech Republic, from Olalde et al's "The Beaker Phenomenon".

    The original paper only went as far as CTS11468, an M269 equivalent, but now Reich and company have him listed as R1b-L21 (R1b1a1b1a1a2c1). The date for I7288 is 2500-2000 BC. If this call is correct, he is our first continental R1b-L21, so this could be important.

    Good call, or not?

    I7288_Czech Beaker_L21_Reich's ancient DNA anno file.jpg
    CTS5082 DER
    PF6463 DER
    CTS11468 DER

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  7. #4474
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    Thanks.

    I wonder what's up with these Y-DNA listings.

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  9. #4475
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    Quote Originally Posted by Generalissimo View Post
    Unless the Y-chromosome data has been re-sequenced since the last release
    That's the only thing that makes sense to me, or somebody's been dosing the coffee at the Reich lab.

    I was pottering about the BAM file for a supposed CW DF49 sample from SE Poland and there's literally nothing there, the file's almost empty.
    Last edited by jdean; 01-25-2021 at 10:18 AM.

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    HEY!

    I got an answer from the Reich Lab, specifically from Iosif Lazaridis.

    He says RISE550 has been called R1b-L51 based not on L617 but on the following, and I am quoting him (I guess that's okay):

    Quote Originally Posted by Iosif Lazaridis

    The call is based on one derived read for R-L51+: PF6535(5465148G>A:A) which is at the 4th base from the end of the read.
    I estimate an overall rate of ~1% for this deamination in all our data, but of course whether this happens is sample-specific and read position-specific.

    So, at present I classify this as an intriguing possibility but not as a clear-cut case of finding R-L51 in Yamnaya which of course would be monumental.
    So, it looks like RISE550 could be R1b-L51, but it is not as clear-cut a case as we all (well, some of us, anyway) would like.

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    Quote Originally Posted by rms2 View Post
    HEY!

    I got an answer from the Reich Lab, specifically from Iosif Lazaridis.

    He says RISE550 has been called R1b-L51 based not on L617 but on the following, and I am quoting him (I guess that's okay):



    So, it looks like RISE550 could be R1b-L51, but it is not as clear-cut a case as we all (well, some of us, anyway) would like.
    That is very interesting. I wish I knew how to work my way through the files, I’d like to know if there were any signs of any other SNPs below L51 besides the L617 call.
    AncestryDNA results:
    England, Wales, & NW Europe 73%
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    Cameroon, Congo 1%

    23&me results:
    British & Irish 62.9%
    French & German 15.0%
    Scandinavian 0.9%
    Broadly Northwestern European 19.4%
    Broadly Southern European 0.9%
    Broadly European 0.1%
    Sub-Saharan African 0.7%

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    What I find heartening is that it seems the current calls at Reich's new ancient DNA site are based on the data and are not just typos and/or other errors.

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    Quote Originally Posted by rms2 View Post
    What I find heartening is that it seems the current calls at Reich's new ancient DNA site are based on the data and are not just typos and/or other errors.
    Me too, also looks like they're taking Y-SNPs a little more seriously now than a couple of years ago.

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    Quote Originally Posted by rms2 View Post
    HEY!

    I got an answer from the Reich Lab, specifically from Iosif Lazaridis.

    He says RISE550 has been called R1b-L51 based not on L617 but on the following, and I am quoting him (I guess that's okay):

    So, it looks like RISE550 could be R1b-L51, but it is not as clear-cut a case as we all (well, some of us, anyway) would like.
    OK, well they should re-sequence this sample if possible.

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