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Thread: Ancient uni-parental descent -- crazy question

  1. #1
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    Ancient uni-parental descent -- crazy question

    So I have a crazy quest -- I would like to see if I'm descended (via my paternal line) from an ancient individual.

    I realize that the probability is exceedingly small.

    I'm T-CTS9882 which is downstream from seven of the males found in the Pik'in Cave in Ancient DNA from Harney et al, "Chalcolithic Israel reveals the role of population mixture in cultural transformation."

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

    I'm Ashkenazi and T's are relatively rare -- I thought that it might be interesting if I can trace my lineage that far back. As I said above, I know that the probabilities are minute.

    I have my BAM file from FTDNA and the BAM files from the paper above. What can I do next?

    Y-full does not have those samples on their tree. I have also played around with usegalaxy.org, but I'm not a geneticist and would have a hard time understanding any results.

    Any help / tools / tips would be appreciated.

    Thanks in advance.

  2. #2
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    Wellcome to AG, grumpydaddybear!

    I'd better listen to what other's say, but I can see noone starts discussion, so I'll tell you what I would do.
    Maybe what I suggest you is not optimal, but let's see other comments.

    1. Get as much information as possible about exact location of Pik'in Cave samples on Y-tree.

    To get the exact location you can use list of SNP's from current YSOGG list.
    You will not be able to check it manually, I've wrote a simple fast made program for myself to make this check.
    I know python, so I wrote the program on python. If you want some details, I can share my experience with you or even share my code with you. It took me 2 days to write and debug the program, at the beginning I knew nothing about bam files, they are not as simple as I thought at the beginning.
    If you know some other programming language, you should probably write the program yourself.

    After this stage you will see, if Pik'in Cave samples have some YSOGG-known SNPs you are negative to.
    If there are 2+ such mutaions we can say almost for sure that you are not their direct male line descendant, because probability of back mutations is small, so chance of two back mutations is too little.

    If such mutations are found and they seem reliable, your search is over - they are a side branch.
    If no such mutations found, you can check their location on y-full tree, and see time estimations. If time-estimation of their branch is close to their C14-dating, you are probably their direct ancestor, if their branch of Y-full is much older then they are a side-branch.

    2. If after point 1 you see they are not a side-branch, you can try to find new, unkown mutations you share with some or all of Pik'in Cave samples.
    Well, I've never wrote such code myself, it will likeky run very slow. Here I would rather listen to advice from others.

  3. The Following User Says Thank You to artemv For This Useful Post:

     grumpydaddybear (05-10-2019)

  4. #3
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    Thank you, Artem

    If you don't mind, i would love to get your python code. I dabble in data analysis, but mostly with R.

    Many of the Ts in Pik'in are along same branch of the tree: from T1a1a (T-L208) to T1a1a1b2 (T-CTS2214). I am downstream to those. But according to Yfull the TMRCA for those two is 8700 bp.

    I have not been able to extract and compare the individual SNPs however. I think that your code would really help.

    Thank you very much

    Edit: Thanks Artem! -- can't send PMs (I'm too junior)
    Last edited by grumpydaddybear; 05-10-2019 at 05:15 PM.

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