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Thread: The Wartberg culture paper (Immel et. al. 2019) - Y-chromosomes

  1. #1
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    The Wartberg culture paper (Immel et. al. 2019) - Y-chromosomes

    Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

    URL to preprint:
    https://www.biorxiv.org/content/10.1101/851188v1.full

    URL to main thread:
    https://anthrogenica.com/showthread....el-et-al-2019)

    I guess it more convenient to post the Y-chromosome results here, and disscuss them in the main thread. The pre-print is out without any supplementary info, but *.bam files are already published. Some of them are very heavy (more than 20 Gb!), so I started the chromosome check with small sized files, because processing heavy files really takes time (as we have no supplementary data at all, processing some files will only show is that was a woman).

    I remind that all the samples are from the same collective grave, that was used by the same group of people for about 100 years.




    file_name my_result
    KH150208_KH150210 woman
    KH150287 pre-I-S9234
    KH150289 I-M423*
    KH150290 woman
    KH150417 (pre?)I-S9234
    KH150418 pre-I-S9234
    KH150419 woman
    KH150422 I-M423*
    KH150618 pre-I-S9234
    KH150621 (pre?)I-S9234

    KH150287
    He is definitely I-Y5334:
    FGC18615+ (1 read)
    S22470+ (1 read)
    FGC18575+ (1 read)

    Has one of I-S9234 synonim mutations, others ancestral:
    Y1049.2- (1 read)
    F313- (1 read)
    FGC18575+ (1 read)

    KH150289
    He is positive to all the M423 synonimes that have reads, and negative to all known downstream branches:
    AM0129+ (1 read)
    Z2594+ (1 read)
    FGC8118+ (1 read)
    AM01260+ (1 read)

    Negative downstreams:
    L161.1- (1 read)
    S10302- (1 read) -> this is synonim of L621
    Y80035- (1 read) -> one more M423 branch(Y24694 on y-full), still not present in ISOGG

    KH150417
    FGC18549+ (1 read)
    L1251.1+ (1 read)

    KH150418
    FGC18544+ (2 reads)
    FGC18648- (1 read)

    KH150422
    Likely one more I-M423*. This one has no calls for L-161.1 synonimes (and ancestral results for other known M423 branches), but I guess this is the same branch as KH150289.

    M423 synonimes:
    AM01285+ (1 read)
    AM01293+ (1 read)
    AM01260+ (2 reads)

    L621 synonimes:
    FGC30451- (1 read)
    F3145- (1 read)
    S10980- (1 read)
    S10302- (1 read)
    S13737- (2 reads)

    Y24694 synonimes:
    Y81096- (1 read)
    Y129078- (1 read)

    KH150618
    Out of S9234 synonimes has just 1 ancestral SNP and 6 derived.
    Interesting result for FGC18624.
    FGC18584+ (1 read)
    FGC18616+ (1 read)
    L1251.1+ (2 reads)
    FGC18554+ (1 read)
    S22054+ (2 reads)
    FGC18558+ (3 reads)
    FGC18608- (1 read)

    FGC18624 G (2 reads) - this is a T->C SNP, but here we get G

    KH150621
    Out of S9234 synonimes all 3 have derived results. But we know S9234 branch is too young, so for 5000 years old sample, so this must be some pre-S9234 branch.
    FGC18584+ (2 reads)
    S26491+ (2 reads)
    S25233+ (2 reads)

    FGC18624 G (2 reads) - this is a T->C SNP, but here we get G, again.
    That's interesting, do we have the same error for both KH150621 and KH150618 samples, or thats a new SNP?
    Last edited by artemv; 12-24-2019 at 12:22 AM.

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  3. #2
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    sample KH150204_KH150634 has many calls on I level. It seems I2.

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  5. #3
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    KH150610 is a woman.

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     Principe (12-24-2019)

  7. #4
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    sample KH150641 seems to be I of some sort. Probably I2c (it has got some calls on I2c level).

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     artemv (12-24-2019)

  9. #5
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    file_name my result
    KH150610 woman
    KH150625 woman
    KH150626 woman
    KH150628 pre-I-S9234
    KH150639 pre-I-S9234
    KH150191 I-S6635 (pre-I-S9234?)
    KH180044 woman
    KH150193_KH150286 woman
    KH150195_KH150196_KH150616 woman
    KH150197 (pre?)-I-S9234
    KH150198 (pre?)-I-S9234
    KH150200 woman
    KH150203 woman
    KH150640 woman

    KH150628
    FGC18616+ (1 read)
    FGC18544+ (2 reads)
    FGC18555- (2 reads)
    FGC18648- (1 read)
    Y7859- (1 read)

    KH150639
    FGC18584+ (2 reads)
    FGC18650+ (2 reads)
    FGC18606+ (1 read)
    FGC18588- (1 read)
    S25233+ (2 reads)

    KH150191
    This is a low coverage sample, just 17Mb.
    PF6915+ (1 read)
    Although he is only positive to one of S6635 synonimes, there are no downstream negatives, and he is likely pre-I-S9234, like most of his mates.

    KH150197
    Upstream positives:
    PF3893+
    L596+
    S6729+
    PF3892+

    S9234 synonimes:
    L1251.1+ (1 read) -> This is a C->T SNP
    We only het one S9234 synonime, and that synonime is a C->T SNP. But given S9234 age this cannot be full S9234, this must be some pre-I-S9234

    KH150198
    One more low coverage sample.
    Upstream positives:
    L596+ (1 read)
    FGC18548+ (2 reads)

    S9234 synonimes:
    FGC18609+ (1 read) -> This is a C->T SNP
    Again just 1 synonime, and again C->T SNP. But as we have no negatives, we can assume this is likely a pre-I-S9234 sample

    Now I only have "heavy weight" file left, it would take some time to process them.

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     Michał (01-02-2020)

  11. #6
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    2 more results for high-quality samples today:

    file name my result
    KH150641 pre-I-S9234
    KH150633 pre-I-S9234

    Quote Originally Posted by Romilius View Post
    sample KH150641 seems to be I of some sort. Probably I2c (it has got some calls on I2c level).
    Yes, I guess this happlogroup was called I2c in some ISOGG tree version, in actual ISOGG this happlogroup is called I2a2.

    Chcking this samples, I have found a mistake in ISOGG data.
    FGC18600(Y7172) is a C->G mutation
    FGC18624(Y7182) is a T->G mutation


    KH150641
    Here we have 21 derived SNPs, 10 ancestral SNPs

     

    Derived:
    FGC18584+ 1 read
    FGC18616+ 3
    S16199+ 1
    FGC18650+ 2
    S22470+ 1
    FGC18544+ 1
    FGC18549+ 1
    FGC18601+ 2
    FGC18651+ 1
    S17221+ 1
    L1251.1+ 4
    FGC18609+ 2
    S22054+ 3
    S9234+ 1
    S22170+ 4
    FGC18607+ 1
    FGC18558+ 5
    BY2776+ 7
    S25233+ 1
    FGC18600+ 2
    FGC18624+ 1


    Ancestral:
    FGC18653 - 2 reads
    S18042 - 3
    S18299 - 3
    FGC18551 - 4
    FGC18648 - 1
    S11571 - 4
    FGC18588 - 2
    FGC18608 - 1
    FGC18559 - (2 reads for ancestral G, one read - "other" T, the only T case - on the edge of a read, so I consider sample is FGC18559-)
    Y7859 - 3 reads



    KH150633
    Here we have 19 derived SNPs and 15 ancestral SNPs.
     

    Derived:
    BY435+ 1 read
    FGC18584+ 3
    FGC18616+ 1
    FGC18544+ 2
    FGC18601+ 2
    FGC18603+ 3
    S10141+ 2
    L1251.1+ 3
    FGC18554+ 2
    FGC18575+ 1
    FGC18609+ 2
    S21750+ 1
    S22054+ 2
    FGC18618+ 1
    FGC18607+ 1
    FGC18558+ 1
    FGC18547+ 1
    FGC18600+ 5


    Ancestral:
    FGC18653- 1 read
    S18042- 1
    S18299- 1
    FGC18555-
    FGC18551- 1
    FGC18553- 3
    FGC18643- 1
    Y7878- 1
    FGC18585- 1
    BY1802- 1
    S16446- 2
    FGC18588- 1
    FGC18608- 1
    FGC18559- 2
    Y7859- 1

    Last edited by artemv; 12-26-2019 at 04:18 PM.

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  13. #7
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    file_name my_result
    KH150189_KH150632_KH150636 pre-I-S9234
    KH150613_KH180043 pre-I-S9234

    No surprises here. I have 12 heavy file files left, all of them 10Gb+. And little hope to find anything new.

    KH150189_KH150632_KH150636
    Total 10 ancestral and 29 derived.
     

    Derived:
    BY435+ 3
    FGC18578+ 1
    FGC18584+ 4
    FGC18616+ 3(this one has 3 C and one T read, likely that T because of deamination, so I consider it C)
    FGC18624+ 4
    S16199+ 1
    S26491+ 1
    FGC18650+ 2
    S22470+ 4
    FGC18544+ 1
    FGC18549+ 3
    FGC18601+ 4
    FGC18603+ 1
    FGC18651+ 1
    S10141+ 2
    S17221+ 1
    L1251.1+ 2
    FGC18554+ 2
    FGC18609+ 2
    S21750+ 2
    S22054+ 1
    FGC18610+ 2
    FGC18618+ 2
    S9234+ 1
    S22170+ 2
    FGC18607+ 4
    FGC18558+ 4
    BY2776+
    FGC18547+

    Ancestral:
    FGC18653- 8 reads
    S18299- 8
    FGC18555- 2
    FGC18551- 2
    FGC18553- 1
    S11571- 5
    Y7878- 4
    FGC18585- 1
    S16446- 2
    FGC18588- 3
    FGC18608- 3
    FGC18559- 3
    Y7859- 5



    KH150613_KH180043
    Total 15 ancestral and 23 derived.
     

    Derived:
    BY435+ 1
    FGC18584+ 2
    FGC18616+ 1
    S16199+ 1
    S22470+ 2
    FGC18544+ 4
    FGC18549+ 3
    FGC18601+ 1
    L1251.1+ 4
    FGC18554+ 3
    FGC18600+ 4
    FGC18606+ 2
    S22054+ 3
    BY1802+? 1 (this is a problematic one. This is an A->T SNP, and we have 1 read for T and 1 for C)
    FGC18610+ 1
    FGC18618+ 2
    S9234+ 2
    FGC18607+ 2
    FGC18558+ 10
    BY2776+ 3 (another case of contradicting reads. 3 reads for A, 1 read for T, so I consider this to be A)
    Y11278+ 1
    S25233+ 2
    FGC18628+ 1

    Ancestral:
    Y7839- 1 read
    FGC18653- 3
    S18042- 4
    S18299- 5
    FGC18555- 3
    FGC18551- 4
    FGC18648- 4
    S11571- 3
    Y7878- 2
    FGC18585- 1
    S16446- 1
    FGC18588- 11
    FGC18608- 3
    FGC18559-
    Y7859-


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  15. #8
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    file_name my_result
    KH150629 pre-I-S9234
    KH150637 pre-I-S9234

    KH150629
    Total 30 derived and 15 ancestral.
     

    Derived:
    BY435+ 4 reads
    FGC18578+ 4
    FGC18584+ 4
    FGC18616+ 3
    FGC18624+ 6
    S16199+ 2
    FGC18650+ 2
    S22470+ 6
    FGC18544+ 2
    FGC18549+ 2
    FGC18601+ 5
    FGC18603+ 2
    S10141+ 2
    S17221+ 4
    L1251.1+ 2
    FGC18554+ 3
    FGC18575+ 3
    FGC18600+ 8
    FGC18609+ 2
    S21750+ 1
    S22054+ 2
    FGC18618+ 4
    S9234+ 3(this SNP has 3 reads for derived G and 1 read for ancestral A, consider it to be derived)
    S22170+ 5
    FGC18607+ 2
    FGC18558+ 9
    BY2776+ 3
    Y11278+ 2
    S25233+ 2
    FGC18628+ 4

    Ancestral:
    Y7839- 1
    FGC18653- 3
    S18299- 1
    FGC18555- 3
    FGC18551- 4
    FGC18553- 2
    FGC18643- 1
    FGC18648- 1
    Y7878- 1
    FGC18585- 2
    S16446- 2
    FGC18588- 2
    FGC18608- 4
    FGC18559- 3
    Y7859- 4



    KH150637
    Total 27 derived and 15 ancestral
     

    Derived:
    BY435+ 1 read
    FGC18578+ 1
    FGC18584+ 3
    FGC18616+ 3
    S16199+ 1
    S26491+ 3
    FGC18650+ 1
    FGC18544+ 2
    FGC18549+ 2
    FGC18601+ 2
    FGC18651+ 1
    S10141+ 1
    S17221+ 1
    L1251.1+ 5
    FGC18554+ 2
    FGC18600+ 3
    FGC18609+ 3
    S21750+ 3
    S22054+ 2
    BY1802+ 1
    FGC18610+ 3
    S9234+ 1
    S22170+ 3
    FGC18558+ 4
    BY2776+ 4
    S25233+ 1
    FGC18628+ 1

    Ancestral:
    FGC18653- 1
    S18042- 4
    S18299- 3
    FGC18555- 2
    FGC18551- 3
    FGC18553- 2
    FGC18643- 1
    FGC18648- 1
    S11571- 3
    Y7878- 3
    FGC18585- 2
    S16446- 4
    FGC18588- 5
    FGC18608- 2
    Y7859- 5


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  17. #9
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    I'm trying to download and process the BAM files left behind.

    There is a problem: KH150612 can't be downloaded... so I start with KH150614_KH150615... I think it will take long time!

    From the authors so far no answer to my e-mail about the Supplemental tables.

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  19. #10
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    I've downloaded KH150612, it worked fine. Will post tomorrow results.
    Although I do not expect anything new.

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