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Thread: South Asian HGDP Haplogroups

  1. #1
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    Post South Asian HGDP Haplogroups

    Here is a spreadsheet containing maternal and paternal haplogroups for all of the South Asian HGDP cell lines I've managed to find.

    Y-SNP calls were extracted from VCF data generated by Bergström et al. - "Insights into human genetic variation and population history from 929 diverse genomes" and inputted into YSEQ's Clade Finder v1.0 to determine Y-DNA subclades. Some of these HGDP cell lines weren't present in any data from this study, so their paternal haplogroups were taken from Sengupta et al. - "Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists". I'm still looking for WGS/chrY sequencing data for these samples but I've had no luck so far. You could probably infer their subclades from other samples in their populations though. The HGDP00111 (classed as Hazara) and HGDP00220 (classed as Pathan) cell lines originate from the same individual, who is most likely Hazara judging from the Y-DNA subclade and autosomal results posted elsewhere.

    mtDNA subclades were determined by downloading FASTA files from these cell lines submitted to GenBank by Lippold et al. - "Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences" and running them through HaploGrep v2.1.25 to determine mtDNA subclades.

    If there are any errors then please let me know.

    Link: https://docs.google.com/spreadsheets...#gid=799017964
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a1
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

    Hidden Content

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  3. #2
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    Wow, this is a really useful resource. Thank you! ����

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    Must have taken lots of effort. Thanks!

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    Quote Originally Posted by aaronbee2010 View Post
    Here is a spreadsheet containing maternal and paternal haplogroups for all of the South Asian HGDP cell lines I've managed to find.

    Y-SNP calls were extracted from VCF data generated by Bergström et al. - "Insights into human genetic variation and population history from 929 diverse genomes" and inputted into YSEQ's Clade Finder v1.0 to determine Y-DNA subclades. Some of these HGDP cell lines weren't present in any data from this study, so their paternal haplogroups were taken from Sengupta et al. - "Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists". I'm still looking for WGS/chrY sequencing data for these samples but I've had no luck so far. You could probably infer their subclades from other samples in their populations though. The HGDP00111 (classed as Hazara) and HGDP00220 (classed as Pathan) cell lines originate from the same individual, who is most likely Hazara judging from the Y-DNA subclade and autosomal results posted elsewhere.

    mtDNA subclades were determined by downloading FASTA files from these cell lines submitted to GenBank by Lippold et al. - "Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences" and running them through HaploGrep v2.1.25 to determine mtDNA subclades.

    If there are any errors then please let me know.

    Link: https://docs.google.com/spreadsheets...#gid=799017964
    Thanks a lot for your work.

    Kalash R1a is very interestingly under this clade https://www.yfull.com/tree/R-Y29452/

    It is shared with an Indian and Lebanese on yfull. Y29452 is under Z2123>Y934 which has a very wide distribution among Indo-Iranians and has lines which seem to be West Iranic, Scythian/Saka (today frequent in the Caucasus and Volga region), East Iranic and based on the Kalash results even Indo-Aryan/Dardic. I somehow wrongly expected Kalash to be Y47 because this clade is almost entirely restricted to Afghanistan and South Asia https://www.yfull.com/tree/R-Y47/ but Y934 is likely older than the date of the Indo-Iranian split into different branches so it likely was carried by earliest Indo-Aryans too.

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  9. #5
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    I'm a possible Y-DNA match to HGDP00254

    He appears to be Pathan from Pakistan based on this: https://www.sciencedirect.com/scienc...02929707623532

    YFull matches as at 2020-08-15.png

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  11. #6
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    I'm in awe at the amount of diversity in all of this.

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  13. #7
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    I had previously thought that the H-M82 clade I belong to was more dominant in Indo-Aryan language speakers and H-M69, H-M52 was more dominant in Dardic and Eastern Iranian populations, but I guess that was wrong. Also, surprised to not see even one belonging to mt-DNA Haplogroup A so far as there's quite a few of us here on Anthrogenica.

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    Barely any R1a-Y7. Sad reacts only.

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  17. #9
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    Quote Originally Posted by MonkeyDLuffy View Post
    Barely any R1a-Y7. Sad reacts only.
    There's only one sample who comes under R2-SK2142. You don't know true pain.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a1
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

    Hidden Content

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    Quote Originally Posted by aaronbee2010 View Post
    There's only one sample who comes under R2-SK2142. You don't know true pain.
    Mutual F.

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