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Thread: South Asian PCA based on the latest 2018 South/Central Asian paper

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    South Asian PCA based on the latest 2018 South/Central Asian paper

    Most of the paper is beyond my comprehension until somebody dumbs it all down, but I saw the estimates of Steppe-Indus-Onge in the supplementary sheet. Well, here is the PCA based on just that:

    Biplot
    https://i.imgur.com/rITreLb.png


    PCA - Variance coverage is ~100%
    https://i.imgur.com/2PaZb8A.png

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    I'm pretty sure the Jatt Sikh samples are mislabeled in some manner. They are scoring exceedingly low Indus Disapora (Majority Iran Farmer + AASI + ANE/West Siberian) in comparison to Punjabi Khatri, Gujarati A, Gujarati Lohana, etc. and more AASI than Bihari Brahmins, Yadavs from UP and Rajasthan, Haryana Baniya, etc. If you compare Jatt Sikhs and Punjabi Khatri, you wouldn't even think they score remotely similar on admixture calculators when in fact on Harappa, I usually get Punjabi Khatri in my top 3. So do my parents.

    Here is the link to the excel admixture breakdowns from the paper.

    https://www.biorxiv.org/content/bior.../292581-2.xlsx

    Here are some scores from my other post:

    Code:
    Punjabi_Khatri - 61% Indus Diaspora + 26.1% Steppe MLBA + 12.9% Onge AASI related 
    
    Kashmiri_Pandit - 62.7% Indus Diaspora + 21.9% Steppe MLBA 15.4% Onge AASI related 
    
    Muslim_Kashmiri - 60.5% Indus Diaspora + 19.6% Steppe MLBA + 19.9% Onge AASI related 
    
    Dogra_Jammu - 60.8% Indus Diaspora + 22.2% Steppe MLBA + 17% Onge AASI related 
    
    Jatt_Sikh - 55% Indus Diaspora + 24.2% Steppe MLBA + 20.8% Onge AASI related 
    
    Gujarati_A - 63.6% Indus Diaspora + 24.5% Steppe MLBA + 11.9% Onge AASI related 
    
    Gujarati_Lohana - 64% Indus Diaspora + 25.1% Steppe MLBA + 10.9% Onge AASI related 
    
    Yadav_Rajasthan - 61.5% Indus Diaspora + 22.4% Steppe MLBA + 16.1% Onge AASI related 
    
    Yadav_UP - 61.1% Indus Diaspora + 21.3% Steppe MLBA + 17.6% Onge AASI related 
    
    Brahmin_Haryana -  58.6% Indus Diaspora + 23.5% Steppe MLBA + 17.9% Onge AASI related 
    
    Rajput_Haryana - 58.8% Indus Disapsora + 20.9% Steppe MLBA  + 20.3% Onge AASI related 
    
    Bhumihar_Bihar - 54.5% Indus Diaspora + 25.4% Steppe MLBA + 20.1% Onge AASI related 
    
    Brahmin_Nepal - 53.6% Indus Diaspora + 23.4% Steppe MLBA + 23.0% Onge ASSI related 
    
    Brahmin_UP - 52.2% Indus Diaspora + 24.4% Steppe MLBA + 23.4% Onge AASI related 
    
    Brahmin_Tiwari - 53% Indus Diaspora + 25.0% Steppe MLBA + 22.0% Onge AASI related 
    
    note: Tiwari Brahmins are from Chattisgarh 
    
    Gujarati B - 57.7% Indus Diaspora + 21% Steppe MLBA + 21.3% Onge AASI related 
    
    Gujarati C - 58.7% Indus Diaspora + 16.2% Steppe MLBA + 25.1% Onge AASI related 
    
    Haryana Baniya - 61.7% Indus Diaspora + 18.2% Steppe MLBA + 20.1% Onge AASI related 
    
    Brahmin_Karnataka - 57.5% Indus Diaspora + 18.6% Steppe MLBA + 23.9% Onge AASI related
    note: Indus Diaspora is the Iran Farmer like component. It is part majority Iran Farmer like but part ASI and part West Siberian like as pegasus explained in the other thread.

    Edit: I am going to also inquire into getting the 41 Jatt Sikh individual's results from Dr. Reich. It's possible there are outliers, mixed individuals or non Jatt Sikhs in the average with them being the largest ethnoreligious group in Indian Punjab. Many non Jatt Sikhs take on Jatt Sikh clan names and in rare cases might even identify as such.

    I'm also unsure of how they are accounting for East Asian admixture. Reich and co decided not to include some East Asian admixed Eastern Indo-Aryan populations such as Bengalis but what happens for the minor but notable East Asian in Nepali Brahmins for example? Does it just go into AASI? I think it's also possible the Nepali Brahmins here a bit different than the Nepali Brahmin members on the forum like the academic samples lukasz had in his Eurogenes K36 data.

    @poi/pnb123, can either if you confirm if they're the same eastern shifted samples (relative to you guys) that lukasz has in his set?
    Last edited by Sapporo; 04-02-2018 at 06:26 AM.

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    Last edited by anthroin; 04-01-2018 at 12:41 PM. Reason: Premature and likely involved very poor understanding

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    Quote Originally Posted by Sapporo View Post
    I'm pretty sure the Jatt Sikh samples are mislabeled in some manner. They are scoring exceedingly low Indus Disapora in comparison to Punjabi Khatri, Gujarati A, Gujarati Lohana, etc. and more AASI than Bihari Brahmins, Yadavs from UP and Rajasthan, Haryana Baniya, etc. If you compare Jatt Sikhs and Punjabi Khatri, you wouldn't even think they score remotely similar on admixture calculators when in fact on Harappa, I usually get Punjabi Khatri in my top 3. So do my parents.

    Here is the link to the excel admixture breakdowns from the paper.

    https://www.biorxiv.org/content/bior.../292581-2.xlsx

    Here are some scores from my other post:

    Code:
    Punjabi_Khatri - 61% Iran Farmer + 26.1% Steppe MLBA + 12.9% Onge AASI related 
    
    Kashmiri_Pandit - 62.7% Iran Farmer + 21.9% Steppe MLBA 15.4% Onge AASI related 
    
    Gujarati_A - 63.6% Iran Farmer + 24.5% Steppe MLBA + 11.9% Onge AASI related 
    
    Gujarati_Lohana - 64% Iran Farmer + 25.1% Steppe MLBA + 10.9% Onge AASI related 
    
    Yadav_Rajasthan - 61.5% Iran Farmer + 22.4% Steppe MLBA + 16.1% Onge AASI related 
    
    Yadav_UP - 61.1% Iran Farmer + 21.3% Steppe MLBA + 17.6% Onge AASI related 
    
    Muslim_Kashmiri - 60.5% Iran Farmer + 19.6% Steppe MLBA + 19.9% Onge AASI related 
    
    Dogra_Jammu - 60.8% Iran Farmer + 22.2% Steppe MLBA + 17% Onge AASI related 
    
    Brahmin_Haryana -  58.6% Iran Farmer + 23.5% Steppe MLBA + 17.9% Onge AASI related 
    
    Jatt_Sikh - 55% Iran Farmer + 24.2% Steppe MLBA + 20.8% Onge AASI related 
    
    Bhumihar_Bihar - 54.5% Iran Farmer + 25.4% Steppe MLBA + 20.1% Onge AASI related 
    
    Brahmin_UP - 52.2% Iran Farmer + 24.4% Steppe MLBA + 23.4% Onge AASI related 
    
    Brahmin_Tiwari - 53% Iran Farmer + 25.0% Steppe MLBA + 22.0% Onge AASI related 
    
    note: Tiwari Brahmins are from Chattisgarh 
    
    Gujarati B - 57.7% Iran Farmer + 21% Steppe MLBA + 21.3% Onge AASI related 
    
    Haryana Baniya - 61.7% Iran Farmer + 18.2% Steppe MLBA + 20.1% Onge AASI related 
    
    Brahmin_Karnataka - 57.5% Iran Farmer + 18.6% Steppe MLBA + 23.9% Onge AASI related
    note: Iran Farmer in this case is Indus diaspora. It is part ASI as pegasus explained in the other thread.

    Edit: I am going to also inquire into getting the 41 Jatt Sikh individual's results from Dr. Reich. It's possible there are outliers, mixed individuals or non Jatt Sikhs in the average with them being the largest ethnoreligious group in Indian Punjab. Many non Jatt Sikhs take on Jatt Sikh clan names and in rare cases might even identify as such.
    How is Iran farmer part ASI? I thought ASI was strictly Onge related Austroloid type DNA. Sorry I'm new at this stuff.

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    Quote Originally Posted by Censored View Post
    How is Iran farmer part ASI? I thought ASI was strictly Onge related Austroloid type DNA. Sorry I'm new at this stuff.
    It's not Iran Farmer but Indus Periphery, which is about 1/4 AASI, per the paper. The paper supplement stipulates that Iran Neolithic has no AASI ancestry.

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    Quote Originally Posted by Varun R View Post
    It's not Iran Farmer but Indus Periphery, which is about 1/4 AASI, per the paper. The paper supplement stipulates that Iran Neolithic has no AASI ancestry.
    Okay, for a second I thought Sapporo was referring to the chart that he posted, my mistake. So would the South Indian component in Harappaworld basically be Onge-type+some Iran neolithic?

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    Everyone read page 96 of the supplementary...

    A very interesting list of groups considered fringe South Asians, Balochi and Brahui in this list. Implications are interesting.
    An even more interesting list of 7 populations excluded due to statistically significant African ancestry... in this list Sindhis, Gujjars, and Kamboj are found...

    They didn't bother addressing any population that doesn't help their cline. ie. the hard ones. It's a cop out to not model Baloch, Brahui, Makrani -- as how you model each of them them shows your theory of the ethnogenesis of the region in numbers and not words. Massive cop out for not modeling Sindhi. Seriously.
    Bengali is too East Eurasian to consider in the South Asian cluster... !!!!

    Furthermore, I'm getting the impression that the suggestion that certain populations are fringe populations (like Baloch), the authors are implying that their Iran N is independent/not-related to to Iran N/AASI story for the rest of South Asia as mediated via Indus-periphery.
    By not including these populations in the model and saying they are atypical, it seems to me they are passively proposing that they are not necessary to explain the ethnogenesis of the region. ie. they are later arrivals, and they are not the source of Iran N, nor received Iran N from the Indus-periphery.

    I haven't read the entire paper in detail at all. Just skimmed through, because what stood out to me IMMEDIATELY were plots with no Iranian population, no Baloch, no Sindhi, no Tajik, no Bengali.
    Magically, on academic papers they decided to make a Jatt Sikh group and a Chaudhary ethnic group!? I highly doubt that idea occurred in a vacuum.... I think the South Asian community on AG's collective efforts to sort things out may have been absorbed via osmosis.
    Kalash, Pathan, Khatri and Lohana at one end of the spectrum and Pulliyar at the other, and Chamar... another.....? I don't even know how to frame it. They cut out the populations we use to bound everyone between.
    Of course the Brahmin groups will stand out with significant Steppe ancestry, the analysis didn't include the majority of ethnic groups that live between the Brahmins and the Pashtun and Kalash.... except the Jatt Sikh.

    They basically define South Asia as 2 populations from Pakistan + India. They excluded the rest of Pakistan, south of the northwestern corner of KPK and Northeastern Punjab as fringe and atypical. In India they exclude all of Bengal and AAs, and additionally, they don't consider Bangladesh.
    Somehow the Kalash fit perfectly, but Burusho are too "W Eurasian" to consider -- Chaudhary is a real ethnicity on the plot, and there are no other populations in Northern Pakistan that exist to plot.
    Somehow Iran N is super important, but let's not model any modern population in the region in which it peaks, or even attempt to explain how they fit in to the ethnogenesis of the region.

    Anyways, don't hold me to any of this. I barely read the paper in detail. These is just my immediate reaction to their choice of modern samples. The way they are framing "who" is South Asian is lazy, and allows them to escape defending an unambiguous theory of the peopling of the region.
    I have this whole theory regarding Sindh, Jatts, Khoja, Lohana, Gujarat, South India, etc. that rests on on how Baloch, Makrani, Brahui, Bandari are modeled. Disappointed I can't build on it.
    Last edited by khanabadoshi; 04-02-2018 at 12:46 AM.
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    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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    @Khana they didn’t even bother to model groups from central Asian or Iran. Not even Afghans or Tajiks. And most of the samples in the paper came from Central Asia and Iran. They should remove the world Central from the title.

    India does not release ancient samples but gets the most modeling. It’s a conspiracy!(just kidding).
    Last edited by jesus; 04-02-2018 at 12:51 AM.

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    Quote Originally Posted by khanabadoshi View Post
    Bengali is too East Eurasian to consider in the South Asian cluster... !!!!
    Didn't poi post a PCA before that showed Bengalis cluster with Sinhalas? If Sinhalas cluster with Bengalis despite barely having any East Eurasian, then why does EE admixture cause Bengalis to drop outside of the PCA plot?

    Do West Bengalis also have significant EE admixture?

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    Quote Originally Posted by jesus View Post
    @Khana they didn’t even bother to model groups from central Asian or Iran. Not even Afghans or Tajiks. And most of the samples in the paper came from Central Asia and Iran. They should remove the world Central from the title.

    India does release the ancient samples but gets the most modeling. It’s a conspiracy!(just kidding).
    Seriously... I was just thinking that... the audacity of a PCA to have a Kalash dot... and no Yaghnobi, Shugnan, Rushan.
    How can a paper talk to me about Iran N, and not plot a single Iranian! ARGHHH!
    Jesus... a landmark paper which attempts to tell us definitively who banged whom on either side of the Hindu Kush felt it prudent to subdivide a group called Brahmin_Catholic into 3 distinct points. Jesus, this same paper has a single point for "Pathan".


    They attempt to explain the Summer holiday travel routes of a bunch of fanny-packed Ancients by showing me signs that their unruly kids took a sharpie and etched, 'Andronovo wuz here in spirit' in every stall of every truckstop in the entire subcontinent, except the truck-stops where the Ancients actually pulled over and had a cup of chai in.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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