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Thread: Nepali Genetics

  1. #1
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    Nepali Genetics

    From the paper: Genetic structure in the Sherpa and neighboring Nepalese populations, Cole et al., 2017
    https://bmcgenomics.biomedcentral.co...864-016-3469-5

    The Newar appeared as the most admixed Nepalese ethnic group, with similar proportions of Tibetan and ANI ancestry (Table 1). The Rai, Magar and Tamang showed 92%, 82% and 79% Tibetan ancestry, respectively. The Indo-Aryan showed 93% ANI ancestry. These ancestral proportions are consistent with results from our PCA and Admixture analysis. These admixture proportions reported here across Nepalese subpopulations also concur with demographic literature of Nepal and previous mtDNA and Y-STR studies (see supp cohort description for Additional file 3) [10, 14].

    Previously, they did mention ANI as one of the ancestral Indian components.

    ...each of the four ancestral Indian ethnic groups (ANI, ASI, AAA and ATB ) (representing ‘Southern Himalaya’).


    I am confused about that line "ANI" and surprised as it was 93%, but how can that be given ASI, AAA, etc. Did the authors screw up?

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  3. #2
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    Not sure about their ANI calculations but on the PCA, the Indo-Aryan Nepalis are clustering slightly off the main South Asian cline near the southern end of the Pakistani cluster with a off cline pull toward the Central Asian cluster. My guess is the Pakistanis that are off the main cline are Burusho (approximately 10-12% East Eurasian admixed). In addition, I presume the Khatris plotting well within the Pakistani cluster are Punjabi Khatris (either Sikh or Hindu).

    Last edited by Sapporo; 03-02-2018 at 07:57 AM.

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    Thank you for sharing, it also includes Manipuri samples. I am keen on understanding the ancestry of Gurung people as well

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    Who does Indo-Aryan represent - Khas Brahmins? Madhesi?

    Is the rest of the 93% ATB (E Asian) or AAA (SE Asian Tribal)? - likely to be the former

    Ok what stood out to me

    High intermarriage among Nepali Indo-Aryans:

    We found ROH16 to be significantly greater than IBD16 for the Nepalese Indo-Aryan supporting consanguinity as an explanation for observed ROH patterns in that population, despite unions between biological kin being prohibited [27].

    IBD analysis confirmed that the Nepalese Indo-Aryan appear to be the only significant consanguineous subgroup.


    Nepali Indo-Aryans are pretty much north Indian. ANI is Basu's ANI component, he modelled Punjabi Khatris as 97% ANI which is described as Central-South Asians (Baloch, Pathan & Sindhi) and so includes Baloch ASI etc. Tamil Brahmins are modelled 80% ANI by Basu:

    The Indo-Aryan, an Indo-European Nepalese ethnic group, strongly resemble the ANI populations given their large component of north Indian ancestry identified by admixture and the F4-ratio.

    The populations of India with a large proportion of ANI component; particularly the KSH with ∼97% ANI ancestry is inseparable from the CS-Asian, particularly Burusho, Pathan, and Sindhi. The hypothesis that the root of ANI is in Central Asia is further bolstered by the recent evidence derived from analysis of ancient DNA samples

    The resultant dataset comprised a common set of 630,918 markers. Reich et al. (9) have characterized the ANI ancestry as “genetically close to Middle Easterners, Central Asians, and Europeans.”

    The ANI and the ATB can clearly be rooted to the CS-Asians and E-Asians
    Last edited by bmoney; 03-02-2018 at 09:09 AM.

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    It is not clear whether East Asian includes ASI type ancestry for Sherpas as the differentiator they have used is ANI

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    Quote Originally Posted by jortita View Post
    It is not clear whether East Asian includes ASI type ancestry for Sherpas as the differentiator they have used is ANI
    Tbh the components they use are confusing - they are lumping Baloch Sindhi and Pashtun as ANI when they all have very different admix profiles

    Clearly the Khatri are getting some ASI in their 97% as they are not 3% South Indian in Harappa

    And yes whats the non ANI breakdown for each pop - how do we split AAA ATB ASI etc

    I just feel ANI is a pointless component if Tamil Brahmins are 80% ANI for example - not sure why the study uses this Basu/Reich component

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    Quote Originally Posted by bmoney View Post
    Who does Indo-Aryan represent - Khas Brahmins? Madhesi?

    Is the rest of the 93% ATB (E Asian) or AAA (SE Asian Tribal)? - likely to be the former
    In this study "Indo Aryan" means Khas, most likely Brahmins only. Chettri would only skew East Asians arbitrarily.

    Also, this study seems to say the same thing on our very high ROH. Reich Lab also had a study on this, but focused on the diseases.

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  15. #8
    Confusing yet very informative

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    I have seen 2 recent studies and they have Nepali Brahmins have very high ROH, so pretty much completely inbred.

    I was expecting my Gedmatch's "Are your parents related" to show close match, but here is my (Western Khas) and my wife's sister (Eastern Khas):

    GedMatch - Are Your Parents Related?

    poi - FTDNA upload
    Code:
    Largest segment = 16.1 cM
    Total of segments > 7 cM = 16.1 cM
    Estimated number of generations to MRCA = 4.9
    
    Results:
    
    Largest individual segment of SNPs with greater than 500 matches: 7.0 cM
    
    Total autosomal SNPs in segments with greater than 500 matches: 2443
    
    Largest Single-Block Genetic Distance = 
    Total Genetic Distance = 
    Interpreting your results:
    
    This analysis indicates that your parents are probably distantly related.
    Sister-in-Law - AncestryDNA upload
    Code:
    Largest segment = 9.8 cM
    Total of segments > 7 cM = 17.0 cM
    Estimated number of generations to MRCA = 5.0
    
    Results:
    
    Largest individual segment of SNPs with greater than 500 matches: 7.0 cM
    
    Total autosomal SNPs in segments with greater than 500 matches: 2094
    
    Largest Single-Block Genetic Distance = 
    Total Genetic Distance = 
    Interpreting your results:
    
    This analysis indicates that your parents are probably distantly related.
    -----

    Search for Runs of Homozygosity (ROHs)
    http://www.math.mun.ca/~dapike/FF23utils/roh.php

    poi - FTDNA Upload
    Code:
    Total autosomal (Chr 1-22):   4.556 % ( 32006 of 702442 SNPs) are NoCalls
    Total autosomal (Chr 1-22):  28.445 % (199812 of 702442 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
    Total autosomal (Chr 1-22):  71.555 % (502630 of 702442 SNPs) are Homozygous   (this tally includes 0 heterozygous SNPs that were treated as homozygous)
    sister-in-law - AncestryDNA Upload
    Code:
    Total autosomal (Chr 1-22):   0.153 % (   973 of 637639 SNPs) are NoCalls
    Total autosomal (Chr 1-22):  29.223 % (186336 of 637639 SNPs) are Heterozygous (this tally excludes 7 heterozygous SNPs that were treated as homozygous)
    Total autosomal (Chr 1-22):  70.777 % (451303 of 637639 SNPs) are Homozygous   (this tally includes 7 heterozygous SNPs that were treated as homozygous)
    Last edited by poi; 03-02-2018 at 04:23 PM.

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  19. #10
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    Is there any connection between any Nepalese groups with Hunza Valley of Pakistan any folklore attached to it or anything?

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