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Thread: MDLP K23b Project - Part 2 of 2- Community PCAs, graphs, & charts

  1. #1
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    Post MDLP K23b Project - Part 2 of 2- Community PCAs, graphs, & charts

    This is part 2 of 2 of the MDLP k23b analysis project. The majority of the analysis will be done under this thread. The goals of part 2 of the project will be as follows:

    1- To perform analysis via a PCA plot of the community member data. Component 1 of the PCA (x-axis) will consist of the sum of all the S. Asian, SE Asian, and NE Asian MDLP components minus all the West Asian components. Component 2 of the PCA (y-axis) will consist of the sum of all the MDLP European components minus all the African components. This choice of the components will nicely break up populations into clusters somewhat consistent with geographical positioning;

    2- Create sorted admixture cluster graphs for the community membership;

    3- Create sorted admixture overlap charts for a couple of the major ethnic groups.

    I encourage members from all ethnicities to post their data here. To make it less time consuming for me, I would appreciate it if you would copy and paste your data as it appears next to the pie chart graphic, as that is the order I will enter data, and I can thus copy and paste it into my spreadsheet, which will minimize errors. I encourage members to post their data by Saturday midnight US Pacific Time, as I am not able to make more than one update to the charts due to time constraints.

    It would be nice if someone can post MDLP K23 admixtures and oracles for some of the newly sequenced ancient genomes, Yamnaya, etc., so that I can incorporate those into the PCAs and graphs.

    The following definitions will apply throughout the project:

    1- S. Asia = SC Asia + S. India
    2- NE & SE Asia = The sum of Amerindian, Ancestral Altaic, Arctic, Tungus Altaic, Paleo Siberian, SE Asian, Australoid, Austronesian, Melano Polynesian
    3- W. Asia = Near East + Caucasian

    4- The rest is self explanatory

    To start here is my data:


    [IMG][/IMG]

    I have highlighted my W. Asian surrogates in green, and S/C Asian ones in brown

    [IMG][/IMG]
    Last edited by Kurd; 03-12-2015 at 07:30 PM.

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  3. #2
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    This is my data consolidated into major regions. I will be using these components when I do community cluster graphs.


    [IMG][/IMG]

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  5. #3
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    My results:

    Code:
    0.64	Amerindian
    1.39	Ancestral_Altaic
    0.23	Archaic_Human
    42.58	Caucasian
    8.49	European_Early_Farmers
    0.29	European_Hunters_Gatherers
    0.64	Melano_Polynesian
    18.91	Near_East
    4.55	North_African
    0.55	Paleo_Siberian
    19.68	South_Central_Asian
    1.64	South_Indian
    0.41	Tungus-Altaic
    IQ Mandaean 1

    Code:
    0.94	Amerindian
    0.03	Archaic_Human
    42.5	Caucasian
    8.82	European_Early_Farmers
    0.73	European_Hunters_Gatherers
    0.57	Melano_Polynesian
    17.38	Near_East
    5.96	North_African
    0.82	Paleo_Siberian
    19.71	South_Central_Asian
    0.02	South_East_Asian
    2.51	South_Indian
    IQ Mandaean 2

    Code:
    0.65	Amerindian
    1.42	Ancestral_Altaic
    0.2	Archaic_Human
    0.39	Arctic
    0.19	Austronesian
    40.73	Caucasian
    0.22	East_African
    4.53	European_Early_Farmers
    20.56	Near_East
    8.27	North_African
    20.91	South_Central_Asian
    1.84	South_Indian

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  7. #4
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    Arbėreshė Wales Germany Palatinate Polish–LithuanianCommonwealth Israel Slovakia
    Here are my results.
    1 European_Hunters_Gatherers 38.55
    2 Caucasian 28.32
    3 European_Early_Farmers 18.97
    4 South_Central_Asian 5.27
    5 Near_East 3.19
    6 North_African 2.07
    7 Ancestral_Altaic 2.06
    8 Melano_Polynesian 1.00

    MDLP K23b reduced painting.jpg

    MDLP K23b admixture by chromosomes.jpg

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  9. #5
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    Turkey Afsharid Dynasty
    Population
    Amerindian 1.80%
    Ancestral_Altaic 3.70%
    South_Central_Asian 15.64%
    Arctic -
    South_Indian 2.81%
    Australoid 0.21%
    Austronesian 1.04%
    Caucasian 40.19%
    Archaic_Human 0.06%
    East_African -
    East_Siberian 0.87%
    European_Early_Farmers 8.27%
    Khoisan -
    Melano_Polynesian -
    Archaic_African -
    Near_East 12.68%
    North_African 1.91%
    Paleo_Siberian -
    African_Pygmy -
    South_East_Asian -
    Subsaharian -
    Tungus-Altaic 4.85%
    European_Hunters_Gatherers 5.97%

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    Quote Originally Posted by Kurd View Post
    To make it less time consuming for me, I would appreciate it if you would copy and paste your data as it appears next to the pie chart graphic, as it is alphabetisized, and I can thus copy and paste it into my spreadsheet, which will minimize errors.
    Sorry about that!

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  13. #7
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    mtDNA (P)
    M18a

    United States of America Canada
    Population
    Amerindian 0.70%
    Ancestral_Altaic 4.21%
    South_Central_Asian 33.13%
    Arctic -
    South_Indian 38.30%
    Australoid 0.22%
    Austronesian -
    Caucasian 7.32%
    Archaic_Human -
    East_African -
    East_Siberian 0.83%
    European_Early_Farmers 3.55%
    Khoisan -
    Melano_Polynesian -
    Archaic_African 0.09%
    Near_East 1.54%
    North_African -
    Paleo_Siberian 2.45%
    African_Pygmy -
    South_East_Asian -
    Subsaharian 0.43%
    Tungus-Altaic 0.91%
    European_Hunters_Gatherers 6.31%
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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  15. #8
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    .....
    Last edited by MfA; 07-18-2016 at 06:35 PM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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  17. #9
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    United States of America Iran United States of America Iran
    Code:
    Population	 
    Amerindian	-    
    Ancestral_Altaic	3.45%
    South_Central_Asian	25.24%
    Arctic	1.11%
    South_Indian	6.00%
    Australoid	0.16%
    Austronesian	-    
    Caucasian	35.50%
    Archaic_Human	0.39%
    East_African	0.11%
    East_Siberian	0.07%
    European_Early_Farmers	5.92%
    Khoisan	-    
    Melano_Polynesian	0.58%
    Archaic_African	-    
    Near_East	12.41%
    North_African	1.23%
    Paleo_Siberian	-    
    African_Pygmy	0.32%
    South_East_Asian	2.06%
    Subsaharian	-    
    Tungus-Altaic	-    
    European_Hunters_Gatherers	5.46%

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  19. #10
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    United States of America Canada
    Ancestral Altaic is actually leftover ANE, so that's not really East Asian. You could join it with European but not sure that would be a lot better since EEF + WHG together is pretty much middle neolithic Gok2-like European admixture. With ANE it could approximate something else, or just treat it separately altogether like "North Eurasian" since it seems to vary a lot (the other components themselves use up most of the ANE).

    It depends if the European users are getting a lot of it which they don't seem to, so it just sticks out like a sore thumb. In South Asians some of that would've gone into European in other calculators, so it shows there's a discrepancy between what's actually European-like and what Admixture lumps into European because of ANE in other calculators for South Asians.

    Or I guess you could put it into South Asian though since it appears that for everyone outside South Asia, it may be coming from South Asian components, but for everyone inside South Asia, it's coming from Gedrosian or European.

    But treating it separately as 'North Eurasian' would allow for useful comparisons and avoid committing to one or the other category where it doesn't seem to fit into any.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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