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Thread: Revised and Updated "Geographic Population Structure Prediction"

  1. #1
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    Revised and Updated "Geographic Population Structure Prediction"

    Has anyone tried the updated site? It's a huge improvement over what they previously offered, and has a lot of interesting stuff to play with. I like how they've made all of the data public. Nice to see the 1000 Genomes samples analyzed on the Geno 2.0 Chip.
    http://www.prosapia.org/

    They have a "Download" section, but I'm too inept to use anything on it. So I just tried the "Calculator". I recommend it to anyone who has their Geno 2.0 results.

    To save everyone some trouble:
    Admixture1=Northeast Asian
    Admixture2=Mediterranean
    Admixture3=Southern African
    Admixture4=Southwest Asian
    Admixture5=Native American
    Admixture6=Oceanian
    Admixture7=Southeast Asian
    Admixture8=Northern European
    Admixture9=Sub-Saharan African

    My Geno 2.0 results:
    Northeast Asian=4%
    Mediterranean=26%
    Southern African=0%
    Southwest Asian=46%
    Native American=2%
    Oceanian=0%
    Southeast Asian=11%
    Northern European=11%
    Sub-Saharan African=0%
    (My Mediterranean is 25%, but I added one percent, so that the sum is 100%)

    When you input numbers, the sum of Admixture 1-9 is supposed to be equal to 1. So I put in:
    Admixture1=0.04
    Admixture2=0.26
    Admixture3=0
    Admixture4=0.46
    Admixture5=0.02
    Admixture6=0
    Admixture7=0.11
    Admixture8=0.11
    Admixture9=0

    My location on the World Map, using 1 reference population:

    "Based on the data that you have entered our tool computed that your closest population is from the Iran region.
    Calculated Latitude of Origin: 32.4192
    Calculated Longitude of Origin: 53.6861
    The region is marked on the map below as markers."

    GPS1Ref.jpg

    Using 10 reference populations:

    "Based on the data that you have entered our tool computed that your closest population is from the Iran region.
    Calculated Latitude of Origin: 34.0001
    Calculated Longitude of Origin: 59.742
    The region is marked on the map below as markers."

    GPS10Ref.jpg

    I expected eastern Iran, not too far from home. If we get enough people to try this, we could perhaps attempt something along the lines of the "Spatial Ancestry" thread. Should be fun to compare results between the two.

    If anyone understands the "Downloads" section, please do share with us. I just couldn't figure it out (I guess that reflects rather badly on my mental agility). It has a really cool complete work-flow, so you can create something similar using your own Admixture experiments.
    Last edited by Sein; 01-24-2014 at 06:02 PM.

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    I ended up in the North Caucasus. Like yourself, added 1% to the Mediterranean to achieve 100%. When using more than one reference population, my point settles in northern Georgia, just east of South Ossetia.


    Code:
    Admixture 1	Admixture 2	Admixture 3	Admixture 4	Admixture 5	Admixture 6	Admixture 7	Admixture 8	Admixture 9
    0.05	0.48	0	0.32	0	0	0.03	0.12	0
    Reference Population: 1

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  5. #3
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    Cool! A rather interesting result.

    I looked at the Iranian results provided in the CSV, they range from 53% "Southwest Asian", to only 32%. Most are around 40%. Does that give any indication as to their geographic origins? Perhaps they are from the south of the country?

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    I have a feeling the Geno 2.0 Iranians are from somewhere central in Iran, perhaps Yazd or thereabouts. Note the Geno 2.0 Iranian average lacks any components modal in Africa, whereas most of the Behar et al. Iranian samples have some degree of African admixture.

    If we presume some degree of African ancestry among Iranians points to a southern location, then the Geno 2.0 Iranians fit somewhere between the zone bound by northerners (e.g. yours truly) and the Behar Iranians. Yazd is a guess. Might be from somewhere like Hamadan province (central-west) for all we know.

    For the record, my SW Asian score is 32%.

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    This is mine using former Eurogenes emulator ''K9b''



    Based on the data that you have entered our tool computed your closest population from Iran region.
    Calculated Latitude of Origin: 37.9661
    Calculated Longitude of Origin: 52.5416
    The region is marked on the map below as markers.
    Code:
    0.011 Northeast Asian	
    0.372 Mediterranean	
    0.000 Southern African
    0.430 Southwest Asian
    0.001 Native American
    0.000 Oceanian	
    0.000 Southeast Asian	
    0.185 Northern European
    0.000 Sub-Saharan African

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    Can you guys who have already done Geno2 try K9b? would be interesting to see how much it is off.
    Last edited by MfA; 01-24-2014 at 01:32 PM.

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    Quote Originally Posted by DMXX View Post
    I have a feeling the Geno 2.0 Iranians are from somewhere central in Iran, perhaps Yazd or thereabouts. Note the Geno 2.0 Iranian average lacks any components modal in Africa, whereas most of the Behar et al. Iranian samples have some degree of African admixture.

    If we presume some degree of African ancestry among Iranians points to a southern location, then the Geno 2.0 Iranians fit somewhere between the zone bound by northerners (e.g. yours truly) and the Behar Iranians. Yazd is a guess. Might be from somewhere like Hamadan province (central-west) for all we know.

    For the record, my SW Asian score is 32%.
    Sounds very reasonable. It's fascinating that you have the minimum amount of "Southwest Asian" for the Iranians they sampled. I'm sure your results are more reflective of northern Iranians, but in comparison to the Iranians they sampled, you seem more similar to the Ingush, but with an intermediate Northern European percentage (you have more than these Iranians, but less than the Ingush).

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    My Dad's ( http://www.anthrogenica.com/showthre...ull=1#post4492 ) results (I added 1% each to the SW asian and SE asian to get to 100%):

    One population:
    onepop.jpg


    Ten populations:
    tenpop.jpg


    The download section is for an offline calculator for the same.
    Paternal YDNA: G-P303+ -> G-Z30522+
    Paternal mtDNA: U7a3b1
    Maternal YDNA: R-Z2123+ -> R-YP526+
    Maternal mtDNA: C4a1 (T195C!)

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    Quote Originally Posted by MfA View Post
    Can you guys who have already done Geno2 try K9b? would be interesting to see how much it is off.
    My K9b results:
    Southwest_Asian=60.94%
    North_European=11.06%
    Mediterranean=10.07%
    Southeast_Asian=7.20%
    Native_American=2.40%
    Northeast_Asian=3.70%
    Oceanian=3.45%
    Sub-Saharan_African=1.18%

    Very noisy in comparison to the actual results. Also underestimates "Mediterranean", and overestimates "Southwest Asian". "Northern European" seems accurate though.

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    Quote Originally Posted by Sein View Post
    My K9b results:
    Southwest_Asian=60.94%
    North_European=11.06%
    Mediterranean=10.07%
    Southeast_Asian=7.20%
    Native_American=2.40%
    Northeast_Asian=3.70%
    Oceanian=3.45%
    Sub-Saharan_African=1.18%

    Very noisy in comparison to the actual results. Also underestimates "Mediterranean", and overestimates "Southwest Asian". "Northern European" seems accurate though.
    In my case, it's really overestimating my North Euro (usually around 8-12%) as well as the others:

    Code:
    Population	  
    Southwest_Asian	42.33%
    Native_American	0.42%
    Northeast_Asian	3.53%
    Mediterranean	31.23%
    North_European	19.15%
    Southeast_Asian	1.69%
    Oceanian	0.82%
    South_African	-    
    Sub-Saharan_African	0.83%
    I don't think there's sufficient carry-over here.

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