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Thread: A genetic map of West Eurasians and their distinction from Europeans1379 days old

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    Default A genetic map of West Eurasians and their distinction from Europeans

    http://dienekes.blogspot.com/2011/01...eurasians.html
    In the following, I have included all populations from Human genetic variation: the first ? components that had "West Eurasian" admixture of at least 75% at K=3.


    I have also added some additional populations from Xing et al. and a number of Dodecad Ancestry Project populations, including some making their debut; sample sizes in several old populations have increased due to participation in the current submission opportunity.


    The number of markers is ~37k in order to include the greatest variety of populations, but as will be seen, the ability to detect structure is not greatly diminished.

    Image 1: http://1.bp.blogspot.com/_Ish7688voT...00/MDS1600.png

    Some South Asian populations were above the 75% cutoff and form their own cluster at the bottom, with the isolated Kalash at some way off. The island of Sardinia is its own island in genetic space as well.


    The most distinctive feature of this plot is the separation of Europeans from West Asians. The big hole framed by Chuvash (bottom), Greeks, Italians, and European Jews (top), Europeans (left), and West Asians (right) and probably reflects barriers to gene flow by the Black Sea and Aegean.

    A fairly linear cluster to the right of this hole contrasts people from the Caucasus (Urkarah, bottom) with those from Arabia (Yemenese Jews, Saudis, Bedouins).

    Using the Galore approach on just the first two MDS dimensions resulted in 13 clusters:

    Image 2: http://2.bp.blogspot.com/_Ish7688voT...600/galore.png

    The distinctiveness of several populations is discovered by MCLUST using just the first two dimensions, confirming our visual impression, e.g., #13: Chuvash, #12: Kalash, #3: Sardinian.

    Other clusters, correspond to multiple populations, e.g., #9: Caucasus, and #10: Arabians.


    In the latter case, as I have mentioned several times before, we should not conclude that these populations are identical, but see whether they can be divided using additional MDS dimensions.


    Indeed, using just 4 dimensions, MCLUST infers 46 clusters.


    Even more clusters can be inferred with the usual set of 177k markers and more MDS dimensions, but, for now, I just wanted to make the point that even the smaller number of SNPs suffices to uncover population variation.


    This allows us to amortize genotyping efforts using different chips with relatively few markers in common with most of the populations included in the Dodecad Project.
    What is your opinion about the separation of Europeans from West Asians?Do you think is a correct one?

    P.S. Sorry for not posting the images but they were too enormous.


    Last edited by jibarodepr; 2011-01-13 at 00:15.

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    Humanist (2011-01-24)

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    46 cluster (4 dimension) clusters specific to the Middle East and Caucasus:

    Population Sample Size
    Adygei 17 ADY
    Armenian_D 7 ARD
    Ashkenazi_D 12 AJD
    Assyrian_D 8 ASD
    Azerbaijan_Jews 8 AZJ
    Bedouin 46 BED
    Cypriots 12 CYP
    Druze 42 DRZ
    Georgia_Jews 4 GEJ
    Georgians 20 GEO
    Iranian_Jews 4 IRJ
    Iranians 20 IRA
    Iraq_Jews 11 IQJ
    Jordanians 20 JOR
    N_Iraq_Kurds 24 KUR
    Lebanese 7 LEB
    Lezgins 18 LEZ
    Morocco_Jews 16 MOJ
    Palestinian 46 PAL
    Samaritans 3 SAM
    Saudis 20 SAU
    Sephardic_Jews 19 SEJ
    Stalskoe 5 STL
    Syrians 16 SYR
    Turks 19 TUR
    Urkarah 18 URK
    Uzbekistan_Jews 2 UZJ
    Yemen_Jews 15 YEJ

    Cluster 2: 1/19 SEJ
    Cluster 5: 12/12 AJD, 1/16 MOJ, 6/19 SEJ
    Cluster 8: 6/7 ARD, 7/8 ASD, 8/8 AZJ, 3/4 GEJ, 4/4 IRJ, 5/11 IQJ, 1/2 UZJ
    Cluster 9: 1/7 ARD, 16/20 GEO
    Cluster 10: 12/12 CYP, 2/19 SEJ
    Cluster 13: 11/17 ADY, 3/20 GEO, 1/18 LEZ, 2/19 TUR
    Cluster 15: 1/8 ASD, 31/42 DRZ, 6/11 IQJ, 3/3 SAM, 1/16 SYR
    Cluster 16: 1/17 ADY, 1/20 GEO
    Cluster 18: 11/46 BED, 1/4 GEJ, 15/20 JOR, 2/7 LEB, 39/46 PAL, 1/20 SAU, 5/16 SYR
    Cluster 19: 8/42 DRZ
    Cluster 20: 3/42 DRZ, 3/20 JOR, 4/7 LEB, 1/46 PAL, 1/20 SAU, 8/16 SYR
    Cluster 21: 1/7 LEB, 1/16 SYR, 14/19 TUR, 1/2 UZJ
    Cluster 23: 15/16 MOJ, 10/19 SEJ
    Cluster 24: 5/17 ADY, 17/18 LEZ, 5/5 STL, 1/19 TUR, 18/18 URK
    Cluster 25: 13/46 BED, 6/46 PAL, 4/20 SAU, 1/15 YEJ
    Cluster 26: 14/15 YEJ
    Cluster 27: 3/20 IRA, 1/20 JOR, 1/20 SAU, 1/16 SYR
    Cluster 29: 15/20 IRA, 24/24 KUR, 2/19 TUR
    Cluster 30: 2/46 BED, 11/20 SAU
    Cluster 31: 1/20 SAU
    Cluster 32: 2/20 IRA, 1/20 SAU
    Cluster 33: 1/20 JOR
    Cluster 34: 9/46 BED
    Cluster 35: 10/46 BED
    Cluster 36: 1/46 BED

    Generalized
    Cluster 5: Ashkenazi and Sephardi Jewish
    Cluster 8: Assyrian, Armenian, Mizrahim
    Cluster 9: Georgian
    Cluster 10: Cypriot
    Cluster 13: Adygei
    Cluster 15: Samaritan, Druze, Iraqi Jewish
    Cluster 18: Levantine-Arabian
    Cluster 19: Druze
    Cluster 20: Syro-Lebanese
    Cluster 21: Turkish
    Cluster 23: Moroccan and Sephardi Jewish
    Cluster 24: Caucasus (“North European” and “Northeast Asian”)
    Cluster 25: Bedouin
    Cluster 26: Yemeni Jewish
    Cluster 29: Iranian and Kurdish(N Iraq)
    Cluster 30: Saudi
    Cluster 34: Bedouin
    Cluster 35: Bedouin

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    jibarodepr (2011-01-24)

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