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Friday, November 4, 2011

The major revision of MDLP: adding Yunusbayev et all.2011 data

Earlier this month i added Bulgarians, Ukrainians and Mordovians from the reference samples in Yunusbayev et all.2011 paper and calculated PCA loadings of new obtained

As promised earlier, i have wasted a couple of hours on plotting PCA loadings (from Eigensoft analysis of my MDL BGA project) in graphical interface of indispensable R-package "BiplotGUI". I've made a lot of efforts combining diffirent types of statistical tests into one meaningful illustration.

Below are results of my experiments with Biplot.

Another cool feature of BiplotGUI is that it fully supports rgl, which is a 3D visualization system based on OpenGL. It provides a medium to high level interface for use in R, currently modelled on classic R graphics, with extensions to allow for interaction and creation of 3D animations/movies.

I've not figured yet how it works, but the next time i will be doing PCA analysis, i'll try to make 3D rotating animations for members of my project. 

(Via) DODECAD:Comparing different ADMIXTURE runs using Zombies

Dienekes Pontikos of DODECAD BGA project  was using our MDLP calculator (based on DIYDodecad methodological paradigma) as proof concept for comparing/mapping the Eurasian components inferred from the Dodecad-dv3 dataset  (West Asian, West European, East European, Mediterranean, Northeast Asian, Southeast Asian) against MDLP components (Scandinavian,Volga_Region, Altaic, Celto_Germanic, Caucassian_Anatolian_Balkanic, Balto_Slavic, North_Atlantic).

This is what he did :

".. To compare components across different projects; there has been a proliferation of different ancestry projects since the launching of Dodecad nearly a year ago, and since all of them slightly different individuals/SNPs/terminology, it is quite useful to be able to gauge how one component from one project maps onto other components in other projects. As proof of concept, I took the MDLP calculator from the Magnus Ducatus Lituaniae Project and generated 50 zombies for each of its 7 ancestral components:
  1. Scandinavian
  2. Volga_Region
  3. Altaic
  4. Celto_Germanic
  5. Caucassian_Anatolian_Balkanic
  6. Balto_Slavic
  7. North_Atlantic
 I then inferred the ancestry of the MDLP zombies using Dodecad v3, and vice versa. Since Dodecad v3 also includes populations (e.g., Africans) not considered by MDLP, I did not try to map those onto MDLP.

I will comment on the MDLP-to-dv3 mapping:
  1. The MDLP "Scandinavian" component appears to be West/East European with a little Mediterranean and a little Northeast Asian
  2. The MDLP "Volga_Region" component appears to be East European with some Northeast Asian
  3. The MDLP "Altaic" component is West Asian+Northeast Asian+Southeast Asian. Note that in Dodecad v3, the Northeast Asian component peaks at Chukchi, Nganasan, and Koryak, and most other east Eurasian populations have much less of it
  4. The MDLP "Celto-Germanic" component is (surprisingly) Mediterranean-dominated. One possible interpretation is that in the context of MDLP this captures one aspect of the difference between Southwestern and Northeastern Europe -higher Mediterranean in the former-, whereas the...
  5. ... MDLP "North-Atlantic" component seems to be entirely West European, and is capturing a different aspect of east-west variation in Europe.
  6. The MDLP "Balto-Slavic" appears the reverse of the "Celto-Germanic" with lower Mediterranean and reversed East/West European
  7. Finally, the MDLP "Caucassian_Anatolian_Balkanic" component is predictably mainly West Asian, but with a little Mediterranean and Southwest Asian as well
A different way of comparing the different components is to include them all in a joint MDS plot, or calculate various types of distances between them (e.g., Fst).

For example, the first couple of dimensions are dominated by the African/Asian components of Dodecad v3 that are not present in MDLP.Notice, however, the position of "Altaic", right where one might expect to find it between West and East Eurasians.

It appears that the "North_Atlantic" component may be centered on a small number of related individuals."

PS. Our MDLP calculator has been occasionally used by various people, and thus results arecurrently being disseminated over the large number of  the different Internet communities of DNA-genealogy/molecular anthroplogy's hobbysts. We are going to collect the results made publicly available by those hobbysts and out them into one spreadsheet for the futher analysis.